diff --git a/.DS_Store b/.DS_Store
index 81914b4f..2b21082f 100644
Binary files a/.DS_Store and b/.DS_Store differ
diff --git a/DESCRIPTION b/DESCRIPTION
index 39b026bf..40311f0c 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: ArchR
 Type: Package
-Date: 2020-10-01
+Date: 2020-11-23
 Title: Analyzing single-cell regulatory chromatin in R.
-Version: 1.0.0
+Version: 1.0.1
 Authors@R: c(
     person("Jeffrey", "Granja", email = "jgranja.stanford@gmail.com", role = c("aut","cre")),
     person("Ryan", "Corces", role = "aut"))
@@ -11,7 +11,7 @@ Roxygen: list(markdown = TRUE)
 License: GPL (>= 2)
 LinkingTo: Rcpp
 LazyData: TRUE
-RoxygenNote: 7.0.2
+RoxygenNote: 7.1.1
 Encoding: UTF-8
 Imports:
     Rcpp (>= 0.12.16),
diff --git a/NAMESPACE b/NAMESPACE
index 398bf483..ce5679a8 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -17,6 +17,7 @@ export(addArchRDebugging)
 export(addArchRGenome)
 export(addArchRLogging)
 export(addArchRThreads)
+export(addArchRVerbose)
 export(addBgdPeaks)
 export(addCellColData)
 export(addClusters)
@@ -68,6 +69,7 @@ export(getArchRDebugging)
 export(getArchRGenome)
 export(getArchRLogging)
 export(getArchRThreads)
+export(getArchRVerbose)
 export(getArrowFiles)
 export(getAvailableMatrices)
 export(getBgdPeaks)
diff --git a/R/AllClasses.R b/R/AllClasses.R
index 9ba68568..f87ff98c 100644
--- a/R/AllClasses.R
+++ b/R/AllClasses.R
@@ -130,7 +130,7 @@ ArchRProject <- function(
 
   message("Getting SampleNames...")
   sampleNames <- unlist(.safelapply(seq_along(ArrowFiles), function(x){
-    message(x, " ", appendLF = FALSE)
+    if(getArchRVerbose()) message(x, " ", appendLF = FALSE)
     .sampleName(ArrowFiles[x])
   }, threads = threads))
   message("")
@@ -159,7 +159,7 @@ ArchRProject <- function(
   #Cell Information
   message("Getting Cell Metadata...")
   metadataList <- .safelapply(seq_along(ArrowFiles), function(x){
-    message(x, " ", appendLF = FALSE)
+    if(getArchRVerbose()) message(x, " ", appendLF = FALSE)
     .getMetadata(ArrowFiles[x])
   }, threads = threads)
   message("")
diff --git a/R/AnnotationGenome.R b/R/AnnotationGenome.R
index d35fa9ba..3d75ac3a 100644
--- a/R/AnnotationGenome.R
+++ b/R/AnnotationGenome.R
@@ -41,7 +41,14 @@ createGenomeAnnotation <- function(
 
     ##################
     message("Getting blacklist..")
-    blacklist <- .getBlacklist(genome = bsg@provider_version)
+
+    genomeName <- tryCatch({
+      bsg@provider_version
+    }, error = function(e){
+      strsplit(bsg@pkgname,"\\.")[[1]][4]
+    })
+
+    blacklist <- .getBlacklist(genome = genomeName)
 
   }else{
 
diff --git a/R/AnnotationPeaks.R b/R/AnnotationPeaks.R
index 60b30642..13df1f22 100644
--- a/R/AnnotationPeaks.R
+++ b/R/AnnotationPeaks.R
@@ -98,7 +98,7 @@ getMatches <- function(ArchRProj = NULL, name = NULL, annoName = NULL){
 #' binary value is stored indicating whether each region is observed within the peak region.
 #' 
 #' @param ArchRProj An `ArchRProject` object.
-#' @param regions A `list` of `GRanges` that are to be overlapped with the `peakSet` in the `ArchRProject`.
+#' @param regions A named `list` of `GRanges` that are to be overlapped with the `peakSet` in the `ArchRProject`.
 #' @param name The name of `peakAnnotation` object to be stored as in `ArchRProject`.
 #' @param force A boolean value indicating whether to force the `peakAnnotation` object indicated by `name` to be overwritten
 #' if it already exists in the given `ArchRProject`.
@@ -136,6 +136,10 @@ addPeakAnnotations <- function(
 
   }else{
 
+    if(is.null(names(regions))){
+      names(regions) <- paste0("Region_", seq_along(regions))
+    }
+
     regionPositions <- lapply(seq_along(regions), function(x){
       
       .logThis(regions[[x]], paste0("regions[[x]]-", x), logFile = logFile)
@@ -184,6 +188,9 @@ addPeakAnnotations <- function(
   # Peak Overlap Matrix
   #############################################################
   peakSet <- getPeakSet(ArchRProj)
+  if(is.null(peakSet)){
+    .logStop("peakSet is NULL. You need a peakset to run addMotifAnnotations! See addReproduciblePeakSet!", logFile = logFile)
+  }
   allPositions <- unlist(regionPositions)
 
   .logDiffTime("Creating Peak Overlap Matrix", t1 = tstart, verbose = TRUE, logFile = logFile)
@@ -431,6 +438,9 @@ addMotifAnnotations <- function(
   #############################################################
   .logDiffTime("Finding Motif Positions with motifmatchr!", t1 = tstart, verbose = TRUE, logFile = logFile)
   peakSet <- ArchRProj@peakSet
+  if(is.null(peakSet)){
+    .logStop("peakSet is NULL. You need a peakset to run addMotifAnnotations! See addReproduciblePeakSet!", logFile = logFile)
+  }
   motifPositions <- motifmatchr::matchMotifs(
       pwms = motifs,
       subject = peakSet,
@@ -606,7 +616,11 @@ addArchRAnnotations <- function(
     }
   }
 
-  genome <- tolower(validBSgenome(getGenome(ArchRProj))@provider_version)
+  genome <- tolower(tryCatch({
+    validBSgenome(getGenome(ArchRProj))$provider_version
+  }, error = function(e){
+    strsplit(validBSgenome(getGenome(ArchRProj))@pkgname,"\\.")[[1]][4]
+  }))
 
   annoPath <- file.path(find.package("ArchR", NULL, quiet = TRUE), "data", "Annotations")
   dir.create(annoPath, showWarnings = FALSE)
@@ -690,6 +704,9 @@ addArchRAnnotations <- function(
   # Peak Overlap Matrix
   #############################################################
   peakSet <- getPeakSet(ArchRProj)
+  if(is.null(peakSet)){
+    .logStop("peakSet is NULL. You need a peakset to run addMotifAnnotations! See addReproduciblePeakSet!", logFile = logFile)
+  }
   chr <- paste0(unique(seqnames(peakSet)))
 
   .logMessage("Annotating Chromosomes", verbose = TRUE, logFile = logFile)
@@ -1061,6 +1078,10 @@ plotEnrichHeatmap <- function(
   mat <- mat[keep, ,drop = FALSE]
   .logThis(mat, "mat-mlog10Padj-Filter", logFile = logFile)
 
+  if(nrow(mat)==0){
+    stop("No enrichments found for your cutoff!")
+  }
+
   passMat <- lapply(seq_len(nrow(mat)), function(x){
     (mat[x, ] >= 0.9*max(mat[x, ])) * 1
   }) %>% Reduce("rbind", .) %>% data.frame
@@ -1070,7 +1091,7 @@ plotEnrichHeatmap <- function(
   mat[mat > pMax] <- pMax
 
   if(nrow(mat)==0){
-    stop("No enrichments found!")
+    stop("No enrichments found for your cutoff!")
   }
 
   mat <- .rowScale(as.matrix(mat), min = 0)
diff --git a/R/ArchRBrowser.R b/R/ArchRBrowser.R
index 27a01fbd..c496cc9f 100644
--- a/R/ArchRBrowser.R
+++ b/R/ArchRBrowser.R
@@ -1749,6 +1749,12 @@ plotBrowserTrack <- function(
 
   title <- paste0(as.character(seqnames(region)),":", start(region)-1, "-", end(region), " ", title)
   
+  #Re-Order
+  groupDF$group2 <- factor(
+    paste0(groupDF$group2), 
+    levels = gtools::mixedsort(unique(paste0(groupDF$group2)))
+  )
+
   p <- ggplot(groupDF, aes(x=bp, y=y, width = tileSize, fill = group2, color = group2)) + 
       geom_tile(size = scTileSize) + 
       facet_grid(group2 ~ ., scales="free_y") + 
diff --git a/R/ArrowRead.R b/R/ArrowRead.R
index 0fa26ae1..20bbdb6c 100644
--- a/R/ArrowRead.R
+++ b/R/ArrowRead.R
@@ -783,6 +783,11 @@ getMatrixFromArrow <- function(
 
     matFiles <- lapply(mat, function(x) x[[2]]) %>% Reduce("c", .)
     mat <- lapply(mat, function(x) x[[1]]) %>% Reduce("cbind", .)
+    if(!all(cellNames %in% colnames(mat))){
+      .logThis(sampledCellNames, "cellNames supplied", logFile = logFile)
+      .logThis(colnames(mat), "cellNames from matrix", logFile = logFile)
+      stop("Error not all cellNames found in partialMatrix")
+    }
     mat <- mat[,sampledCellNames, drop = FALSE]
     mat <- .checkSparseMatrix(mat, length(sampledCellNames))
 
@@ -793,6 +798,11 @@ getMatrixFromArrow <- function(
   }else{
 
     mat <- Reduce("cbind", mat)
+    if(!all(cellNames %in% colnames(mat))){
+      .logThis(cellNames, "cellNames supplied", logFile = logFile)
+      .logThis(colnames(mat), "cellNames from matrix", logFile = logFile)
+      stop("Error not all cellNames found in partialMatrix")
+    }
     mat <- mat[,cellNames, drop = FALSE]
     mat <- .checkSparseMatrix(mat, length(cellNames))
     
@@ -902,6 +912,16 @@ getMatrixFromArrow <- function(
       stop("Means Variances and Ns lengths not identical")
     }
 
+    #Check if samples have NAs due to N = 1 sample or some other weird thing.
+    #Set it to min non NA variance
+    dfVars <- lapply(seq_len(nrow(dfVars)), function(x){
+      vx <- dfVars[x, ]
+      if(any(is.na(vx))){
+        vx[is.na(vx)] <- min(vx[!is.na(vx)])
+      }
+      vx
+    }) %>% Reduce("rbind", .)
+
     combinedMeans <- rowSums(t(t(dfMeans) * ns)) / sum(ns)
     summedVars <- rowSums(t(t(dfVars) * (ns - 1)) + t(t(dfMeans^2) * ns))
     combinedVars <- (summedVars - sum(ns)*combinedMeans^2)/(sum(ns)-1)
@@ -925,8 +945,6 @@ getMatrixFromArrow <- function(
     length(.availableCells(ArrowFiles[y], useMatrix))
   }) %>% unlist
 
-
-
   #Compute RowVars
   summaryDF <- .safelapply(seq_along(featureDF), function(x){
     
diff --git a/R/ArrowUtils.R b/R/ArrowUtils.R
index 7fa584b5..f8e4af75 100644
--- a/R/ArrowUtils.R
+++ b/R/ArrowUtils.R
@@ -379,10 +379,20 @@
   o <- h5createGroup(outArrow, groupName)
 
   mData <- ArrowInfo[[groupName]]
+  cellNames <- .h5read(inArrow, "Metadata/CellNames")
+  idx <- which(cellNames %in% stringr::str_split(cellsKeep, pattern="#", simplify=TRUE)[,2])
   
+  if(length(idx)==0){
+    stop("No cells matching in arrow file!")
+  }
+
   for(i in seq_len(nrow(mData))){
     h5name <- paste0(groupName, "/", mData$name[i])
-    h5write(.h5read(inArrow, h5name), file = outArrow, name = h5name)
+    mDatai <- .h5read(inArrow, h5name)
+    if(length(mDatai)==length(cellNames)){
+      mDatai <- mDatai[idx]
+    }
+    h5write(mDatai, file = outArrow, name = h5name)
   }
 
   #2. scATAC-Fragments
diff --git a/R/CreateArrow.R b/R/CreateArrow.R
index 10db9ec3..d793bc69 100644
--- a/R/CreateArrow.R
+++ b/R/CreateArrow.R
@@ -473,7 +473,7 @@ createArrowFiles <- function(
 
       .logDiffTime("Continuing through after error ggplot for Fragment Size Distribution", t1 = tstart, logFile = logFile)
       #print(x)
-      message("\n")
+      if(getArchRVerbose()) message("\n")
 
   })
   gc()
@@ -537,7 +537,7 @@ createArrowFiles <- function(
 
       .logDiffTime("Continuing through after error ggplot for TSS by Frags", t1 = tstart, logFile = logFile)
       #message(x)
-      message("\n")
+      if(getArchRVerbose()) message("\n")
 
   })
 
@@ -1119,7 +1119,7 @@ createArrowFiles <- function(
     TRUE
   }, error = function(x){
     tryCatch({
-      message("Attempting to index ", file," as tabix..")
+      if(getArchRVerbose()) message("Attempting to index ", file," as tabix..")
       indexTabix(file, format = "bed")
       TRUE
     }, error = function(y){
@@ -1138,7 +1138,7 @@ createArrowFiles <- function(
     }
   }, error = function(x){
     tryCatch({
-      message("Attempting to index ", file," as bam...")
+      if(getArchRVerbose()) message("Attempting to index ", file," as bam...")
       indexBam(file)
       TRUE
     }, error = function(y){
@@ -1278,7 +1278,7 @@ createArrowFiles <- function(
           o <- .suppressAll(h5createDataset(tmpFile, chrRGLengths, storage.mode = "integer", dims = c(lengthRG, 1), level = 0))
           o <- .suppressAll(h5createDataset(tmpFile, chrRGValues, storage.mode = "character", 
             dims = c(lengthRG, 1), level = 0, size = max(nchar(RG@values)) + 1))
-          o <- h5write(obj = cbind(dt$V2,dt$V3-dt$V2), file = tmpFile, name = chrPos)
+          o <- h5write(obj = cbind(dt$V2,dt$V3 - dt$V2 + 1), file = tmpFile, name = chrPos)
           o <- h5write(obj = RG@lengths, file = tmpFile, name = chrRGLengths)
           o <- h5write(obj = RG@values, file = tmpFile, name = chrRGValues)
 
@@ -1314,7 +1314,7 @@ createArrowFiles <- function(
           o <- .suppressAll(h5createDataset(tmpChrFile, chrRGValues, storage.mode = "character", 
             dims = c(lengthRG, 1), level = 0, size = max(nchar(RG@values)) + 1))
           
-          o <- h5write(obj = cbind(dt$V2,dt$V3-dt$V2), file = tmpChrFile, name = chrPos)
+          o <- h5write(obj = cbind(dt$V2,dt$V3 - dt$V2 + 1), file = tmpChrFile, name = chrPos)
           o <- h5write(obj = RG@lengths, file = tmpChrFile, name = chrRGLengths)
           o <- h5write(obj = RG@values, file = tmpChrFile, name = chrRGValues)
 
@@ -1650,7 +1650,7 @@ createArrowFiles <- function(
           o <- .suppressAll(h5createDataset(tmpFile, chrRGValues, storage.mode = "character", 
                     dims = c(lengthRG, 1), level = 0, size = max(nchar(RG@values)) + 1))
 
-          o <- h5write(obj = cbind(dt$start,dt$end-dt$start), file = tmpFile, name = chrPos)
+          o <- h5write(obj = cbind(dt$start, dt$end - dt$start + 1), file = tmpFile, name = chrPos)
           o <- h5write(obj = RG@lengths, file = tmpFile, name = chrRGLengths)
           o <- h5write(obj = RG@values, file = tmpFile, name = chrRGValues)
 
@@ -1686,7 +1686,7 @@ createArrowFiles <- function(
           o <- .suppressAll(h5createDataset(tmpChrFile, chrRGValues, storage.mode = "character", 
                     dims = c(lengthRG, 1), level = 0, size = max(nchar(RG@values)) + 1))
 
-          o <- h5write(obj = cbind(dt$start,dt$end-dt$start), file = tmpChrFile, name = chrPos)
+          o <- h5write(obj = cbind(dt$start, dt$end - dt$start + 1), file = tmpChrFile, name = chrPos)
           o <- h5write(obj = RG@lengths, file = tmpChrFile, name = chrRGLengths)
           o <- h5write(obj = RG@values, file = tmpChrFile, name = chrRGValues)
 
@@ -1930,14 +1930,29 @@ createArrowFiles <- function(
           chrPos <- paste0("Fragments/",chr,"/Ranges")
           chrRGLengths <- paste0("Fragments/",chr,"/RGLengths")
           chrRGValues <- paste0("Fragments/",chr,"/RGValues")
-          o <- h5createGroup(outArrow, paste0("Fragments/",chr))
-          o <- .suppressAll(h5createDataset(outArrow, chrPos, storage.mode = "integer", dims = c(length(fragments), 2), level = 0))
-          o <- .suppressAll(h5createDataset(outArrow, chrRGLengths, storage.mode = "integer", dims = c(lengthRG, 1), level = 0))
-          o <- .suppressAll(h5createDataset(outArrow, chrRGValues, storage.mode = "character", dims = c(lengthRG, 1), level = 0, 
-                  size = max(nchar(mcols(fragments)$RG@values)) + 1))
-          o <- h5write(obj = cbind(start(fragments),width(fragments)), file = outArrow, name = chrPos)
-          o <- h5write(obj = mcols(fragments)$RG@lengths, file = outArrow, name = chrRGLengths)
-          o <- h5write(obj = mcols(fragments)$RG@values, file = outArrow, name = chrRGValues)
+
+          if(lengthRG == 0){
+          
+            .logMessage(msg = paste0(prefix, " detected 0 Fragments in cells passing filtering threshold for ", chr), logFile = logFile)
+          
+            o <- h5createGroup(outArrow, paste0("Fragments/",chr))
+            o <- .suppressAll(h5createDataset(outArrow, chrPos, storage.mode = "integer", dims = c(0, 2), level = 0))
+            o <- .suppressAll(h5createDataset(outArrow, chrRGLengths, storage.mode = "integer", dims = c(0, 1), level = 0))
+            o <- .suppressAll(h5createDataset(outArrow, chrRGValues, storage.mode = "character", dims = c(0, 1), level = 0, 
+                    size = 10))
+            
+          }else{
+
+            o <- h5createGroup(outArrow, paste0("Fragments/",chr))
+            o <- .suppressAll(h5createDataset(outArrow, chrPos, storage.mode = "integer", dims = c(length(fragments), 2), level = 0))
+            o <- .suppressAll(h5createDataset(outArrow, chrRGLengths, storage.mode = "integer", dims = c(lengthRG, 1), level = 0))
+            o <- .suppressAll(h5createDataset(outArrow, chrRGValues, storage.mode = "character", dims = c(lengthRG, 1), level = 0, 
+                    size = max(nchar(mcols(fragments)$RG@values)) + 1))
+            
+            o <- h5write(obj = cbind(start(fragments),width(fragments)), file = outArrow, name = chrPos)
+            o <- h5write(obj = mcols(fragments)$RG@lengths, file = outArrow, name = chrRGLengths)
+            o <- h5write(obj = mcols(fragments)$RG@values, file = outArrow, name = chrRGValues)
+          }
 
           #Free Some Memory!
           rm(fragments)
@@ -1995,15 +2010,26 @@ createArrowFiles <- function(
           chrRGLengths <- paste0(chr, "._.RGLengths")
           chrRGValues <- paste0(chr, "._.RGValues")
 
-          #HDF5 Write
-          o <- .suppressAll(h5createDataset(tmpChrFile, chrPos, storage.mode = "integer", dims = c(length(fragments), 2), level = 0))
-          o <- .suppressAll(h5createDataset(tmpChrFile, chrRGLengths, storage.mode = "integer", dims = c(lengthRG, 1), level = 0))
-          o <- .suppressAll(h5createDataset(tmpChrFile, chrRGValues, storage.mode = "character", dims = c(lengthRG, 1), level = 0, 
-                  size = max(nchar(mcols(fragments)$RG@values)) + 1))
-
-          o <- h5write(obj = cbind(start(fragments),width(fragments)), file = tmpChrFile, name = chrPos)
-          o <- h5write(obj = mcols(fragments)$RG@lengths, file = tmpChrFile, name = chrRGLengths)
-          o <- h5write(obj = mcols(fragments)$RG@values, file = tmpChrFile, name = chrRGValues)
+          if(lengthRG == 0){
+                   
+            #HDF5 Write
+            o <- .suppressAll(h5createDataset(tmpChrFile, chrPos, storage.mode = "integer", dims = c(0, 2), level = 0))
+            o <- .suppressAll(h5createDataset(tmpChrFile, chrRGLengths, storage.mode = "integer", dims = c(0, 1), level = 0))
+            o <- .suppressAll(h5createDataset(tmpChrFile, chrRGValues, storage.mode = "character", dims = c(0, 1), level = 0, 
+                    size = 10))
+
+          }else{
+           
+            #HDF5 Write
+            o <- .suppressAll(h5createDataset(tmpChrFile, chrPos, storage.mode = "integer", dims = c(length(fragments), 2), level = 0))
+            o <- .suppressAll(h5createDataset(tmpChrFile, chrRGLengths, storage.mode = "integer", dims = c(lengthRG, 1), level = 0))
+            o <- .suppressAll(h5createDataset(tmpChrFile, chrRGValues, storage.mode = "character", dims = c(lengthRG, 1), level = 0, 
+                    size = max(nchar(mcols(fragments)$RG@values)) + 1))
+
+            o <- h5write(obj = cbind(start(fragments),width(fragments)), file = tmpChrFile, name = chrPos)
+            o <- h5write(obj = mcols(fragments)$RG@lengths, file = tmpChrFile, name = chrRGLengths)
+            o <- h5write(obj = mcols(fragments)$RG@values, file = tmpChrFile, name = chrRGValues)
+          }
 
           #Free Some Memory!
           rm(fragments)
diff --git a/R/Embedding.R b/R/Embedding.R
index ba59be35..e0ead19c 100644
--- a/R/Embedding.R
+++ b/R/Embedding.R
@@ -207,9 +207,18 @@ addUMAP <- function(
 
 }
 
+#New Save UWOT
+.saveUWOT <- function(model, file){
+  tryCatch({
+    uwot::save_uwot(model = model, file = file, verbose = TRUE)
+  }, error = function(e){
+    .saveUWOT_Deprecated(model = model, file = file) #backwards to previous version
+  })
+}
+
 #save_uwot does not work because tarring doesnt work for some reason on Stanford's compute server
 #Adapted from save_uwot
-.saveUWOT <- function(model, file){
+.saveUWOT_Deprecated <- function(model, file){
   file <- file.path(normalizePath(dirname(file)), basename(file))
   wd <- getwd()
   mod_dir <- tempfile(pattern = "dir")
@@ -243,8 +252,17 @@ addUMAP <- function(
   return(o)
 }
 
+#New Save UWOT
+.loadUWOT <- function(file){
+  tryCatch({
+    uwot::load_uwot(file = file, verbose = TRUE)
+  }, error = function(e){
+    .loadUWOT_Deprecated(file = file, nDim = nDim) #backwards to previous version
+  })
+}
+
 #Adapted from load_uwot
-.loadUWOT <- function(file, nDim = NULL){
+.loadUWOT_Deprecated <- function(file, nDim = NULL){
     model <- NULL
     tryCatch({
         mod_dir <- tempfile(pattern = "dir")
diff --git a/R/FilterCells.R b/R/FilterCells.R
index 6ef51514..54a89ac1 100644
--- a/R/FilterCells.R
+++ b/R/FilterCells.R
@@ -99,7 +99,7 @@ filterDoublets <- function(ArchRProj = NULL, cutEnrich = 1, cutScore = -Inf, fil
   }
   
   ArchRProj <- addProjectSummary(ArchRProj = ArchRProj, name = "filterDoublets", 
-    summary = c("Date" = Sys.time(), cutEnrich = cutEnrich, cutScore = cutScore, filterRatio = filterRatio))
+    summary = c(cutEnrich = cutEnrich, cutScore = cutScore, filterRatio = filterRatio))
 
   ArchRProj
 
diff --git a/R/GgplotUtils.R b/R/GgplotUtils.R
index c0339437..609caa08 100644
--- a/R/GgplotUtils.R
+++ b/R/GgplotUtils.R
@@ -952,8 +952,10 @@ theme_ArchR <- function(
 
 .checkCairo <- function(){
   tryCatch({
+    tmp <- dev.cur()
     Cairo::Cairo(type='raster')
     dev.off()
+    dev.set(tmp)
     TRUE
   }, error = function(e){
     FALSE
diff --git a/R/GlobalDefaults.R b/R/GlobalDefaults.R
index 26854c57..aae3753b 100644
--- a/R/GlobalDefaults.R
+++ b/R/GlobalDefaults.R
@@ -8,7 +8,8 @@ ArchRDefaults <- list(
   ArchR.logging = TRUE,
   ArchR.genome = NA,
   ArchR.chrPrefix = TRUE,
-  ArchR.debugging = FALSE 
+  ArchR.debugging = FALSE,
+  ArchR.verbose = TRUE
 )
 
 .onAttach <- function(libname, pkgname){
@@ -27,9 +28,30 @@ ArchRDefaults <- list(
   if(!.checkCairo()){
     packageStartupMessage("WARNING : Cairo check shows Cairo is not functional.\n          ggplot2 rasterization will not be available without Cario.\n          This may cause issues editing plots with many thousands of points from single cells.")
   }
+  if(.checkJupyter()){
+    packageStartupMessage("Detected Jupyer Notebook session. Disabling Log Messages!\n\tIf this is undesired use `addArchRVerbose(TRUE)`")
+    addArchRVerbose(verbose = FALSE)
+  }
   invisible()
 }
 
+#Check Jupyer Status
+.checkJupyter <- function(){
+  tryCatch({
+    sysID <- Sys.getenv("JPY_PARENT_PID")
+    if(!is.character(sysID)){
+      return(FALSE)
+    }
+    if(sysID == ""){
+      FALSE
+    }else{
+      TRUE
+    }
+  },error= function(e){
+    FALSE
+  })
+}
+
 #' Install extra packages used in ArchR that are not installed by default
 #' 
 #' This function will install extra packages used in ArchR that are not installed by default.
diff --git a/R/GroupCoverages.R b/R/GroupCoverages.R
index 549ec840..63859218 100644
--- a/R/GroupCoverages.R
+++ b/R/GroupCoverages.R
@@ -195,7 +195,11 @@ addGroupCoverages <- function(
   args$ArrowFiles <- getArrowFiles(ArchRProj)
   args$availableChr <- .availableSeqnames(getArrowFiles(ArchRProj))
   args$chromLengths <- getChromLengths(ArchRProj)
-  args$cellsInArrow <- split(rownames(getCellColData(ArchRProj)), getCellColData(ArchRProj)$Sample)
+  #args$cellsInArrow <- split(rownames(getCellColData(ArchRProj)), getCellColData(ArchRProj)$Sample)
+  args$cellsInArrow <-   cellsInArrow <- split(
+    rownames(getCellColData(ArchRProj)), 
+    stringr::str_split(rownames(getCellColData(ArchRProj)), pattern="\\#", simplify=TRUE)[,1]
+  )
   args$covDir <- file.path(getOutputDirectory(ArchRProj), "GroupCoverages", groupBy)
   args$parallelParam <- parallelParam
   args$threads <- threads
@@ -218,9 +222,6 @@ addGroupCoverages <- function(
   nCells <- lapply(seq_along(batchOut),function(x) batchOut[[x]]$nCells) %>% unlist
   nFragments <- lapply(seq_along(batchOut),function(x) batchOut[[x]]$nFragments) %>% unlist
 
-  #Enable Hdf5 File Locking
-  h5enableFileLocking()
-
   #Add To Project
   coverageMetadata <- DataFrame(
     Group = stringr::str_split(names(unlistGroups), pattern = "\\._.", simplify=TRUE)[,1],
@@ -245,6 +246,9 @@ addGroupCoverages <- function(
 
   ArchRProj@projectMetadata$GroupCoverages[[groupBy]] <- SimpleList(Params = Params, coverageMetadata = coverageMetadata)
 
+  #Enable Hdf5 File Locking
+  h5enableFileLocking()
+
   .logDiffTime(sprintf("Finished Creation of Coverage Files!"), tstart, addHeader = FALSE)
   .endLogging(logFile = logFile)
 
@@ -671,7 +675,7 @@ addGroupCoverages <- function(
 .getCoverageMetadata <- function(ArchRProj = NULL, groupBy = NULL, useGroups = NULL, minCells = NULL){
   coverageMetadata <- ArchRProj@projectMetadata$GroupCoverages[[groupBy]]$coverageMetadata
   if(is.null(coverageMetadata)){
-    stop("No Coverage Metadata found for : ", groupBy)
+    stop("No Coverage Metadata found for : ", groupBy, ". Please run addGroupCoverages!")
   }
   if(!is.null(useGroups)){
     if(sum(coverageMetadata[,1] %in% useGroups) == 0){
diff --git a/R/GroupExport.R b/R/GroupExport.R
index b13b5a1e..87bf3719 100644
--- a/R/GroupExport.R
+++ b/R/GroupExport.R
@@ -222,7 +222,11 @@ getGroupBW <- function(
 
   o <- suppressWarnings(file.remove(list.files(bwDir2, full.names = TRUE)))
 
-  cellsInArrow <- split(rownames(getCellColData(ArchRProj)), getCellColData(ArchRProj)$Sample)
+  #cellsInArrow <- split(rownames(getCellColData(ArchRProj)), getCellColData(ArchRProj)$Sample)
+  cellsInArrow <- split(
+    rownames(getCellColData(ArchRProj)), 
+    stringr::str_split(rownames(getCellColData(ArchRProj)), pattern="\\#", simplify=TRUE)[,1]
+  )
   availableChr <- .availableSeqnames(head(getArrowFiles(ArchRProj)))
   chromLengths <- getChromLengths(ArchRProj)
   chromSizes <- getChromSizes(ArchRProj)
diff --git a/R/IntegrativeAnalysis.R b/R/IntegrativeAnalysis.R
index 909e0f30..543d1eff 100644
--- a/R/IntegrativeAnalysis.R
+++ b/R/IntegrativeAnalysis.R
@@ -821,7 +821,7 @@ addCoAccessibility <- function(
   o$idx2 <- NULL
   o <- o[!is.na(o$correlation),]
 
-  o$TStat <- (o$correlation / sqrt((max(1-o$correlation^2, 0.00000000000000001))/(length(knnObj)-2))) #T-statistic P-value
+  o$TStat <- (o$correlation / sqrt((pmax(1-o$correlation^2, 0.00000000000000001, na.rm = TRUE))/(length(knnObj)-2))) #T-statistic P-value
   o$Pval <- 2*pt(-abs(o$TStat), length(knnObj) - 2)
   o$FDR <- p.adjust(o$Pval, method = "fdr")
   o$VarQuantile1 <- .getQuantiles(o$Variability1)
@@ -1028,9 +1028,16 @@ addPeak2GeneLinks <- function(
   tstart <- Sys.time()
 
   dfAll <- .safelapply(seq_along(ArrowFiles), function(x){
+    cNx <- paste0(names(ArrowFiles)[x], "#", h5read(ArrowFiles[x], paste0(useMatrix, "/Info/CellNames")))
+    pSx <- tryCatch({
+      h5read(ArrowFiles[x], paste0(useMatrix, "/Info/predictionScore"))
+    }, error = function(e){
+      if(getArchRVerbose()) message("No predictionScore found. Continuing without predictionScore!")
+      rep(9999999, length(cNx))
+    })
     DataFrame(
-      cellNames = paste0(names(ArrowFiles)[x], "#", h5read(ArrowFiles[x], paste0(useMatrix, "/Info/CellNames"))),
-      predictionScore = h5read(ArrowFiles[x], paste0(useMatrix, "/Info/predictionScore"))
+      cellNames = cNx,
+      predictionScore = pSx
     )
   }, threads = threads) %>% Reduce("rbind", .)
 
@@ -1173,7 +1180,7 @@ addPeak2GeneLinks <- function(
   o$Correlation <- rowCorCpp(as.integer(o$A), as.integer(o$B), assay(seATAC), assay(seRNA))
   o$VarAssayA <- .getQuantiles(matrixStats::rowVars(assay(seATAC)))[o$A]
   o$VarAssayB <- .getQuantiles(matrixStats::rowVars(assay(seRNA)))[o$B]
-  o$TStat <- (o$Correlation / sqrt((max(1-o$Correlation^2, 0.00000000000000001))/(ncol(seATAC)-2))) #T-statistic P-value
+  o$TStat <- (o$Correlation / sqrt((pmax(1-o$Correlation^2, 0.00000000000000001, na.rm = TRUE))/(ncol(seATAC)-2))) #T-statistic P-value
   o$Pval <- 2*pt(-abs(o$TStat), ncol(seATAC) - 2)
   o$FDR <- p.adjust(o$Pval, method = "fdr")
   out <- o[, c("A", "B", "Correlation", "FDR", "VarAssayA", "VarAssayB")]
diff --git a/R/IterativeLSI.R b/R/IterativeLSI.R
index 97f1dcac..57300734 100644
--- a/R/IterativeLSI.R
+++ b/R/IterativeLSI.R
@@ -803,9 +803,7 @@ addIterativeLSI <- function(
       UMAPParams$n_threads <- floor(threads / 2)
       uwotUmap <- do.call(uwot::umap, UMAPParams)
       
-      #Plot
-      pdf(file.path(outDir, paste0("Save-LSI-Iteration-",j,".pdf")), width = 6, height = 6)
-      
+      #Plot      
       p1 <- ggPoint(
         uwotUmap[,1], 
         uwotUmap[,2], 
@@ -831,6 +829,7 @@ addIterativeLSI <- function(
           theme(axis.text.x = element_blank(), axis.ticks.x = element_blank(), 
                 axis.text.y = element_blank(), axis.ticks.y = element_blank())
 
+      pdf(file.path(outDir, paste0("Save-LSI-Iteration-",j,".pdf")), width = 6, height = 6)
       .fixPlotSize(p1, plotWidth = 6, plotHeight = 6)
       grid::grid.newpage()
       .fixPlotSize(p2, plotWidth = 6, plotHeight = 6)
diff --git a/R/LoggerUtils.R b/R/LoggerUtils.R
index f704cf94..bc498e08 100644
--- a/R/LoggerUtils.R
+++ b/R/LoggerUtils.R
@@ -56,6 +56,33 @@ getArchRDebugging <- function(){
   ArchRDebugging
 }
 
+#' Set ArchR Verbosity for Log Messaging
+#' 
+#' This function will set ArchR logging verbosity.
+#'
+#' @param verbose A boolean describing whether to printMessages in addition to logging with ArchR.
+#' @export
+addArchRVerbose <- function(verbose = TRUE){
+  .validInput(input = verbose, name = "verbose", valid = "boolean")
+  message("Setting addArchRVerbose = ", verbose)
+  options(ArchR.verbose = verbose)
+  return(invisible(0))
+}
+
+#' Set ArchR Verbosity for Log Messaging
+#' 
+#' This function will get ArchR logging verbosity.
+#'
+#' @export
+getArchRVerbose <- function(){
+  ArchRVerbose <- options()[["ArchR.verbose"]]
+  if(!is.logical(ArchRVerbose)){
+    options(ArchR.verbose = TRUE)
+    return(TRUE)
+  }
+  ArchRVerbose
+}
+
 #' Create a Log File for ArchR
 #' 
 #' This function will create a log file for ArchR functions. If ArchRLogging is not TRUE
@@ -113,9 +140,9 @@ createLogFile <- function(
       }else{
         msg <- sprintf("%s : %s, %s %s %s", Sys.time(), main, dt, units, tail)
       }
-      message(msg)
+      if(getArchRVerbose()) message(msg)
     }, error = function(x){
-      message("Time Error : ", x)
+      if(getArchRVerbose()) message("Time Error : ", x)
     })
 
   }
@@ -172,7 +199,7 @@ createLogFile <- function(
   }
   }
 
-  message("ArchR logging to : ", logFile, 
+  if(getArchRVerbose()) message("ArchR logging to : ", logFile, 
     "\nIf there is an issue, please report to github with logFile!")
   
   #Begin With
@@ -220,8 +247,12 @@ createLogFile <- function(
   useLogs = getArchRLogging()
   ){
 
-  msg <- utils::capture.output(message(...), type = "message")
-  msg <- paste0(msg, collapse = "\n")
+  if(getArchRVerbose()){
+    msg <- utils::capture.output(message(...), type = "message")
+    msg <- paste0(msg, collapse = "\n")
+  }else{
+    msg <- "SuppressedMessaged due to getArchRVerbose() is FALSE!"
+  }
 
   if(is.null(msg)){
     stop("Message must be provided when logging!")
@@ -556,7 +587,7 @@ createLogFile <- function(
     cat(paste0("Elapsed Time Minutes = ", mn), file = logFile, append = TRUE)
     cat(paste0("\nElapsed Time Hours = ", hr), file = logFile, append = TRUE)
     cat("\n\n-------\n\n\n\n", file = logFile, append = TRUE)
-    message("ArchR logging successful to : ", logFile)
+    if(getArchRVerbose()) message("ArchR logging successful to : ", logFile)
   }, error = function(x){
   })
 
diff --git a/R/MarkerFeatures.R b/R/MarkerFeatures.R
index 0cf5bf56..0ed03a5b 100644
--- a/R/MarkerFeatures.R
+++ b/R/MarkerFeatures.R
@@ -410,6 +410,10 @@ getMarkerFeatures <- function(
     
     }
 
+    .logThis(o, paste0(group, "_", seqnames[y], "_diffResult"), logFile = logFile)
+
+    o
+
   }) %>% Reduce("rbind", .)
 
   idxFilter <- rowSums(pairwiseDF[,c("mean1","mean2")]) != 0
diff --git a/R/MatrixDeviations.R b/R/MatrixDeviations.R
index 6fd0d467..fd9de175 100644
--- a/R/MatrixDeviations.R
+++ b/R/MatrixDeviations.R
@@ -378,11 +378,17 @@ addDeviationsMatrix <- function(
 
   if("z" %in% tolower(out)){
     z <- t(vapply(results, function(x) x[["z"]], rep(0, length(cn))))
+    if(length(cn)==1){
+      z <- matrix(z, ncol=length(cn))
+    }
   }else{
     z <- matrix(0, nrow = ncol(annotationsMatrix), ncol = length(cn))
   }
   if("deviations" %in% tolower(out)){
     dev <- t(vapply(results, function(x) x[["dev"]], rep(0, length(cn))))
+    if(length(cn)==1){
+      dev <- matrix(dev, ncol=length(cn))
+    }
   }else{
     dev <- matrix(0, nrow = ncol(annotationsMatrix), ncol = length(cn))
   }
diff --git a/R/MatrixGeneScores.R b/R/MatrixGeneScores.R
index 1325d4ce..ef34822d 100644
--- a/R/MatrixGeneScores.R
+++ b/R/MatrixGeneScores.R
@@ -100,6 +100,10 @@ addGeneScoreMatrix <- function(
     stop("Error Input Arrow Files do not all exist!")
   }
 
+  if(inherits(mcols(genes)$symbol, "list") | inherits(mcols(genes)$symbol, "SimpleList")){
+    stop("Found a list in genes symbol! This is an incorrect format. Please correct your genes!")
+  }
+
   .startLogging(logFile = logFile)
   .logThis(mget(names(formals()),sys.frame(sys.nframe())), "addGeneScoreMatrix Input-Parameters", logFile = logFile)
 
@@ -191,6 +195,10 @@ addGeneScoreMatrix <- function(
   .validInput(input = force, name = "force", valid = c("boolean"))
   .validInput(input = tmpFile, name = "tmpFile", valid = c("character", "null"))
 
+  if(inherits(mcols(genes)$symbol, "list") | inherits(mcols(genes)$symbol, "SimpleList")){
+    stop("Found a list in genes symbol! This is an incorrect format. Please correct your genes!")
+  }
+
   ArrowFile <- ArrowFiles[i]
   sampleName <- .sampleName(ArrowFile)
 
diff --git a/R/ProjectMethods.R b/R/ProjectMethods.R
index 5609cf0f..1cb18b7d 100644
--- a/R/ProjectMethods.R
+++ b/R/ProjectMethods.R
@@ -363,24 +363,56 @@ getPeakSet <- function(ArchRProj = NULL){
 #' 
 #' @param ArchRProj An `ArchRProject` object.
 #' @param peakSet A `GRanges` object containing the set of regions that define all peaks in the desired peak set.
+#' @param genomeAnnotation The genomeAnnotation (see `createGenomeAnnotation()`) to be used for generating peak metadata such as nucleotide
+#' information (GC content) or chromosome sizes.
 #' @param force If a `peakSet` object has already been added to the given `ArchRProject`, the value of `force` determines
 #' whether or not to overwrite this `peakSet`.
 #' @export
-addPeakSet <- function(ArchRProj = NULL, peakSet = NULL, force = FALSE){
+addPeakSet <- function(
+  ArchRProj = NULL, 
+  peakSet = NULL, 
+  genomeAnnotation = getGenomeAnnotation(ArchRProj),
+  force = FALSE
+  ){
+  
   .validInput(input = ArchRProj, name = "ArchRProj", valid = "ArchRProject")
   .validInput(input = peakSet, name = "peakSet", valid = c("GRanges"))
   .validInput(input = force, name = "force", valid = c("boolean"))
+  genomeAnnotation <- .validGenomeAnnotation(genomeAnnotation)
+  
   if(is.null(ArchRProj@peakSet) | force){
+   
     #Index The Peak Set
     peakSet <- lapply(split(peakSet, seqnames(peakSet)), function(x){
       mcols(x)$idx <- seq_along(x)
       x
     }) %>% Reduce("c", .) %>% sortSeqlevels %>% sort
+
+    #Get NucleoTide Content
+    peakSet <- tryCatch({
+      .requirePackage(genomeAnnotation$genome)
+      .requirePackage("Biostrings",source="bioc")
+      BSgenome <- eval(parse(text = genomeAnnotation$genome))
+      BSgenome <- validBSgenome(BSgenome)
+      nucFreq <- BSgenome::alphabetFrequency(getSeq(BSgenome, peakSet))
+      mcols(peakSet)$GC <- round(rowSums(nucFreq[,c("G","C")]) / rowSums(nucFreq),4)
+      mcols(peakSet)$N <- round(nucFreq[,c("N")] / rowSums(nucFreq),4)
+      peakSet
+    }, error = function(e){
+      peakSet
+    })
+
+    #Add PeakSet
     ArchRProj@peakSet <- peakSet
+
   }else{
+  
     stop("Error peakSet exists! Set force=TRUE to override!")
+  
   }
+  
   return(ArchRProj)
+
 }
 
 ##########################################################################################
@@ -571,6 +603,10 @@ getGenes <- function(ArchRProj = NULL, symbols = NULL){
     genes <- genes[which(tolower(genes$symbol) %in% tolower(symbols))]
   }
 
+  if(inherits(mcols(genes)$symbol, "list") | inherits(mcols(genes)$symbol, "SimpleList")){
+    stop("Found a list in genes symbol! This is an incorrect format. Please correct your genes!")
+  }
+
   genes
 
 }
diff --git a/R/RNAIntegration.R b/R/RNAIntegration.R
index 53a367f6..8e11b27e 100644
--- a/R/RNAIntegration.R
+++ b/R/RNAIntegration.R
@@ -43,6 +43,7 @@
 #' @param reduction The Seurat reduction method to use for integrating modalities. See `Seurat::FindTransferAnchors()` for possible reduction methods.
 #' @param addToArrow A boolean value indicating whether to add the log2-normalized transcript counts from the integrated matched RNA to the Arrow files.
 #' @param scaleTo Each column in the integrated RNA matrix will be normalized to a column sum designated by `scaleTo` prior to adding to Arrow files.
+#' @param genesUse If desired a character vector of gene names to use for integration instead of determined ones from Seurat::variableGenes.
 #' @param nameCell A column name to add to `cellColData` for the predicted scRNA-seq cell in the specified `ArchRProject`. This is useful for identifying which cell was closest to the scATAC-seq cell.
 #' @param nameGroup A column name to add to `cellColData` for the predicted scRNA-seq group in the specified `ArchRProject`. See `groupRNA` for more details.
 #' @param nameScore A column name to add to `cellColData` for the predicted scRNA-seq score in the specified `ArchRProject`. These scores represent
@@ -77,6 +78,7 @@ addGeneIntegrationMatrix <- function(
   reduction = "cca",
   addToArrow = TRUE,
   scaleTo = 10000,
+  genesUse = NULL,
   nameCell = "predictedCell",
   nameGroup = "predictedGroup",
   nameScore = "predictedScore",
@@ -110,6 +112,7 @@ addGeneIntegrationMatrix <- function(
   .validInput(input = reduction, name = "reduction", valid = c("character"))
   .validInput(input = addToArrow, name = "addToArrow", valid = c("boolean"))
   .validInput(input = scaleTo, name = "scaleTo", valid = c("numeric"))
+  .validInput(input = genesUse, name = "genesUse", valid = c("character", "null"))
   .validInput(input = nameCell, name = "nameCell", valid = c("character"))
   .validInput(input = nameGroup, name = "nameGroup", valid = c("character"))
   .validInput(input = nameScore, name = "nameScore", valid = c("character"))
@@ -385,7 +388,9 @@ addGeneIntegrationMatrix <- function(
     .logDiffTime(sprintf("%s Identifying Variable Genes", prefix), tstart, verbose = verbose, logFile = logFile)
     subRNA <- FindVariableFeatures(object = subRNA, nfeatures = nGenes, verbose = FALSE)
     subRNA <- ScaleData(object = subRNA, verbose = FALSE)
-    genesUse <- VariableFeatures(object = subRNA)
+    if(is.null(genesUse)){
+      genesUse <- VariableFeatures(object = subRNA)
+    }
 
     ##############################################################################################
     #2. Get Gene Score Matrix and Create Seurat ATAC
diff --git a/R/ReproduciblePeakSet.R b/R/ReproduciblePeakSet.R
index fd6393df..8699e748 100644
--- a/R/ReproduciblePeakSet.R
+++ b/R/ReproduciblePeakSet.R
@@ -262,7 +262,7 @@ addReproduciblePeakSet <- function(
 
 	}else if(tolower(peakMethod) == "tiles"){
 
-		.logMessage("Calling Peaks with TileMatrix", logFile = logFile)
+		.logMessage("Calling Peaks with TileMatrix. We recommend using the Macs2 Version.\nThis method is still under development.", logFile = logFile)
 
 		useMatrix <- "TileMatrix"
 		
@@ -325,11 +325,13 @@ addReproduciblePeakSet <- function(
 		#Compute Row Sums Across All Samples
 		.logDiffTime("Computing Total Accessibility Across All Features", tstart, addHeader = FALSE, verbose = verbose)
 		totalAcc <- .getRowSums(ArrowFiles = ArrowFiles, useMatrix = useMatrix, seqnames = chrToRun)
+  	.logThis(totalAcc, "PeakCallTiles-totalAcc", logFile=logFile)		
 		nTiles <- nrow(totalAcc)
 		gc()
 
 		#Pre-Filter 0s
 		topFeatures <- totalAcc[which(totalAcc$rowSums != 0), ]
+  	.logThis(topFeatures, "PeakCallTiles-topFeatures", logFile=logFile)		
 
 		#Group Matrix
 		#Consider reading in group-wise if this is getting too large?
@@ -344,9 +346,12 @@ addReproduciblePeakSet <- function(
       asSparse = TRUE,
       verbose = FALSE
     )
-		
+  	.logThis(groupMat, "PeakCallTiles-groupMat", logFile=logFile)		
+
 		.logDiffTime(sprintf("Created Pseudo-Grouped Tile Matrix (%s GB)", round(object.size(groupMat) / 10^9, 3)), tstart, addHeader = FALSE, verbose = verbose)
     expectation <- Matrix::colSums(groupMat) / nTiles
+    .logMessage(paste0("colSums = ", Matrix::colSums(groupMat)), logFile = logFile)
+    .logMessage(paste0("nTiles = ", nTiles), logFile = logFile)
     .logMessage(paste0("Expectation = ", expectation), logFile = logFile)
 
 		#####################################################
@@ -401,6 +406,8 @@ addReproduciblePeakSet <- function(
 
     }, threads = threads) %>% Reduce("rbind", .)
 
+  	.logThis(groupPeaks, "PeakCallTiles-groupPeaks", logFile=logFile)
+
     groupPeaks <- groupPeaks[order(groupPeaks$normmlogp, decreasing=TRUE), ]
 
 		#####################################################
diff --git a/R/Trajectory.R b/R/Trajectory.R
index c1931e30..ceee126d 100644
--- a/R/Trajectory.R
+++ b/R/Trajectory.R
@@ -72,7 +72,9 @@ addTrajectory <- function(
   }
 
   if(sum(unique(groupDF[,1]) %in% trajectory) < 3){
-    .logStop("trajectory must span at least 3 groups in groupBy!", logFile = logFile)
+    if(!force){
+      .logStop("trajectory must span at least 3 groups in groupBy!", logFile = logFile)
+    }
   }
 
   if(is.null(embedding)){
@@ -475,6 +477,13 @@ plotTrajectoryHeatmap <- function(
   }
 
   mat <- assay(seTrajectory)
+
+  if(!is.null(grepExclude)){
+    idxExclude <- grep(grepExclude, rownames(mat))
+    if(length(idxExclude) > 0){
+      mat <- mat[-grep(grepExclude, rownames(mat)), , drop = FALSE]
+    }
+  }
   
   #Rows with NA
   rSNA <- rowSums(is.na(mat))
@@ -676,7 +685,7 @@ plotTrajectory <- function(
   .validInput(input = pal, name = "pal", valid = c("character", "null"))
   .validInput(input = size, name = "size", valid = c("numeric"))
   .validInput(input = rastr, name = "rastr", valid = c("boolean"))
-  .validInput(input = quantCut, name = "quantCut", valid = c("numeric"))
+  .validInput(input = quantCut, name = "quantCut", valid = c("numeric", "null"))
   .validInput(input = quantHex, name = "quantHex", valid = c("numeric"))
   .validInput(input = discreteSet, name = "discreteSet", valid = c("character", "null"))
   .validInput(input = continuousSet, name = "continuousSet", valid = c("character", "null"))
@@ -693,6 +702,10 @@ plotTrajectory <- function(
   .startLogging(logFile = logFile)
   .logThis(mget(names(formals()),sys.frame(sys.nframe())), "Input-Parameters", logFile=logFile)
 
+  if(is.null(quantCut)){
+    quantCut <- c(0, 1)
+  }
+
   #Make Sure ColorBy is valid!
   if(length(colorBy) > 1){
     stop("colorBy must be of length 1!")
diff --git a/R/VisualizeData.R b/R/VisualizeData.R
index 6f2daa8d..d675abd4 100644
--- a/R/VisualizeData.R
+++ b/R/VisualizeData.R
@@ -95,12 +95,12 @@ plotPDF <- function(
 
         if(inherits(plotList[[i]], "patchwork")){
 
-          message("Plotting Patchwork!")
+          if(getArchRVerbose()) message("Plotting Patchwork!")
           print(plotList[[i]])
         
         }else{
 
-          message("Plotting Ggplot!")
+          if(getArchRVerbose()) message("Plotting Ggplot!")
 
           if(!is.null(attr(plotList[[i]], "ratioYX"))){
             .fixPlotSize(plotList[[i]], plotWidth = width, plotHeight = height, height = attr(plotList[[i]], "ratioYX"), newPage = FALSE)
@@ -116,7 +116,7 @@ plotPDF <- function(
       
       }else if(inherits(plotList[[i]], "gtable")){
 
-        message("Plotting Gtable!")
+        if(getArchRVerbose()) message("Plotting Gtable!")
         
         print(grid::grid.draw(plotList[[i]]))
         if(i != length(plotList)){
@@ -124,7 +124,7 @@ plotPDF <- function(
         }
       }else if(inherits(plotList[[i]], "HeatmapList") | inherits(plotList[[i]], "Heatmap") ){ 
 
-        message("Plotting ComplexHeatmap!")
+        if(getArchRVerbose()) message("Plotting ComplexHeatmap!")
 
         padding <- 15
         draw(plotList[[i]], 
@@ -135,7 +135,7 @@ plotPDF <- function(
 
       }else{
 
-        message("Plotting Other")
+        if(getArchRVerbose()) message("Plotting Other")
        
         print(plotList[[i]])
 
@@ -147,7 +147,7 @@ plotPDF <- function(
 
   }, error = function(x){
 
-    message(x)
+    if(getArchRVerbose()) message(x)
 
   })
 
@@ -320,7 +320,7 @@ plotEmbedding <- function(
       }
 
       if(!is.null(imputeWeights)){
-        message("Imputing Matrix")
+        if(getArchRVerbose()) message("Imputing Matrix")
         colorMat <- matrix(colorParams$color, nrow=1)
         colnames(colorMat) <- rownames(df)
         colorMat <- imputeMatrix(mat = colorMat, imputeWeights = imputeWeights, logFile = logFile)
@@ -367,7 +367,7 @@ plotEmbedding <- function(
     .logThis(colorMat, "colorMat-Before-Impute", logFile = logFile)
 
     if(!is.null(imputeWeights)){
-      message("Imputing Matrix")
+      if(getArchRVerbose()) message("Imputing Matrix")
       colorMat <- imputeMatrix(mat = as.matrix(colorMat), imputeWeights = imputeWeights, logFile = logFile)
       if(!inherits(colorMat, "matrix")){
         colorMat <- matrix(colorMat, ncol = nrow(df))
@@ -401,11 +401,11 @@ plotEmbedding <- function(
 
   }
 
-  message("Plotting Embedding")
+  if(getArchRVerbose()) message("Plotting Embedding")
 
   ggList <- lapply(seq_along(colorList), function(x){
 
-    message(x, " ", appendLF = FALSE)
+    if(getArchRVerbose()) message(x, " ", appendLF = FALSE)
 
     plotParamsx <- .mergeParams(colorList[[x]], plotParams)
 
@@ -483,7 +483,7 @@ plotEmbedding <- function(
 
   })
   names(ggList) <- name
-  message("")
+  if(getArchRVerbose()) message("")
 
   if(length(ggList) == 1){
     ggList <- ggList[[1]]
@@ -663,7 +663,7 @@ plotGroups <- function(
 
   pl <- lapply(seq_along(colorList), function(x){
 
-    message(paste0(x, " "), appendLF = FALSE)
+    if(getArchRVerbose()) message(paste0(x, " "), appendLF = FALSE)
 
     if(is.null(ylim)){
       ylim <- range(colorList[[x]]$color,na.rm=TRUE) %>% extendrange(f = 0.05)
@@ -692,7 +692,7 @@ plotGroups <- function(
   })
 
   names(pl) <- name
-  message("")
+  if(getArchRVerbose()) message("")
   
   if(length(name)==1){
     pl[[1]]
@@ -764,7 +764,7 @@ plotGroups <- function(
   cellNamesList <- split(rownames(getCellColData(ArchRProj)), getCellColData(ArchRProj)$Sample)
   
   values <- .safelapply(seq_along(cellNamesList), function(x){
-    message(x, " ", appendLF = FALSE)
+    if(getArchRVerbose()) message(x, " ", appendLF = FALSE)
     valuesx <- tryCatch({
       o <- h5closeAll()
       ArrowFile <- getSampleColData(ArchRProj)[names(cellNamesList)[x],"ArrowFiles"]
@@ -792,7 +792,7 @@ plotGroups <- function(
     valuesx
   }, threads = threads) %>% Reduce("cbind", .)
   values <- values[, ArchRProj$cellNames, drop = FALSE]
-  message("")
+  if(getArchRVerbose()) message("")
   gc()
   .logThis(values, "Feature-Matrix", logFile = logFile)
 
@@ -804,7 +804,7 @@ plotGroups <- function(
   #Values Summary
   if(!is.null(log2Norm)){
     if(log2Norm){
-      message("Log2 Normalizing...")
+      if(getArchRVerbose()) message("Log2 Normalizing...")
       values <- log2(values + 1)
     }
   }
diff --git a/man/ArchRPalettes.Rd b/man/ArchRPalettes.Rd
index 61cc1e60..c74ad672 100644
--- a/man/ArchRPalettes.Rd
+++ b/man/ArchRPalettes.Rd
@@ -4,7 +4,9 @@
 \name{ArchRPalettes}
 \alias{ArchRPalettes}
 \title{List of color palettes that can be used in plots}
-\format{An object of class \code{list} of length 30.}
+\format{
+An object of class \code{list} of length 30.
+}
 \usage{
 ArchRPalettes
 }
diff --git a/man/addArchRVerbose.Rd b/man/addArchRVerbose.Rd
new file mode 100644
index 00000000..dadc3508
--- /dev/null
+++ b/man/addArchRVerbose.Rd
@@ -0,0 +1,14 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/LoggerUtils.R
+\name{addArchRVerbose}
+\alias{addArchRVerbose}
+\title{Set ArchR Verbosity for Log Messaging}
+\usage{
+addArchRVerbose(verbose = TRUE)
+}
+\arguments{
+\item{verbose}{A boolean describing whether to printMessages in addition to logging with ArchR.}
+}
+\description{
+This function will set ArchR logging verbosity.
+}
diff --git a/man/addGeneIntegrationMatrix.Rd b/man/addGeneIntegrationMatrix.Rd
index 9b89ffdb..dba7957d 100644
--- a/man/addGeneIntegrationMatrix.Rd
+++ b/man/addGeneIntegrationMatrix.Rd
@@ -28,6 +28,7 @@ addGeneIntegrationMatrix(
   reduction = "cca",
   addToArrow = TRUE,
   scaleTo = 10000,
+  genesUse = NULL,
   nameCell = "predictedCell",
   nameGroup = "predictedGroup",
   nameScore = "predictedScore",
@@ -98,6 +99,8 @@ correlation to sequencing depth that is greater than the \code{corCutOff}, it wi
 
 \item{scaleTo}{Each column in the integrated RNA matrix will be normalized to a column sum designated by \code{scaleTo} prior to adding to Arrow files.}
 
+\item{genesUse}{If desired a character vector of gene names to use for integration instead of determined ones from Seurat::variableGenes.}
+
 \item{nameCell}{A column name to add to \code{cellColData} for the predicted scRNA-seq cell in the specified \code{ArchRProject}. This is useful for identifying which cell was closest to the scATAC-seq cell.}
 
 \item{nameGroup}{A column name to add to \code{cellColData} for the predicted scRNA-seq group in the specified \code{ArchRProject}. See \code{groupRNA} for more details.}
diff --git a/man/addPeakAnnotations.Rd b/man/addPeakAnnotations.Rd
index d96db49d..72775a9f 100644
--- a/man/addPeakAnnotations.Rd
+++ b/man/addPeakAnnotations.Rd
@@ -15,7 +15,7 @@ addPeakAnnotations(
 \arguments{
 \item{ArchRProj}{An \code{ArchRProject} object.}
 
-\item{regions}{A \code{list} of \code{GRanges} that are to be overlapped with the \code{peakSet} in the \code{ArchRProject}.}
+\item{regions}{A named \code{list} of \code{GRanges} that are to be overlapped with the \code{peakSet} in the \code{ArchRProject}.}
 
 \item{name}{The name of \code{peakAnnotation} object to be stored as in \code{ArchRProject}.}
 
diff --git a/man/addPeakSet.Rd b/man/addPeakSet.Rd
index 26b597d7..81dcd3e6 100644
--- a/man/addPeakSet.Rd
+++ b/man/addPeakSet.Rd
@@ -4,13 +4,21 @@
 \alias{addPeakSet}
 \title{Add a peak set to an ArchRProject}
 \usage{
-addPeakSet(ArchRProj = NULL, peakSet = NULL, force = FALSE)
+addPeakSet(
+  ArchRProj = NULL,
+  peakSet = NULL,
+  genomeAnnotation = getGenomeAnnotation(ArchRProj),
+  force = FALSE
+)
 }
 \arguments{
 \item{ArchRProj}{An \code{ArchRProject} object.}
 
 \item{peakSet}{A \code{GRanges} object containing the set of regions that define all peaks in the desired peak set.}
 
+\item{genomeAnnotation}{The genomeAnnotation (see \code{createGenomeAnnotation()}) to be used for generating peak metadata such as nucleotide
+information (GC content) or chromosome sizes.}
+
 \item{force}{If a \code{peakSet} object has already been added to the given \code{ArchRProject}, the value of \code{force} determines
 whether or not to overwrite this \code{peakSet}.}
 }
diff --git a/man/getArchRVerbose.Rd b/man/getArchRVerbose.Rd
new file mode 100644
index 00000000..0ed46322
--- /dev/null
+++ b/man/getArchRVerbose.Rd
@@ -0,0 +1,11 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/LoggerUtils.R
+\name{getArchRVerbose}
+\alias{getArchRVerbose}
+\title{Set ArchR Verbosity for Log Messaging}
+\usage{
+getArchRVerbose()
+}
+\description{
+This function will get ArchR logging verbosity.
+}