diff --git a/.Rbuildignore b/.Rbuildignore
index 8bb0571..ca52a6f 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -14,3 +14,4 @@ ucsc.knownGenes.db
 ^appveyor\.yml$
 
 setupEnv.R
+^\.github$
diff --git a/.github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yml
new file mode 100644
index 0000000..95605be
--- /dev/null
+++ b/.github/workflows/check-bioc.yml
@@ -0,0 +1,333 @@
+## Read more about GitHub actions the features of this GitHub Actions workflow
+## at https://lcolladotor.github.io/biocthis/articles/biocthis.html#use_bioc_github_action
+##
+## For more details, check the biocthis developer notes vignette at
+## https://lcolladotor.github.io/biocthis/articles/biocthis_dev_notes.html
+##
+## You can add this workflow to other packages using:
+## > biocthis::use_bioc_github_action()
+##
+## Using GitHub Actions exposes you to many details about how R packages are
+## compiled and installed in several operating system.s
+### If you need help, please follow the steps listed at
+## https://github.com/r-lib/actions#where-to-find-help
+##
+## If you found an issue specific to biocthis's GHA workflow, please report it
+## with the information that will make it easier for others to help you.
+## Thank you!
+
+## Acronyms:
+## * GHA: GitHub Action
+## * OS: operating system
+
+on:
+  push:
+  pull_request:
+
+name: R-CMD-check-bioc
+
+## These environment variables control whether to run GHA code later on that is
+## specific to testthat, covr, and pkgdown.
+##
+## If you need to clear the cache of packages, update the number inside
+## cache-version as discussed at https://github.com/r-lib/actions/issues/86.
+## Note that you can always run a GHA test without the cache by using the word
+## "/nocache" in the commit message.
+env:
+  has_testthat: 'true'
+  run_covr: 'true'
+  run_pkgdown: 'false'
+  has_RUnit: 'false'
+  cache-version: 'cache-v1'
+  run_docker: 'false'
+
+jobs:
+  build-check:
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+    container: ${{ matrix.config.cont }}
+    ## Environment variables unique to this job.
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - { os: ubuntu-latest, r: '4.2', bioc: '3.16', cont: "bioconductor/bioconductor_docker:RELEASE_3_16", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
+          - { os: ubuntu-latest, r: 'next', bioc: '3.17', cont: "bioconductor/bioconductor_docker:RELEASE_3_17", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
+          - { os: macOS-latest, r: '4.2', bioc: '3.16'}
+          - { os: windows-latest, r: '4.2', bioc: '3.16'}
+          ## Check https://github.com/r-lib/actions/tree/master/examples
+          ## for examples using the http-user-agent
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RSPM: ${{ matrix.config.rspm }}
+      NOT_CRAN: true
+      TZ: UTC
+      GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+
+      ## Set the R library to the directory matching the
+      ## R packages cache step further below when running on Docker (Linux).
+      - name: Set R Library home on Linux
+        if: runner.os == 'Linux'
+        run: |
+          mkdir /__w/_temp/Library
+          echo ".libPaths('/__w/_temp/Library')" > ~/.Rprofile
+
+      ## Most of these steps are the same as the ones in
+      ## https://github.com/r-lib/actions/blob/master/examples/check-standard.yaml
+      ## If they update their steps, we will also need to update ours.
+      - name: Checkout Repository
+        uses: actions/checkout@v3
+
+      ## R is already included in the Bioconductor docker images
+      - name: Setup R from r-lib
+        if: runner.os != 'Linux'
+        uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+
+      ## pandoc is already included in the Bioconductor docker images
+      - name: Setup pandoc from r-lib
+        if: runner.os != 'Linux'
+        uses: r-lib/actions/setup-pandoc@v2
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+        shell: Rscript {0}
+
+      - name: Restore R package cache
+        if: "!contains(github.event.head_commit.message, '/nocache') && runner.os != 'Linux'"
+        uses: actions/cache@v3
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_16-r-4.2-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_16-r-4.2-
+
+      - name: Cache R packages on Linux
+        if: "!contains(github.event.head_commit.message, '/nocache') && runner.os == 'Linux' "
+        uses: actions/cache@v3
+        with:
+          path: /home/runner/work/_temp/Library
+          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_16-r-4.2-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_16-r-4.2-
+
+      - name: Install Linux system dependencies
+        if: runner.os == 'Linux'
+        run: |
+          sysreqs=$(Rscript -e 'cat("apt-get update -y && apt-get install -y", paste(gsub("apt-get install -y ", "", remotes::system_requirements("ubuntu", "20.04")), collapse = " "))')
+          echo $sysreqs
+          sudo -s eval "$sysreqs"
+
+      - name: Install macOS system dependencies
+        if: matrix.config.os == 'macOS-latest'
+        run: |
+          ## Enable installing XML from source if needed
+          brew install libxml2
+          echo "XML_CONFIG=/usr/local/opt/libxml2/bin/xml2-config" >> $GITHUB_ENV
+
+          ## Required to install magick as noted at
+          ## https://github.com/r-lib/usethis/commit/f1f1e0d10c1ebc75fd4c18fa7e2de4551fd9978f#diff-9bfee71065492f63457918efcd912cf2
+          brew install imagemagick@6
+
+          ## For textshaping, required by ragg, and required by pkgdown
+          brew install harfbuzz fribidi
+
+          ## For installing usethis's dependency gert
+          brew install libgit2
+
+          ## Required for tcltk
+          brew install xquartz --cask
+
+      - name: Install Windows system dependencies
+        if: runner.os == 'Windows'
+        run: |
+          ## Edit below if you have any Windows system dependencies
+        shell: Rscript {0}
+        
+      - name: Init tinytex
+        uses: r-lib/actions/setup-tinytex@v2
+        
+      - name: Install tinytex packages
+        run: |
+          system("tlmgr --version")
+          install.packages("tinytex")
+          tinytex::tlmgr_install(pkgs = c("bera", "caption", "changepage", "enumitem", "everysel", "fancyhdr", "footmisc", "grfext", "index", "marginfix", "mathtools", 
+                                 "ms", "nowidow", "parnotes", "parskip", "placeins", "preprint", "ragged2e", "side", "soul", "titlesec", "tocbibind", "xstring"))
+        shell: Rscript {0}
+
+      - name: Install BiocManager
+        run: |
+          message(paste('****', Sys.time(), 'installing BiocManager ****'))
+          remotes::install_cran("BiocManager")
+        shell: Rscript {0}
+
+      - name: Set BiocVersion
+        run: |
+          BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE, force = TRUE)
+        shell: Rscript {0}
+
+      - name: Install dependencies pass 1
+        run: |
+          ## Try installing the package dependencies in steps. First the local
+          ## dependencies, then any remaining dependencies to avoid the
+          ## issues described at
+          ## https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016675.html
+          ## https://github.com/r-lib/remotes/issues/296
+          ## Ideally, all dependencies should get installed in the first pass.
+
+          ## Set the repos source depending on the OS
+          ## Alternatively use https://storage.googleapis.com/bioconductor_docker/packages/
+          ## though based on https://bit.ly/bioc2021-package-binaries
+          ## the Azure link will be the main one going forward.
+          gha_repos <- if(
+              .Platform$OS.type == "unix" && Sys.info()["sysname"] != "Darwin"
+          ) c(
+              "AnVIL" = "https://bioconductordocker.blob.core.windows.net/packages/3.16/bioc",
+              BiocManager::repositories()
+              ) else BiocManager::repositories()
+
+          ## For running the checks
+          message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****'))
+          install.packages(c("rcmdcheck", "BiocCheck"), repos = gha_repos)
+
+          ## Pass #1 at installing dependencies
+          ## This pass uses AnVIL-powered fast binaries
+          ## details at https://github.com/nturaga/bioc2021-bioconductor-binaries
+          ## The speed gains only apply to the docker builds.
+          message(paste('****', Sys.time(), 'pass number 1 at installing dependencies: local dependencies ****'))
+          remotes::install_local(dependencies = TRUE, repos = gha_repos, build_vignettes = FALSE, upgrade = TRUE)
+        continue-on-error: true
+        shell: Rscript {0}
+
+      - name: Install dependencies pass 2
+        run: |
+          ## Pass #2 at installing dependencies
+          ## This pass does not use AnVIL and will thus update any packages
+          ## that have seen been updated in Bioconductor
+          message(paste('****', Sys.time(), 'pass number 2 at installing dependencies: any remaining dependencies ****'))
+          remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE, force = TRUE)
+        shell: Rscript {0}
+
+      - name: Install BiocGenerics
+        if:  env.has_RUnit == 'true'
+        run: |
+          ## Install BiocGenerics
+          BiocManager::install("BiocGenerics")
+        shell: Rscript {0}
+
+      - name: Install covr
+        if: github.ref == 'refs/heads/master' && env.run_covr == 'true' && runner.os == 'Linux'
+        run: |
+          remotes::install_cran("covr")
+        shell: Rscript {0}
+
+      - name: Install pkgdown
+        if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
+        run: |
+          remotes::install_cran("pkgdown")
+        shell: Rscript {0}
+
+      - name: Session info
+        run: |
+          options(width = 100)
+          pkgs <- installed.packages()[, "Package"]
+          sessioninfo::session_info(pkgs, include_base = TRUE)
+        shell: Rscript {0}
+
+      - name: Run CMD check
+        env:
+          _R_CHECK_CRAN_INCOMING_: false
+          DISPLAY: 99.0
+        run: |
+          options(crayon.enabled = TRUE)
+          rcmdcheck::rcmdcheck(
+              args = c("--no-manual", "--no-vignettes", "--timings"),
+              build_args = c("--no-manual", "--keep-empty-dirs", "--no-resave-data"),
+              error_on = "error",
+              check_dir = "check"
+          )
+        shell: Rscript {0}
+
+      ## Might need an to add this to the if:  && runner.os == 'Linux'
+      - name: Reveal testthat details
+        if:  env.has_testthat == 'true'
+        run: find . -name testthat.Rout -exec cat '{}' ';'
+
+      - name: Run RUnit tests
+        if:  env.has_RUnit == 'true'
+        run: |
+          BiocGenerics:::testPackage()
+        shell: Rscript {0}
+
+      - name: Run BiocCheck
+        env:
+          DISPLAY: 99.0
+        run: |
+          BiocCheck::BiocCheck(
+              dir('check', 'tar.gz$', full.names = TRUE),
+              `quit-with-status` = TRUE,
+              `no-check-R-ver` = TRUE,
+              `no-check-bioc-help` = TRUE
+          )
+        shell: Rscript {0}
+
+      - name: Test coverage
+        if: github.ref == 'refs/heads/master' && env.run_covr == 'true' && runner.os == 'Linux'
+        run: |
+          covr::codecov()
+        shell: Rscript {0}
+
+      - name: Install package
+        if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
+        run: R CMD INSTALL .
+
+      - name: Build pkgdown site
+        if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+        ## Note that you need to run pkgdown::deploy_to_branch(new_process = FALSE)
+        ## at least one locally before this will work. This creates the gh-pages
+        ## branch (erasing anything you haven't version controlled!) and
+        ## makes the git history recognizable by pkgdown.
+
+      - name: Install deploy dependencies
+        if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
+        run: |
+          apt-get update && apt-get -y install rsync
+
+      - name: Deploy pkgdown site to GitHub pages 🚀
+        if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
+        uses: JamesIves/github-pages-deploy-action@releases/v4
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@master
+        with:
+          name: ${{ runner.os }}-biocversion-RELEASE_3_16-r-4.2-results
+          path: check
+
+        ## Note that DOCKER_PASSWORD is really a token for your dockerhub
+        ## account, not your actual dockerhub account password.
+        ## This comes from
+        ## https://seandavi.github.io/BuildABiocWorkshop/articles/HOWTO_BUILD_WORKSHOP.html#6-add-secrets-to-github-repo
+        ## Check https://github.com/docker/build-push-action/tree/releases/v1
+        ## for more details.
+      - uses: docker/build-push-action@v1
+        if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && runner.os == 'Linux' "
+        with:
+          username: ${{ secrets.DOCKER_USERNAME }}
+          password: ${{ secrets.DOCKER_PASSWORD }}
+          repository: gagneurlab/outrider
+          tag_with_ref: true
+          tag_with_sha: true
+          tags: latest
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
deleted file mode 100644
index 87cb157..0000000
--- a/.gitlab-ci.yml
+++ /dev/null
@@ -1,47 +0,0 @@
-variables:
-  PKGNAME:     "OUTRIDER"
-  PKGDIR:      "./"
-  R_LIBS_U:    "tmp_lib"
-  RVER:        "3.6.0-Bioc3.9"
-  TEXVER:      "2016"
-  # CI_DEBUG_TRACE: "true"
-
-stages:
-  - testing
-
-before_script:
-  - module load "i12g/R/$RVER"
-  - module load "i12g/texlive/$TEXVER"
-  - export R_LIBS_U="`realpath ${CI_JOB_ID}_${R_LIBS_U}`"
-  - mkdir $R_LIBS_U
-  - R --vanilla CMD build --no-build-vignettes --no-manual $PKGDIR
-  - PKG_FILE_NAME=$(ls -1t *.tar.gz | head -n 1)
-  - R_LIBS_USER=$R_LIBS_U Rscript --vanilla -e "install.packages('${PKG_FILE_NAME}', lib='$R_LIBS_U', repo=NULL)"
-
-R-check:
-  stage: testing
-  when: always
-  tags: [shell]
-  script:
-    - R_LIBS_USER=$R_LIBS_U R --vanilla CMD check --no-vignettes --timings "${PKG_FILE_NAME}"
-
-R-BiocCheck:
-  stage: testing
-  when: always
-  tags: [shell]
-  script:
-    - R_LIBS_USER=$R_LIBS_U R --vanilla CMD BiocCheck --no-check-vignettes "${PKG_FILE_NAME}"
-
-R-coverage:
-  stage: testing
-  when: always
-  tags: [shell]
-  script:
-    - R_LIBS_USER=$R_LIBS_U Rscript --vanilla -e "library('$PKGNAME'); covr::package_coverage('$PKGDIR')"
-
-R-check_vignettes:
-  stage: testing
-  when: always
-  tags: [shell]
-  script:
-    - cd "$PKGDIR/vignettes/" && R_LIBS_USER=$R_LIBS_U R --vanilla CMD Sweave --engine=knitr::knitr --pdf "$PKGNAME.Rnw"
diff --git a/.travis.yml b/.travis.yml
deleted file mode 100644
index 978852b..0000000
--- a/.travis.yml
+++ /dev/null
@@ -1,54 +0,0 @@
-language: r
-sudo: required
-dist: xenial
-cache:
-  - directories:
-    - $HOME/R/Library
-
-
-addons:
-  apt:
-    packages:
-      - libxml2-dev
-      - tk-dev
-      - libgit2-dev
-
-r:
-  - bioc-devel
-  - bioc-release
-  - 3.6.0
-
-stages:
-  - Setup Cache
-  - Test
-
-# setup cache first
-jobs:
-  include:
-    - stage: Setup Cache
-      r: bioc-devel
-      script: true
-    - stage: Setup Cache
-      r: bioc-release
-      script: true
-    - stage: Setup Cache
-      r: 3.6.0
-      script: true
-
-before_install:
-  - tlmgr install index marginfix bera nowidow parnotes
-
-install:
-  - Rscript setupEnv.R
-  - R --version
-  - R -e "BiocManager::version()"
-
-script:
-  - R CMD build .
-  - R -e 'BiocCheck::BiocCheck(".", `no-check-vignettes`=TRUE)'
-  - R CMD check --no-vignettes --timings *tar.gz
-  - R -e 'devtools::run_examples(run=TRUE, document=TRUE)'
-  - cd vignettes && R CMD Sweave --engine=knitr::knitr --pdf OUTRIDER.Rnw
-
-after_success:
-  - test $TRAVIS_BUILD_STAGE_NAME = "Test" && Rscript -e 'covr::codecov()'
diff --git a/DESCRIPTION b/DESCRIPTION
index 8fa4dab..03f6ffa 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: OUTRIDER
 Title: OUTRIDER - OUTlier in RNA-Seq fInDER
 Type: Package
-Version: 1.16.1
+Version: 1.16.2
 Date: 2020-10-20
 URL: https://github.com/gagneurlab/OUTRIDER
 BugRepots: https://github.com/gagneurlab/OUTRIDER/issues
@@ -9,11 +9,13 @@ Authors@R: c(
     person("Felix", "Brechtmann", role=c("aut"), 
             email="brechtma@in.tum.de"),
     person("Christian", "Mertes", role=c("aut", "cre"), 
-            email="mertes@in.tum.de"),
+            email="mertes@in.tum.de", comment=c(ORCID="0000-0002-1091-205X")),
     person("Agne", "Matuseviciute", role=c("aut")),
     person(c("Michaela", "Fee"), "Müller", role=c("ctb")),
-    person("Vicente", "Yepez", role=c("aut"), email="yepez@in.tum.de"),
-    person("Julien", "Gagneur", role=c("aut"), email="gagneur@in.tum.de"))
+    person("Vicente", "Yepez", role=c("aut"), email="yepez@in.tum.de",
+            comment=c(ORCID="0000-0001-7916-3643")),
+    person("Julien", "Gagneur", role=c("aut"), email="gagneur@in.tum.de",
+            comment=c(ORCID="0000-0002-8924-8365")))
 Description: Identification of aberrant gene expression in RNA-seq data.
     Read count expectations are modeled by an autoencoder to control for
     confounders in the data. Given these expectations, the RNA-seq read counts
@@ -27,7 +29,7 @@ biocViews: ImmunoOncology, RNASeq, Transcriptomics, Alignment, Sequencing,
 License: MIT + file LICENSE
 NeedsCompilation: yes
 Encoding: UTF-8
-RoxygenNote: 7.1.1
+RoxygenNote: 7.2.3
 Depends:
     R (>= 3.6), 
     BiocParallel,
@@ -53,7 +55,6 @@ Imports:
     pcaMethods,
     PRROC,
     RColorBrewer,
-    Rcpp,
     reshape2,
     S4Vectors,
     scales,
diff --git a/NAMESPACE b/NAMESPACE
index aa2cc67..3ab9fc0 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -73,6 +73,7 @@ importFrom(BiocGenerics,plotDispEsts)
 importFrom(BiocParallel,SerialParam)
 importFrom(BiocParallel,bpisup)
 importFrom(BiocParallel,bplapply)
+importFrom(BiocParallel,bpmapply)
 importFrom(BiocParallel,bpparam)
 importFrom(BiocParallel,bpstart)
 importFrom(BiocParallel,bpstop)
diff --git a/NEWS b/NEWS
index 237c70f..215e368 100644
--- a/NEWS
+++ b/NEWS
@@ -1,3 +1,9 @@
+CHANGES IN VERSION 1.16.2
+-----------------------------
+    o Add option to restrict FDR correction to sets of genes of interest
+    o Add opttion to retrieve results based on those FDR values on subsets of 
+      genes
+    
 CHANGES IN VERSION 1.7.1
 -----------------------------
     o Move to S3/S4 methods to be compatible with FRASER
diff --git a/R/OUTRIDER.R b/R/OUTRIDER.R
index 6e39227..0016258 100644
--- a/R/OUTRIDER.R
+++ b/R/OUTRIDER.R
@@ -22,6 +22,12 @@
 #' @inheritParams controlForConfounders
 #' @param controlData If TRUE, the default, the raw counts are controled 
 #'             for confounders by the autoencoder
+#' @param subsets A named list of named lists specifying any number of gene 
+#'             subsets (can differ per sample). For each subset, FDR correction
+#'             will be limited to genes in the subset, and the FDR corrected 
+#'             pvalues stored as an assay in the ods object in addition to the 
+#'             transcriptome-wide FDR corrected pvalues. See the examples for 
+#'             how to use this argument. 
 #' @param ... Further arguments passed on to \code{controlForConfounders}
 #' @return OutriderDataSet with all the computed values. The values are stored
 #'             as assays and can be accessed by: \code{assay(ods, 'value')}.
@@ -44,9 +50,19 @@
 #' plotAberrantPerSample(ods)
 #' plotVolcano(ods, 1)
 #' 
+#' # example of restricting FDR correction to subsets of genes of interest 
+#' genesOfInterest <- list("sample_1"=sample(rownames(ods), 3), 
+#'                          "sample_2"=sample(rownames(ods), 8), 
+#'                          "sample_6"=sample(rownames(ods), 5))
+#' genesOfInterest
+#' ods <- OUTRIDER(ods, subsets=list("exampleSubset"=genesOfInterest))
+#' padj(ods, subsetName="exampleSubset")[1:10,1:10]
+#' res <- results(ods, all=TRUE)
+#' res
+#' 
 #' @export
 OUTRIDER <- function(ods, q, controlData=TRUE, implementation='autoencoder', 
-                    BPPARAM=bpparam(), ...){
+                     subsets=NULL, BPPARAM=bpparam(), ...){
     checkOutriderDataSet(ods)
     implementation <- tolower(implementation)
     
@@ -65,7 +81,7 @@ OUTRIDER <- function(ods, q, controlData=TRUE, implementation='autoencoder',
     }
     
     message(date(), ": P-value calculation ...")
-    ods <- computePvalues(ods, BPPARAM=BPPARAM)
+    ods <- computePvalues(ods, subsets=subsets, BPPARAM=BPPARAM)
     
     message(date(), ": Zscore calculation ...")
     ods <- computeZscores(ods, 
diff --git a/R/getNSetterFuns.R b/R/getNSetterFuns.R
index 6d14e1b..3cc938a 100644
--- a/R/getNSetterFuns.R
+++ b/R/getNSetterFuns.R
@@ -4,6 +4,8 @@
 #' the values within the OUTRIDER model.
 #' 
 #' @param ods,object An OutriderDataSet object.
+#' @param subsetName Name of a gene subset for which to store or retrieve 
+#'              FDR corrected p values 
 #' @param ... Further arguments passed on to the underlying assay function.
 #' @return A matrix or vector dependent on the type of data retrieved.
 #' 
@@ -58,18 +60,26 @@ pValue <- function(ods){
 
 #' @rdname getter_setter_functions
 #' @export padj
-padj <- function(ods){
-    if(!'padjust' %in% assayNames(ods)){
+padj <- function(ods, subsetName=NULL){
+    assayName <- 'padjust'
+    if(!is.null(subsetName)){
+        assayName <- paste0(assayName, "_", subsetName)
+    }
+    if(!assayName %in% assayNames(ods)){
         stop('Please compute first the P-values before retrieving', '
                 the adjusted ones.')
     }
-    assay(ods, 'padjust')
+    assay(ods, assayName)
 }
 
-`padj<-` <- function(ods, ..., value){
+`padj<-` <- function(ods, subsetName=NULL, ..., value){
     stopifnot(is.matrix(value))
     stopifnot(dim(ods) == dim(value))
-    assay(ods, 'padjust', ...) <- value
+    assayName <- 'padjust'
+    if(!is.null(subsetName)){
+        assayName <- paste0(assayName, "_", subsetName)
+    }
+    assay(ods, assayName, ...) <- value
     return(ods)
 }
 
diff --git a/R/method-evaluation.R b/R/method-evaluation.R
index 43a780a..0cdd431 100644
--- a/R/method-evaluation.R
+++ b/R/method-evaluation.R
@@ -1,8 +1,9 @@
 aberrant.OUTRIDER <- function(object, padjCutoff=0.05, zScoreCutoff=0, 
-                    by=c("none", "sample", "gene")){
+                    by=c("none", "sample", "gene"), subsetName=NULL, ...){
     checkFullAnalysis(object)
     
-    aberrantEvents <- padj(object) <= padjCutoff
+    aberrantEvents <- padj(object, subsetName=subsetName) <= padjCutoff
+    
     if(isScalarNumeric(zScoreCutoff, na.ok=FALSE)){
         aberrantEvents <- aberrantEvents & abs(zScore(object)) >= zScoreCutoff
     }
@@ -26,6 +27,10 @@ aberrant.OUTRIDER <- function(object, padjCutoff=0.05, zScoreCutoff=0,
 #'             if NA or NULL no Z-score cutoff is used
 #' @param by if the results should be summarized by 'sample', 
 #'             'gene' or not at all (default).
+#' @param subsetName The name of a subset of genes of interest for which FDR 
+#'             corected pvalues have been previously computed. Those FDR values 
+#'             on the subset will then be used to determine aberrant status. 
+#'             Default is NULL (using transcriptome-wide FDR corrected pvalues).
 #' @param ... Currently not in use.
 #'
 #' @return The number of aberrent events by gene or sample or a TRUE/FALSE 
diff --git a/R/method-gridSearch.R b/R/method-gridSearch.R
index 4d980a0..ee114ab 100644
--- a/R/method-gridSearch.R
+++ b/R/method-gridSearch.R
@@ -200,7 +200,14 @@ injectOutliers <- function(ods, freq, zScore, inj, lnorm, sdlog){
         # only insert outliers if they are different from before 
         # and not too large
         if(art_out < max_out & counts[idxRow, idxCol] != art_out){
-            counts[idxRow, idxCol] <- art_out
+
+          # do not introduce outlier such that all samples have 0 counts for that gene.
+          # if all other samples (excluding idxCol) are 0 and art_out is 0 do not inject that outlier.
+          if(all(counts[idxRow,-idxCol] == 0) & art_out == 0){
+              index[idxRow, idxCol] <- 0
+          }else{
+              counts[idxRow, idxCol] <- art_out
+          }
         }else{
             index[idxRow, idxCol] <- 0
             zScore
diff --git a/R/method-results.R b/R/method-results.R
index 1e35b0c..d1e68c3 100644
--- a/R/method-results.R
+++ b/R/method-results.R
@@ -1,5 +1,5 @@
 compileResults.OUTRIDER <- function(object, padjCutoff=0.05, zScoreCutoff=0, 
-                    round=2, all=FALSE, ...){
+                    round=2, all=FALSE, subsetName=NULL, ...){
     
     #
     # input check and parsing
@@ -19,14 +19,17 @@ compileResults.OUTRIDER <- function(object, padjCutoff=0.05, zScoreCutoff=0,
         round <- 2
     }
     
+    meanCorrectedCounts <- rowMeans(counts(object, normalized=TRUE))
     if(isFALSE(all)){
         abByGene <- aberrant(object, 
                 padjCutoff=padjCutoff, zScoreCutoff=zScoreCutoff, by="gene")
         abBySample <- aberrant(object, 
                 padjCutoff=padjCutoff, zScoreCutoff=zScoreCutoff, by="sample")
         object <- object[abByGene > 0, abBySample > 0]
+        meanCorrectedCounts <- meanCorrectedCounts[abByGene > 0]
     }
     
+    # warning if no rows to return 
     if(nrow(object) == 0){
         if(isFALSE(all)){
             warning('No significant events: use all=TRUE to print all events.')
@@ -34,43 +37,50 @@ compileResults.OUTRIDER <- function(object, padjCutoff=0.05, zScoreCutoff=0,
             warning('Please provide an object with at least one feature.')
         }
         return(data.table(
-                geneID=NA_character_,
-                sampleID=NA_character_,
-                pValue=NA_real_,
-                padjust=NA_real_,
-                zScore=NA_real_,
-                l2fc=NA_real_,
-                rawcounts=NA_integer_,
-                normcounts=NA_real_,
-                meanCorrected=NA_real_,
-                theta=NA_real_,
-                aberrant=NA,
-                AberrantBySample=NA_integer_,
-                AberrantByGene=NA_integer_,
-                padj_rank=NA_real_)[0])
+            geneID=NA_character_,
+            sampleID=NA_character_,
+            pValue=NA_real_,
+            padjust=NA_real_,
+            zScore=NA_real_,
+            l2fc=NA_real_,
+            rawcounts=NA_integer_,
+            normcounts=NA_real_,
+            meanCorrected=NA_real_,
+            theta=NA_real_,
+            aberrant=NA,
+            AberrantBySample=NA_integer_,
+            AberrantByGene=NA_integer_,
+            padj_rank=NA_real_,
+            FDR_set=NA_character_)[0])
     }
     
     #
     # extract data
-    # 
+    #
     ans <- data.table(
         geneID           = rownames(object), 
         sampleID         = rep(colnames(object), each=nrow(object)),
         pValue           = c(pValue(object)),
-        padjust          = c(padj(object)),
+        padjust          = c(padj(object, subsetName=subsetName)),
         zScore           = c(zScore(object)),
         l2fc             = c(assay(object, "l2fc")),
         rawcounts        = c(counts(object)),
         normcounts       = c(counts(object, normalized=TRUE)),
-        meanCorrected    = rowMeans(counts(object, normalized=TRUE)),
+        meanCorrected    = meanCorrectedCounts,
         theta            = theta(object),
         aberrant         = c(aberrant(object, 
-                padjCutoff=padjCutoff, zScoreCutoff=zScoreCutoff)),
+                padjCutoff=padjCutoff, zScoreCutoff=zScoreCutoff,
+                subsetName=subsetName)),
         AberrantBySample = rep(each=nrow(object), aberrant(object, 
-                padjCutoff=padjCutoff, zScoreCutoff=zScoreCutoff, by="sample")),
+                padjCutoff=padjCutoff, zScoreCutoff=zScoreCutoff, by="sample",
+                subsetName=subsetName)),
         AberrantByGene   = aberrant(object, 
-                padjCutoff=padjCutoff, zScoreCutoff=zScoreCutoff, by="gene"),
-        padj_rank        = c(apply(padj(object), 2, rank)))
+                padjCutoff=padjCutoff, zScoreCutoff=zScoreCutoff, by="gene",
+                subsetName=subsetName),
+        padj_rank        = c(apply(padj(object), 2, rank)),
+        FDR_set          = ifelse(is.null(subsetName), "transcriptome-wide", 
+                                    subsetName)
+    )
     
     # round columns if requested
     if(is.numeric(round)){
@@ -80,16 +90,65 @@ compileResults.OUTRIDER <- function(object, padjCutoff=0.05, zScoreCutoff=0,
     }
     
     # 
-    # keep only aberrent events and sort by padj value
+    # keep only aberrant events and sort by padj value
     # 
     if(isFALSE(all)){
         ans <- ans[aberrant == TRUE]
+        
+    } else{
+        # if return full subset is requested, retrieve those as all non-NA padj
+        ans <- ans[!is.na(padjust),]
     }
     ans <- ans[order(padjust)]
     
     return(ans)
 }
 
+compileResultsAll.OUTRIDER <- function(object, padjCutoff=0.05, zScoreCutoff=0, 
+                                    round=2, all=FALSE, 
+                                    returnTranscriptomewideResults=TRUE, ...){
+    #
+    # input check and parsing
+    # 
+    checkOutriderDataSet(object)
+    checkFullAnalysis(object)
+    
+    # get all padjust assays (transcriptome-wide and on subsets)
+    padjAssays <- grep('padjust', assayNames(object), value=TRUE)
+    
+    # dont retrieve transcriptome-wide results if requested
+    if(isFALSE(returnTranscriptomewideResults)){
+        if(length(padjAssays) == 1 && padjAssays == 'padjust'){
+            warning("Retrieving transcriptome-wide results as no other ",
+                    "padjust assays are available in the ods object.")
+        } else{
+            padjAssays <- padjAssays[padjAssays != 'padjust']
+        }
+    }
+    
+    # get results for all available padjust assays
+    resSubsets <- lapply(padjAssays, function(padjAssay){
+        if(padjAssay == 'padjust'){
+            subsetName <- NULL
+        } else{
+            subsetName <- gsub("padjust_", "", padjAssay)
+        }
+        resSub <- compileResults.OUTRIDER(object=object, 
+                            padjCutoff=padjCutoff, zScoreCutoff=zScoreCutoff, 
+                            all=all, round=round, 
+                            subsetName=subsetName, ...)
+        return(resSub)
+    })
+    res <- rbindlist(resSubsets)
+        
+    # sort it if existing
+    if(length(res) > 0){
+        res <- res[order(padjust)]
+    }
+    
+    return(res)
+}
+
 #' 
 #' Accessor function for the 'results' object in an OutriderDataSet object. 
 #' 
@@ -105,9 +164,15 @@ compileResults.OUTRIDER <- function(object, padjCutoff=0.05, zScoreCutoff=0,
 #'             more user friendly
 #' @param all By default FALSE, only significant read counts are listed in the 
 #'             results. If TRUE all results are assembled resulting in a 
-#'             data.table of length samples x genes
+#'             data.table of length samples x genes. If FDR corrected pvalues 
+#'             for subsets of genes of interest have been calculated, this 
+#'             indicates whether the whole subset will be listed in the results.
+#' @param returnTranscriptomewideResults If FDR corrected pvalues for subsets 
+#'              of genes of interest have been calculated, this parameter 
+#'              indicates whether additionally the transcriptome-wide results 
+#'              should be returned as well (default), or whether only results 
+#'              for those subsets should be retrieved.
 #' @param ... Additional arguments, currently not used
-#' 
 #' @return A data.table where each row is an outlier event and the columns
 #'             contain additional information about this event. Eg padj, l2fc
 #' 
@@ -122,10 +187,20 @@ compileResults.OUTRIDER <- function(object, padjCutoff=0.05, zScoreCutoff=0,
 #' res <- results(ods, all=TRUE)
 #' res
 #' 
+#' # example of retrieving results with FDR correction limited to a 
+#' # set of genes of interest
+#' genesOfInterest <- list("sample_1"=sample(rownames(ods), 3), 
+#'                          "sample_2"=sample(rownames(ods), 8), 
+#'                          "sample_6"=sample(rownames(ods), 5))
+#' genesOfInterest
+#' ods <- computePvalues(ods, subsets=list("exampleSubset"=genesOfInterest))
+#' res <- results(ods, all=TRUE, returnTranscriptomewideResults=FALSE)
+#' res
+#' 
 #' @name results
 #' @rdname results
 #' @aliases results results,OutriderDataSet-method
 #' 
 #' @export
-setMethod("results", "OutriderDataSet", compileResults.OUTRIDER)
+setMethod("results", "OutriderDataSet", compileResultsAll.OUTRIDER)
 
diff --git a/R/pValMatrix.R b/R/pValMatrix.R
index 3dbb05b..f011e80 100644
--- a/R/pValMatrix.R
+++ b/R/pValMatrix.R
@@ -11,6 +11,12 @@
 #'             the alternative hypothesis used to calculate the P-values,
 #'             defaults to "two.sided"
 #' @param method Method used for multiple testing
+#' @param subsets A named list of named lists specifying any number of gene 
+#'             subsets (can differ per sample). For each subset, FDR correction
+#'             will be limited to genes in the subset, and the FDR corrected 
+#'             pvalues stored as an assay in the ods object in addition to the 
+#'             transcriptome-wide FDR corrected pvalues. See the examples for 
+#'             how to use this argument. 
 #' @param BPPARAM Can be used to parallelize the computation, defaults to
 #'             bpparam()
 #' @param ... additional params, currently not used.
@@ -36,6 +42,16 @@
 #' 
 #' assays(ods)[['pValue']][1:10,1:10]
 #' 
+#' # example of restricting FDR correction to subsets of genes of interest
+#' genesOfInterest <- list("sample_1"=sample(rownames(ods), 3), 
+#'                          "sample_2"=sample(rownames(ods), 8), 
+#'                          "sample_6"=sample(rownames(ods), 5))
+#' ods <- computePvalues(ods, subsets=list("exampleSubset"=genesOfInterest))
+#' padj(ods, subsetName="exampleSubset")[1:10,1:10]
+#' ods <- computePvalues(ods, 
+#'                  subsets=list("anotherExampleSubset"=rownames(ods)[1:5]))
+#' padj(ods, subsetName="anotherExampleSubset")[1:10,1:10]
+#' 
 #' @exportMethod computePvalues
 setGeneric("computePvalues", 
         function(object, ...) standardGeneric("computePvalues"))
@@ -44,13 +60,26 @@ setGeneric("computePvalues",
 #' @export
 setMethod("computePvalues", "OutriderDataSet", function(object, 
             alternative=c("two.sided", "greater", "less"), method='BY', 
-            BPPARAM=bpparam()){
+            subsets=NULL, BPPARAM=bpparam()){
     
     alternative <- match.arg(alternative)
     object <- pValMatrix(object, alternative, BPPARAM=BPPARAM)
     
     if(method != 'None'){
         object <- padjMatrix(object, method)
+        
+        # calculate FDR for each provided subset and assign to ods
+        if(!is.null(subsets)){
+            stopifnot(is.list(subsets))
+            stopifnot(!is.null(names(subsets)))
+            for(setName in names(subsets)){
+                geneListSubset <- subsets[[setName]]
+                object <- padjOnSubset(ods=object, method=method, 
+                                    BPPARAM=BPPARAM,
+                                    genesToTest=geneListSubset,
+                                    subsetName=setName)
+            }
+        }
     }
     object
 })
@@ -145,3 +174,84 @@ padjMatrix <- function(ods, method='BH'){
     return(ods)
 }
 
+#' 
+#' FDR correction on subset of genes
+#' 
+#' Function to correct the computed pValues using BY FDR correction, limited to 
+#' a subset of genes.
+#'
+#' @param ods OutriderDataSet
+#' @param method adjustment method, by default 'BY'
+#' @param genesToTest A named list with the subset of genes to test per sample.
+#'     The names must correspond to the sampleIDs in the ods object.
+#' @param subsetName The name under which the resulting FDR corrected pvalues 
+#'     will be stored as an assay with name 'padjust_'+subsetName.
+#' @return OutriderDataSet containing adjusted pValues
+#' 
+#' @noRd
+padjOnSubset <- function(ods, genesToTest, subsetName, method='BY', 
+                            BPPARAM=bpparam()){
+    
+    # check input
+    stopifnot(!is.null(genesToTest))
+    stopifnot(is.list(genesToTest) || is.vector(genesToTest))
+    
+    # replicate subset genes for each sample if given as vector
+    if(!is.list(genesToTest)){
+        genesToTest <- rep(list(genesToTest), ncol(ods))
+        names(genesToTest) <- colnames(ods)
+    }
+    
+    # check that names are present and correspond to samples in ods
+    stopifnot(!is.null(names(genesToTest)))
+    if(!all(names(genesToTest) %in% colnames(ods))){
+        stop("names(genesToTest) need to be sampleIDs in the given ods object.")
+    }
+    
+    # compute FDR on the given subsets of genes
+    fdrSubset <- bpmapply(colnames(ods), FUN=function(sampleId){
+                                         
+            # get genes to test for this sample
+            genesToTestSample <- genesToTest[[sampleId]]
+            padj <- rep(NA, nrow(ods))
+            
+            # if no genes present in the subset for this sample, return NAs
+            if(is.null(genesToTestSample)){
+                return(padj)
+            }
+            
+            # get idx of junctions corresponding to genes to test
+            if(is.character(genesToTestSample)){
+                rowIdx <- sort(which(rownames(ods) %in% genesToTestSample))
+            } else{
+                stop("Genes in the list to test must be a character vector ",
+                    "of geneIDs.")
+            }
+                             
+            # check that rowIdx is not empty vector
+            if(length(rowIdx) == 0){
+                warning("No genes from the given subset found in the ods ",
+                            "object for sample: ", sampleId)
+                return(padj)
+            }
+                                         
+            # retrieve pvalues of genes to test
+            p <- pValue(ods)[rowIdx, sampleId]
+                     
+            # FDR correction on subset
+            padjSub <- p.adjust(p, method=method)
+                                         
+            # return FDR on subset, filled with NA for all other genes
+            padj[rowIdx] <- padjSub
+            return(padj)
+            
+        }, SIMPLIFY=TRUE, BPPARAM=BPPARAM)
+    rownames(fdrSubset) <- rownames(ods)
+    colnames(fdrSubset) <- colnames(ods)
+    
+    # add FDR subset info to ods object and return
+    padj(ods, subsetName=subsetName) <- fdrSubset
+    validObject(ods)
+    return(ods)
+}
+
diff --git a/R/package-OUTRIDER.R b/R/package-OUTRIDER.R
index 0d39f9e..88be64b 100644
--- a/R/package-OUTRIDER.R
+++ b/R/package-OUTRIDER.R
@@ -24,6 +24,7 @@
 #'          isScalarValue isScalarNA chunk seq_col seq_row
 #' 
 #' @importFrom BiocParallel bplapply bpparam SerialParam bpisup bpstart bpstop
+#'          bpmapply
 #' 
 #' @importFrom GenomicFeatures makeTxDbFromGFF exonsBy
 #' 
diff --git a/README.md b/README.md
index 8f1a2c5..647cda3 100644
--- a/README.md
+++ b/README.md
@@ -1,13 +1,17 @@
 # OUTRIDER #
+[![Build](https://github.com/gagneurlab/OUTRIDER/actions/workflows/check-bioc.yml/badge.svg)](https://github.com/gagneurlab/OUTRIDER/actions/workflows/check-bioc.yml)
+[![Version](https://img.shields.io/github/v/release/gagneurlab/OUTRIDER)](https://github.com/gagneurlab/OUTRIDER/releases)
+[![Coverage status](https://codecov.io/gh/gagneurlab/OUTRIDER/branch/master/graph/badge.svg)](https://codecov.io/github/gagneurlab/OUTRIDER?branch=master)
+[![License](https://img.shields.io/github/license/mashape/apistatus.svg?maxAge=2592000)](https://github.com/gagneurlab/OUTRIDER/blob/master/LICENSE)
+
 OUTRIDER is a tool to find aberrantly expressed genes in RNA-seq samples.
 The method is published in the [AJHG](https://doi.org/10.1016/j.ajhg.2018.10.025)
 and available through [Bioconductor](http://bioconductor.org/packages/release/bioc/html/OUTRIDER.html).
+It is also part of the workflow [DROP](https://github.com/gagneurlab/drop), which is described in [Nature Protocols](https://www.nature.com/articles/s41596-020-00462-5).
 
-[![Pipeline status](https://travis-ci.org/gagneurlab/OUTRIDER.svg?branch=master)](https://travis-ci.org/gagneurlab/OUTRIDER)
-[![AppVeyor build status](https://ci.appveyor.com/api/projects/status/a2f6io5isq0jhobf/branch/master?svg=true)](https://ci.appveyor.com/project/c-mertes/outrider/branch/master)
-[![Version](https://img.shields.io/badge/Version-1.7.1-green.svg)](https://github.com/gagneurlab/OUTRIDER/tree/master)
-[![Coverage status](https://codecov.io/gh/gagneurlab/OUTRIDER/branch/master/graph/badge.svg)](https://codecov.io/github/gagneurlab/OUTRIDER?branch=master)
-[![License](https://img.shields.io/github/license/mashape/apistatus.svg?maxAge=2592000)](https://github.com/gagneurlab/OUTRIDER/blob/master/LICENSE)
+Please cite our method paper if you use it in a publication:
+
+> Brechtmann F, Mertes C, Matusevičiūtė A, *et al.* OUTRIDER: A Statistical Method for Detecting Aberrantly Expressed Genes in RNA Sequencing Data. *Am J Hum Genet. 2018;103(6):907-917*. https://doi.org/10.1016/j.ajhg.2018.10.025
 
 
 ## Installation
@@ -43,7 +47,7 @@ install.packages('devtools')
 devtools::install_github('gagneurlab/OUTRIDER', dependencies=TRUE)
 
 # installing a specific version/tag of OUTRIDER
-devtools::install_github('gagneurlab/OUTRIDER@1.3.5', dependencies=TRUE)
+devtools::install_github('gagneurlab/OUTRIDER@1.16.2', dependencies=TRUE)
 ```
 
 To check which versions/tags are available you can check the GitHub repo
@@ -70,7 +74,7 @@ To install those packages, please run as administrator:
 
 For Ubuntu or debian based systems:
 ```
-sudo apt-get install build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev zlib1g-dev libmysqld-dev
+sudo apt-get install build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev zlib1g-dev libmariadbd-dev
 ```
 
 For centOS or RHEL based systems:
diff --git a/appveyor.yml b/appveyor.yml
deleted file mode 100644
index 13b9136..0000000
--- a/appveyor.yml
+++ /dev/null
@@ -1,79 +0,0 @@
-# 
-# Use the Bootstrap code from the rwinlib project for CRAN 
-# https://github.com/rwinlib
-#
-init:
-  ps: |
-        $ErrorActionPreference = "Stop"
-        Invoke-WebRequest https://raw.githubusercontent.com/rwinlib/base/master/scripts/appveyor-tool.ps1 -OutFile "..\appveyor-tool.ps1"
-        Import-Module '..\appveyor-tool.ps1'
-
-install:
-  - ps: Bootstrap
-  # install ImageMagick and set path correctly at first position
-  # only needed for building the vignette
-  #- ps: InstallMiktex
-  #- choco install -y -PackageParameters LegacySupport=true imagemagick
-  #- set "PATH=C:\Program Files\ImageMagick-7.0.8-Q16;%PATH%"
-
-#cache:
-#  - C:\RLibrary
-
-environment:
-  # parameters to setup R environment
-  # https://github.com/krlmlr/r-appveyor/blob/master/README.md
-  PKGTYPE: win.binary
-  BIOC_USE_DEVEL: FALSE
-  USE_RTOOLS: TRUE
-  KEEP_VIGNETTES: TRUE
-  GCC_PATH: mingw_64
-  R_ARCH: x64
-#  APPVEYOR_SAVE_CACHE_ON_ERROR: TRUE
-  
-  matrix:
-#    - R_VERSION: devel
-#      BIOC_USE_DEVEL: TRUE
-#    - R_VERSION: devel
-#      BIOC_USE_DEVEL: TRUE
-#      GCC_PATH: mingw_32
-#      R_ARCH: i386    
-    - R_VERSION: release
-#    - R_VERSION: 3.6.0
-      
-build_script:
-  - travis-tool.sh install_bioc BiocManager BiocCheck
-  - R -e "BiocManager::install(Ncpus=5, ask=FALSE, upgrade=TRUE)"
-  - Rscript setupEnv.R
-
-test_script:
-    - R CMD build --no-build-vignettes .
-    - R CMD check --install-args=--build --no-vignettes --no-manual --timings *tar.gz
-    - R -e "BiocCheck::BiocCheck(list.files(path='.', pattern='.tar.gz'))"
-    - R -e "devtools::run_examples(document=FALSE)"
-    # runs currently into an error saying: "LaTeX Error: Missing \begin{document}."
-    #    - cd vignettes && R CMD Sweave --engine=knitr::knitr --pdf OUTRIDER.Rnw
-
-on_failure:
-  - 7z a failure.zip *.Rcheck\*
-  - appveyor PushArtifact failure.zip
-  - appveyor PushArtifact \*_*.tar.gz
-  - appveyor PushArtifact \*_*.zip
-
-artifacts:
-  - path: '*.Rcheck\**\*.log'
-    name: Logs
-
-  - path: '*.Rcheck\**\*.out'
-    name: Logs
-
-  - path: '*.Rcheck\**\*.fail'
-    name: Logs
-
-  - path: '*.Rcheck\**\*.Rout'
-    name: Logs
-
-  - path: '\*_*.tar.gz'
-    name: Bits
-
-  - path: '\*_*.zip'
-    name: Bits
diff --git a/man/OUTRIDER.Rd b/man/OUTRIDER.Rd
index e9e2768..ec684a6 100644
--- a/man/OUTRIDER.Rd
+++ b/man/OUTRIDER.Rd
@@ -9,6 +9,7 @@ OUTRIDER(
   q,
   controlData = TRUE,
   implementation = "autoencoder",
+  subsets = NULL,
   BPPARAM = bpparam(),
   ...
 )
@@ -25,6 +26,13 @@ for confounders by the autoencoder}
 implementation. Also 'pca' and 'peer' can be used to control
 for confounding effects}
 
+\item{subsets}{A named list of named lists specifying any number of gene 
+subsets (can differ per sample). For each subset, FDR correction
+will be limited to genes in the subset, and the FDR corrected 
+pvalues stored as an assay in the ods object in addition to the 
+transcriptome-wide FDR corrected pvalues. See the examples for 
+how to use this argument.}
+
 \item{BPPARAM}{A 
 \code{\link[BiocParallel:BiocParallelParam-class]{BiocParallelParam}}
         instance to be used for parallel computing.}
@@ -72,4 +80,14 @@ res
 plotAberrantPerSample(ods)
 plotVolcano(ods, 1)
 
+# example of restricting FDR correction to subsets of genes of interest 
+genesOfInterest <- list("sample_1"=sample(rownames(ods), 3), 
+                         "sample_2"=sample(rownames(ods), 8), 
+                         "sample_6"=sample(rownames(ods), 5))
+genesOfInterest
+ods <- OUTRIDER(ods, subsets=list("exampleSubset"=genesOfInterest))
+padj(ods, subsetName="exampleSubset")[1:10,1:10]
+res <- results(ods, all=TRUE)
+res
+
 }
diff --git a/man/aberrant.Rd b/man/aberrant.Rd
index 44b3b8c..5ce6152 100644
--- a/man/aberrant.Rd
+++ b/man/aberrant.Rd
@@ -11,7 +11,9 @@ aberrant(object, ...)
   object,
   padjCutoff = 0.05,
   zScoreCutoff = 0,
-  by = c("none", "sample", "gene")
+  by = c("none", "sample", "gene"),
+  subsetName = NULL,
+  ...
 )
 }
 \arguments{
@@ -26,6 +28,11 @@ if NA or NULL no Z-score cutoff is used}
 
 \item{by}{if the results should be summarized by 'sample', 
 'gene' or not at all (default).}
+
+\item{subsetName}{The name of a subset of genes of interest for which FDR 
+corected pvalues have been previously computed. Those FDR values 
+on the subset will then be used to determine aberrant status. 
+Default is NULL (using transcriptome-wide FDR corrected pvalues).}
 }
 \value{
 The number of aberrent events by gene or sample or a TRUE/FALSE 
diff --git a/man/computePvalues.Rd b/man/computePvalues.Rd
index f1f9108..6d48e60 100644
--- a/man/computePvalues.Rd
+++ b/man/computePvalues.Rd
@@ -12,6 +12,7 @@ computePvalues(object, ...)
   object,
   alternative = c("two.sided", "greater", "less"),
   method = "BY",
+  subsets = NULL,
   BPPARAM = bpparam()
 )
 }
@@ -26,6 +27,13 @@ defaults to "two.sided"}
 
 \item{method}{Method used for multiple testing}
 
+\item{subsets}{A named list of named lists specifying any number of gene 
+subsets (can differ per sample). For each subset, FDR correction
+will be limited to genes in the subset, and the FDR corrected 
+pvalues stored as an assay in the ods object in addition to the 
+transcriptome-wide FDR corrected pvalues. See the examples for 
+how to use this argument.}
+
 \item{BPPARAM}{Can be used to parallelize the computation, defaults to
 bpparam()}
 }
@@ -50,6 +58,16 @@ ods <- computePvalues(ods)
 
 assays(ods)[['pValue']][1:10,1:10]
 
+# example of restricting FDR correction to subsets of genes of interest
+genesOfInterest <- list("sample_1"=sample(rownames(ods), 3), 
+                         "sample_2"=sample(rownames(ods), 8), 
+                         "sample_6"=sample(rownames(ods), 5))
+ods <- computePvalues(ods, subsets=list("exampleSubset"=genesOfInterest))
+padj(ods, subsetName="exampleSubset")[1:10,1:10]
+ods <- computePvalues(ods, 
+                 subsets=list("anotherExampleSubset"=rownames(ods)[1:5]))
+padj(ods, subsetName="anotherExampleSubset")[1:10,1:10]
+
 }
 \seealso{
 p.adjust
diff --git a/man/getter_setter_functions.Rd b/man/getter_setter_functions.Rd
index 2c7e61d..18a6cbc 100644
--- a/man/getter_setter_functions.Rd
+++ b/man/getter_setter_functions.Rd
@@ -22,7 +22,7 @@ zScore(ods)
 
 pValue(ods)
 
-padj(ods)
+padj(ods, subsetName = NULL)
 
 \S4method{dispersions}{OutriderDataSet}(object, ...)
 
@@ -31,6 +31,9 @@ theta(ods)
 \arguments{
 \item{ods, object}{An OutriderDataSet object.}
 
+\item{subsetName}{Name of a gene subset for which to store or retrieve 
+FDR corrected p values}
+
 \item{...}{Further arguments passed on to the underlying assay function.}
 }
 \value{
diff --git a/man/results.Rd b/man/results.Rd
index 37fee56..9702ab2 100644
--- a/man/results.Rd
+++ b/man/results.Rd
@@ -13,6 +13,7 @@ results(object, ...)
   zScoreCutoff = 0,
   round = 2,
   all = FALSE,
+  returnTranscriptomewideResults = TRUE,
   ...
 )
 }
@@ -31,7 +32,15 @@ more user friendly}
 
 \item{all}{By default FALSE, only significant read counts are listed in the 
 results. If TRUE all results are assembled resulting in a 
-data.table of length samples x genes}
+data.table of length samples x genes. If FDR corrected pvalues 
+for subsets of genes of interest have been calculated, this 
+indicates whether the whole subset will be listed in the results.}
+
+\item{returnTranscriptomewideResults}{If FDR corrected pvalues for subsets 
+of genes of interest have been calculated, this parameter 
+indicates whether additionally the transcriptome-wide results 
+should be returned as well (default), or whether only results 
+for those subsets should be retrieved.}
 }
 \value{
 A data.table where each row is an outlier event and the columns
@@ -53,4 +62,14 @@ ods <- OUTRIDER(ods)
 res <- results(ods, all=TRUE)
 res
 
+# example of retrieving results with FDR correction limited to a 
+# set of genes of interest
+genesOfInterest <- list("sample_1"=sample(rownames(ods), 3), 
+                         "sample_2"=sample(rownames(ods), 8), 
+                         "sample_6"=sample(rownames(ods), 5))
+genesOfInterest
+ods <- computePvalues(ods, subsets=list("exampleSubset"=genesOfInterest))
+res <- results(ods, all=TRUE, returnTranscriptomewideResults=FALSE)
+res
+
 }
diff --git a/setupEnv.R b/setupEnv.R
deleted file mode 100644
index 209e9ed..0000000
--- a/setupEnv.R
+++ /dev/null
@@ -1,71 +0,0 @@
-BTYPE <- ifelse(.Platform$OS.type == 'unix', "source", "both")
-NCPUS <- 6
-START_TIME <- Sys.time()
-
-print_log <- function(...){
-    hash_line <- paste0(rep("#", 10), collapse="")
-    message(paste0("\n", hash_line, "\n### ", date(), ": ", ..., "\n", hash_line, "\n"))
-}
-
-installIfReq <- function(p, type=BTYPE, Ncpus=NCPUS, ...){
-    for(j in p){
-        if(!requireNamespace(j, quietly=TRUE)){
-            print_log("Install ", j)
-            INSTALL(j, type=type, Ncpus=Ncpus, ...)
-        }
-    }
-}
-
-# install Bioconductor
-if(!requireNamespace("BiocManager", quietly=TRUE)){
-    print_log("Install BiocManager")
-    install.packages("BiocManager", Ncpus=NCPUS)
-}
-INSTALL <- BiocManager::install
-
-# since the current XML package is not compatible with 3.6 anymore
-if(!requireNamespace("XML", quietly=TRUE) & R.version[['major']] == "3"){
-    installIfReq(p="devtools", type=BTYPE, Ncpus=NCPUS)
-    devtools::install_version("XML", version="3.99-0.3")
-}
-
-# because of https://github.com/r-windows/rtools-installer/issues/3
-if("windows" == .Platform$OS.type){
-    print_log("Install XML on windows ...")
-    BTYPE <- "win.binary"
-    installIfReq(p=c("XML", "xml2", "RSQLite", "progress", "AnnotationDbi", "BiocCheck"))
-    
-    print_log("Install source packages only for windows ...")
-    INSTALL(c("GenomeInfoDbData", "org.Hs.eg.db", "TxDb.Hsapiens.UCSC.hg19.knownGene"), type="both")
-} else {
-    BTYPE <- "source"
-}
-
-# install needed packages
-# add testthat to pre installation dependencies due to: https://github.com/r-lib/pkgload/issues/89
-for(p in c("XML", "xml2", "testthat", "devtools", "covr", "roxygen2", "BiocCheck", "R.utils", 
-            "GenomeInfoDbData", "rtracklayer", "hms")){
-    installIfReq(p=p, type=BTYPE, Ncpus=NCPUS)
-}
-
-# install OUTRIDER with its dependencies with a timeout due to 
-# travis (50 min) and appveyor (60 min) set installation warmup to 30 min max
-maxTime <- max(30, (60*30 - difftime(Sys.time(), START_TIME, units="sec")))
-R.utils::withTimeout(timeout=maxTime, {
-    try({
-        print_log("Update packages")
-        INSTALL(ask=FALSE, type=BTYPE, Ncpus=NCPUS)
-    
-        print_log("Install OUTRIDER")
-        devtools::install(".", dependencies=TRUE, upgrade=TRUE, 
-                type=BTYPE, Ncpus=NCPUS)
-    })
-})
-
-# fix knitr for 3.6 for more details see BiocStyle issue 78
-# https://github.com/Bioconductor/BiocStyle/issues/78
-if(R.version[['major']] == "3"){
-    options(repos=c(CRAN="http://cran.rstudio.com"))
-    installIfReq(p="devtools", type=BTYPE, Ncpus=NCPUS)
-    devtools::install_version("knitr", version="1.29", type="source")
-}
diff --git a/src/RcppExports.cpp b/src/RcppExports.cpp
index 779b0ac..47e4407 100644
--- a/src/RcppExports.cpp
+++ b/src/RcppExports.cpp
@@ -6,6 +6,11 @@
 
 using namespace Rcpp;
 
+#ifdef RCPP_USE_GLOBAL_ROSTREAM
+Rcpp::Rostream<true>&  Rcpp::Rcout = Rcpp::Rcpp_cout_get();
+Rcpp::Rostream<false>& Rcpp::Rcerr = Rcpp::Rcpp_cerr_get();
+#endif
+
 // predictMatY
 arma::mat predictMatY(arma::mat x, arma::mat E, arma::mat D, arma::vec b);
 RcppExport SEXP _OUTRIDER_predictMatY(SEXP xSEXP, SEXP ESEXP, SEXP DSEXP, SEXP bSEXP) {