diff --git a/404.html b/404.html index d07a58c..47b0ca1 100644 --- a/404.html +++ b/404.html @@ -32,7 +32,7 @@ bugphyzz - 0.99.9 + 1.1.0 diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html index 4a69fa7..5b3f838 100644 --- a/CODE_OF_CONDUCT.html +++ b/CODE_OF_CONDUCT.html @@ -17,7 +17,7 @@ bugphyzz - 0.99.9 + 1.1.0 diff --git a/CONTRIBUTING.html b/CONTRIBUTING.html index 6566d40..082bb7b 100644 --- a/CONTRIBUTING.html +++ b/CONTRIBUTING.html @@ -17,7 +17,7 @@ bugphyzz - 0.99.9 + 1.1.0 diff --git a/SUPPORT.html b/SUPPORT.html index 480b8fa..d5ac2a0 100644 --- a/SUPPORT.html +++ b/SUPPORT.html @@ -17,7 +17,7 @@ bugphyzz - 0.99.9 + 1.1.0 diff --git a/articles/attributes.html b/articles/attributes.html index 21b109e..c942f11 100644 --- a/articles/attributes.html +++ b/articles/attributes.html @@ -32,7 +32,7 @@ bugphyzz - 0.99.9 + 1.1.0 @@ -126,7 +126,7 @@

Session info#> collate en_US.UTF-8 #> ctype en_US.UTF-8 #> tz UTC -#> date 2024-10-25 +#> date 2024-10-30 #> pandoc 3.4 @ /usr/bin/ (via rmarkdown) #> #> ─ Packages ─────────────────────────────────────────────────────────────────── @@ -136,7 +136,7 @@

Session info#> bit64 4.5.2 2024-09-22 [1] RSPM (R 4.4.0) #> blob 1.2.4 2023-03-17 [1] RSPM (R 4.4.0) #> bslib 0.8.0 2024-07-29 [2] RSPM (R 4.4.0) -#> bugphyzz * 0.99.9 2024-10-25 [1] Bioconductor +#> bugphyzz * 1.1.0 2024-10-30 [1] Bioconductor #> cachem 1.1.0 2024-05-16 [2] RSPM (R 4.4.0) #> cli 3.6.3 2024-06-21 [2] RSPM (R 4.4.0) #> crayon 1.5.3 2024-06-20 [2] RSPM (R 4.4.0) @@ -168,7 +168,7 @@

Session info#> memoise 2.0.1 2021-11-26 [2] RSPM (R 4.4.0) #> pillar 1.9.0 2023-03-22 [2] RSPM (R 4.4.0) #> pkgconfig 2.0.3 2019-09-22 [2] RSPM (R 4.4.0) -#> pkgdown 2.1.1.9000 2024-10-25 [1] Github (r-lib/pkgdown@4f5c10e) +#> pkgdown 2.1.1.9000 2024-10-30 [1] Github (r-lib/pkgdown@ffe60d5) #> purrr * 1.0.2 2023-08-10 [2] RSPM (R 4.4.0) #> R6 2.5.1 2021-08-19 [2] RSPM (R 4.4.0) #> ragg 1.3.3 2024-09-11 [2] RSPM (R 4.4.0) @@ -189,7 +189,7 @@

Session info#> utf8 1.2.4 2023-10-22 [2] RSPM (R 4.4.0) #> vctrs 0.6.5 2023-12-01 [2] RSPM (R 4.4.0) #> vroom 1.6.5 2023-12-05 [1] RSPM (R 4.4.0) -#> withr 3.0.1 2024-07-31 [2] RSPM (R 4.4.0) +#> withr 3.0.2 2024-10-28 [2] RSPM (R 4.4.0) #> xfun 0.48 2024-10-03 [2] RSPM (R 4.4.0) #> yaml 2.3.10 2024-07-26 [2] RSPM (R 4.4.0) #> diff --git a/articles/bugphyzz.html b/articles/bugphyzz.html index 9aab7cc..3a2a7db 100644 --- a/articles/bugphyzz.html +++ b/articles/bugphyzz.html @@ -32,7 +32,7 @@ bugphyzz - 0.99.9 + 1.1.0 @@ -652,7 +652,7 @@

Session information#> collate en_US.UTF-8 #> ctype en_US.UTF-8 #> tz UTC -#> date 2024-10-25 +#> date 2024-10-30 #> pandoc 3.4 @ /usr/bin/ (via rmarkdown) #> #> ─ Packages ─────────────────────────────────────────────────────────────────── @@ -663,7 +663,7 @@

Session information#> ape 5.8 2024-04-11 [1] RSPM (R 4.4.0) #> backports 1.5.0 2024-05-23 [1] RSPM (R 4.4.0) #> base64enc 0.1-3 2015-07-28 [2] RSPM (R 4.4.0) -#> beachmat 2.21.8 2024-10-21 [1] Bioconductor 3.20 (R 4.4.1) +#> beachmat 2.21.9 2024-10-27 [1] Bioconductor 3.20 (R 4.4.1) #> beeswarm 0.4.0 2021-06-01 [1] RSPM (R 4.4.0) #> Biobase * 2.65.1 2024-10-21 [1] Bioconductor 3.20 (R 4.4.1) #> BiocFileCache 2.13.2 2024-10-21 [1] Bioconductor 3.20 (R 4.4.1) @@ -682,7 +682,7 @@

Session information#> bookdown 0.41 2024-10-16 [1] RSPM (R 4.4.0) #> boot 1.3-31 2024-08-28 [2] RSPM (R 4.4.0) #> bslib 0.8.0 2024-07-29 [2] RSPM (R 4.4.0) -#> bugphyzz * 0.99.9 2024-10-25 [1] Bioconductor +#> bugphyzz * 1.1.0 2024-10-30 [1] Bioconductor #> cachem 1.1.0 2024-05-16 [2] RSPM (R 4.4.0) #> checkmate 2.3.2 2024-07-29 [1] RSPM (R 4.4.0) #> cli 3.6.3 2024-06-21 [2] RSPM (R 4.4.0) @@ -702,7 +702,7 @@

Session information#> digest 0.6.37 2024-08-19 [2] RSPM (R 4.4.0) #> DirichletMultinomial 1.47.2 2024-10-21 [1] Bioconductor 3.20 (R 4.4.1) #> dplyr * 1.1.4 2023-11-17 [1] RSPM (R 4.4.0) -#> edgeR 4.3.20 2024-10-21 [1] Bioconductor 3.20 (R 4.4.1) +#> edgeR 4.3.21 2024-10-25 [1] Bioconductor 3.20 (R 4.4.1) #> EnrichmentBrowser * 2.35.1 2024-05-06 [1] Bioconductor 3.20 (R 4.4.0) #> evaluate 1.0.1 2024-10-10 [2] RSPM (R 4.4.0) #> fansi 1.0.6 2023-12-08 [2] RSPM (R 4.4.0) @@ -722,8 +722,8 @@

Session information#> graph * 1.83.0 2024-05-01 [1] Bioconductor 3.20 (R 4.4.0) #> gridExtra 2.3 2017-09-09 [1] RSPM (R 4.4.0) #> GSEABase 1.67.1 2024-10-23 [1] Bioconductor 3.20 (R 4.4.1) -#> gtable 0.3.5 2024-04-22 [1] RSPM (R 4.4.0) -#> Hmisc 5.1-3 2024-05-28 [1] RSPM (R 4.4.0) +#> gtable 0.3.6 2024-10-25 [1] RSPM (R 4.4.0) +#> Hmisc 5.2-0 2024-10-28 [1] RSPM (R 4.4.0) #> htmlTable 2.4.3 2024-07-21 [1] RSPM (R 4.4.0) #> htmltools 0.5.8.1 2024-04-04 [2] RSPM (R 4.4.0) #> htmlwidgets 1.6.4 2023-12-06 [2] RSPM (R 4.4.0) @@ -746,7 +746,7 @@

Session information#> lpSolve 5.6.21 2024-09-12 [1] RSPM (R 4.4.0) #> magrittr 2.0.3 2022-03-30 [2] RSPM (R 4.4.0) #> MASS 7.3-61 2024-06-13 [2] RSPM (R 4.4.0) -#> Matrix 1.7-1 2024-10-18 [3] RSPM (R 4.4.0) +#> Matrix 1.7-1 2024-10-18 [2] RSPM (R 4.4.0) #> MatrixGenerics * 1.17.1 2024-10-23 [1] Bioconductor 3.20 (R 4.4.1) #> matrixStats * 1.4.1 2024-09-08 [1] RSPM (R 4.4.0) #> mediation 4.5.0 2019-10-08 [1] RSPM (R 4.4.0) @@ -764,7 +764,7 @@

Session information#> permute 0.9-7 2022-01-27 [1] RSPM (R 4.4.0) #> pillar 1.9.0 2023-03-22 [2] RSPM (R 4.4.0) #> pkgconfig 2.0.3 2019-09-22 [2] RSPM (R 4.4.0) -#> pkgdown 2.1.1.9000 2024-10-25 [1] Github (r-lib/pkgdown@4f5c10e) +#> pkgdown 2.1.1.9000 2024-10-30 [1] Github (r-lib/pkgdown@ffe60d5) #> plyr 1.8.9 2023-10-02 [1] RSPM (R 4.4.0) #> png 0.1-8 2022-11-29 [1] RSPM (R 4.4.0) #> purrr * 1.0.2 2023-08-10 [2] RSPM (R 4.4.0) @@ -790,7 +790,7 @@

Session information#> ScaledMatrix 1.13.0 2024-05-01 [1] Bioconductor 3.20 (R 4.4.0) #> scales 1.3.0 2023-11-28 [1] RSPM (R 4.4.0) #> scater 1.33.4 2024-10-21 [1] Bioconductor 3.20 (R 4.4.1) -#> scuttle 1.15.4 2024-10-21 [1] Bioconductor 3.20 (R 4.4.1) +#> scuttle 1.15.5 2024-10-27 [1] Bioconductor 3.20 (R 4.4.1) #> sessioninfo 1.2.2 2021-12-06 [2] RSPM (R 4.4.0) #> SingleCellExperiment * 1.27.2 2024-05-24 [1] Bioconductor 3.20 (R 4.4.0) #> slam 0.1-54 2024-10-15 [1] RSPM (R 4.4.0) @@ -806,7 +806,7 @@

Session information#> tidyr 1.3.1 2024-01-24 [1] RSPM (R 4.4.0) #> tidyselect 1.2.1 2024-03-11 [1] RSPM (R 4.4.0) #> tidytree 0.4.6 2023-12-12 [1] RSPM (R 4.4.0) -#> treeio 1.29.1 2024-10-21 [1] Bioconductor 3.20 (R 4.4.1) +#> treeio 1.29.2 2024-10-28 [1] Bioconductor 3.20 (R 4.4.1) #> TreeSummarizedExperiment * 2.13.0 2024-05-01 [1] Bioconductor 3.20 (R 4.4.0) #> UCSC.utils 1.1.0 2024-05-01 [1] Bioconductor 3.20 (R 4.4.0) #> utf8 1.2.4 2023-10-22 [2] RSPM (R 4.4.0) @@ -815,7 +815,7 @@

Session information#> vipor 0.4.7 2023-12-18 [1] RSPM (R 4.4.0) #> viridis 0.6.5 2024-01-29 [1] RSPM (R 4.4.0) #> viridisLite 0.4.2 2023-05-02 [1] RSPM (R 4.4.0) -#> withr 3.0.1 2024-07-31 [2] RSPM (R 4.4.0) +#> withr 3.0.2 2024-10-28 [2] RSPM (R 4.4.0) #> xfun 0.48 2024-10-03 [2] RSPM (R 4.4.0) #> XML 3.99-0.17 2024-06-25 [1] RSPM (R 4.4.0) #> xtable 1.8-4 2019-04-21 [2] RSPM (R 4.4.0) diff --git a/articles/index.html b/articles/index.html index 71ffdd5..786db06 100644 --- a/articles/index.html +++ b/articles/index.html @@ -17,7 +17,7 @@ bugphyzz - 0.99.9 + 1.1.0 diff --git a/articles/sources.html b/articles/sources.html index 8b57d39..5ee7b98 100644 --- a/articles/sources.html +++ b/articles/sources.html @@ -32,7 +32,7 @@ bugphyzz - 0.99.9 + 1.1.0 diff --git a/authors.html b/authors.html index 14fba55..3c8b48b 100644 --- a/authors.html +++ b/authors.html @@ -17,7 +17,7 @@ bugphyzz - 0.99.9 + 1.1.0 @@ -95,13 +95,13 @@

Citation

Gamboa S, Waldron L, Eckenrode K, Ye J, Wokaty J (2024). bugphyzz: A harmonized data resource and software for enrichment analysis of microbial physiologies. -R package version 0.99.9, https://github.com/waldronlab/bugphyzz. +R package version 1.1.0, https://github.com/waldronlab/bugphyzz. 

@Manual{,
   title = {bugphyzz: A harmonized data resource and software for enrichment analysis of microbial physiologies},
   author = {Samuel Gamboa and Levi Waldron and Kelly Eckenrode and Jonathan Ye and Jennifer Wokaty},
   year = {2024},
-  note = {R package version 0.99.9},
+  note = {R package version 1.1.0},
   url = {https://github.com/waldronlab/bugphyzz},
 }
diff --git a/index.html b/index.html index 3fea22e..cf772d2 100644 --- a/index.html +++ b/index.html @@ -33,7 +33,7 @@ bugphyzz - 0.99.9 + 1.1.0 diff --git a/news/index.html b/news/index.html index 402e15c..292189e 100644 --- a/news/index.html +++ b/news/index.html @@ -17,7 +17,7 @@ bugphyzz - 0.99.9 + 1.1.0 diff --git a/pkgdown.yml b/pkgdown.yml index d669d43..713cd36 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -1,11 +1,11 @@ pandoc: '3.4' pkgdown: 2.1.1.9000 -pkgdown_sha: 4f5c10eb59676f0ca2462eb06d7d7232c573a693 +pkgdown_sha: ffe60d5f60934e95285d416dae12c05e24ed1dac articles: articles/attributes: attributes.html bugphyzz: bugphyzz.html sources: sources.html -last_built: 2024-10-25T19:05Z +last_built: 2024-10-30T16:11Z urls: reference: https://waldronlab.io/bugphyzz/reference article: https://waldronlab.io/bugphyzz/articles diff --git a/reference/getTaxonSignatures.html b/reference/getTaxonSignatures.html index 181b748..5f3c862 100644 --- a/reference/getTaxonSignatures.html +++ b/reference/getTaxonSignatures.html @@ -19,7 +19,7 @@ bugphyzz - 0.99.9 + 1.1.0 @@ -103,7 +103,7 @@

Examples

taxid <- "562"
 taxonName <- "Escherichia coli"
 bp <- importBugphyzz()
-#> Using data downloaded on 2024-10-25 19:03:19.
+#> Using data downloaded on 2024-10-30 16:09:43.
 sig_names_1 <- getTaxonSignatures(taxid, bp)
 sig_names_2 <- getTaxonSignatures(taxonName, bp, taxIdType = "Taxon_name")
 
diff --git a/reference/importBugphyzz.html b/reference/importBugphyzz.html
index ace7e09..6806412 100644
--- a/reference/importBugphyzz.html
+++ b/reference/importBugphyzz.html
@@ -20,7 +20,7 @@
       
       
         bugphyzz
-        0.99.9
+        1.1.0
@@ -163,7 +163,7 @@

SourcesExamples


 bp <- importBugphyzz()
-#> Using data downloaded on 2024-10-25 19:03:19.
+#> Using data downloaded on 2024-10-30 16:09:43.
 names(bp)
 #>  [1] "animal pathogen"                      
 #>  [2] "antimicrobial sensitivity"            
diff --git a/reference/index.html b/reference/index.html
index 067ef9d..94a3e69 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -17,7 +17,7 @@
       
       
         bugphyzz
-        0.99.9
+        1.1.0
diff --git a/reference/makeSignatures.html b/reference/makeSignatures.html index 23fab19..a779c9b 100644 --- a/reference/makeSignatures.html +++ b/reference/makeSignatures.html @@ -19,7 +19,7 @@ bugphyzz - 0.99.9 + 1.1.0 @@ -138,7 +138,7 @@

Value

Examples


 bp <- importBugphyzz()
-#> Using data downloaded on 2024-10-25 19:03:19.
+#> Using data downloaded on 2024-10-30 16:09:43.
 sigs <- purrr::map(bp, makeSignatures)
 sigs <- purrr::list_flatten(sigs, name_spec = "{inner}")
 
diff --git a/reference/physiologies.html b/reference/physiologies.html
index bfef6b7..9d0b60c 100644
--- a/reference/physiologies.html
+++ b/reference/physiologies.html
@@ -19,7 +19,7 @@
       
       
         bugphyzz
-        0.99.9
+        1.1.0
diff --git a/reference/showPhys.html b/reference/showPhys.html index 46a1273..febb1f1 100644 --- a/reference/showPhys.html +++ b/reference/showPhys.html @@ -19,7 +19,7 @@ bugphyzz - 0.99.9 + 1.1.0