diff --git a/man/ArchRProject.Rd b/man/ArchRProject.Rd
index 00e30b1b..1f00a53c 100644
--- a/man/ArchRProject.Rd
+++ b/man/ArchRProject.Rd
@@ -11,16 +11,16 @@ ArchRProject(ArrowFiles = NULL, outputDirectory = "ArchR_Output",
 \arguments{
 \item{ArrowFiles}{A character vector containing the names of ArrowFiles to be used.}
 
-\item{outputDirectory}{A name for the relative path of the outputDirectory for ArchR results}
+\item{outputDirectory}{A name for the relative path of the outputDirectory for ArchR results. Relative to the current working directory.}
 
-\item{copyArrows}{A boolean indicating whether ArrowFiles should be copied into outputDirectory}
+\item{copyArrows}{A boolean value indicating whether ArrowFiles should be copied into \code{outputDirectory}.}
 
-\item{showLogo}{A boolean indicating whether to show ArchR Logo after successful creation of an ArchRProject.}
+\item{geneAnnotation}{The \code{geneAnnotation} object (see \code{createGeneAnnotation()}) to be used for downstream analyses such as calculating TSS Enrichment Scores, Gene Scores, etc.}
 
-\item{geneAnno}{The geneAnnotation (see createGeneAnnotation) is used for downstream analyses such as calculate TSS Enrichment Scores, Gene Scores, etc.}
+\item{genomeAnnotation}{The \code{genomeAnnotation} object (see \code{createGenomeAnnotation()}) to be used for downstream analyses requiring genome information such as nucleotide information or chromosome sizes.}
 
-\item{genomeAnno}{The genomeAnnotation (see createGenomeAnnotation) is used for downstream analyses for genome information such as nucleotide information or chromosome sizes.}
+\item{showLogo}{A boolean value indicating whether to show the ascii ArchR logo after successful creation of an ArchRProject.}
 }
 \description{
-This function will create an ArchRProject with given ArrowFiles.
+This function will create an ArchRProject from the provided ArrowFiles.
 }
diff --git a/man/ArchRRegionTrack.Rd b/man/ArchRRegionTrack.Rd
index b8b93d57..0ca9a213 100644
--- a/man/ArchRRegionTrack.Rd
+++ b/man/ArchRRegionTrack.Rd
@@ -2,7 +2,7 @@
 % Please edit documentation in R/ArchRBrowser.R
 \name{ArchRRegionTrack}
 \alias{ArchRRegionTrack}
-\title{Plot ArchR Region Track}
+\title{Plot an ArchR Region Track}
 \usage{
 ArchRRegionTrack(ArchRProj = NULL, region = NULL,
   groupBy = "Clusters", useGroups = NULL, useCoverages = FALSE,
@@ -10,8 +10,8 @@ ArchRRegionTrack(ArchRProj = NULL, region = NULL,
   sizes = c(10, 2, 4), features = getPeakSet(ArchRProj),
   geneSymbol = NULL, upstream = 50000, downstream = 50000,
   tileSize = 100, minCells = 25, normMethod = "ReadsInTSS",
-  threads = 1, ylim = NULL, baseSize = 7, borderWidth = 0.4,
-  tickWidth = 0.4, facetbaseSize = 7,
+  threads = getArchRThreads(), ylim = NULL, baseSize = 7,
+  borderWidth = 0.4, tickWidth = 0.4, facetbaseSize = 7,
   geneAnno = getGeneAnnotation(ArchRProj), title = "", ...)
 }
 \arguments{
@@ -19,19 +19,19 @@ ArchRRegionTrack(ArchRProj = NULL, region = NULL,
 
 \item{region}{A \code{GRanges} region that indicates the region to be plotted. If more than one region exists in the \code{GRanges} object, all will be plotted. If no region is supplied, then the \code{geneSymbol} argument can be used to center the plot window at the transcription start site of the supplied gene.}
 
-\item{groupBy}{A string that indicates how cells should be grouped. This string corresponds to one of the standard or user-supplied \code{cellColData} metadata columns (for example, "Clusters"). Cells with the same value annotated in this metadata column will be grouped together and the average signal will be used.}
+\item{groupBy}{A string that indicates how cells should be grouped. This string corresponds to one of the standard or user-supplied \code{cellColData} metadata columns (for example, "Clusters"). Cells with the same value annotated in this metadata column will be grouped together and the average signal will be plotted.}
 
 \item{useGroups}{A character vector that is used to select a subset of groups by name from the designated \code{groupBy} column in \code{cellColData}. This limits the groups to be plotted.}
 
-\item{useCoverages}{A boolean indicating whether to use group coverages of pseudobulks (see createGroupCoverages) for track plotting instead of ArrowFiles}
+\item{useCoverages}{A boolean indicating whether to use group coverages instead of ArrowFiles for track plotting. See \code{addGroupCoverages()} for information on plotting ArrowFiles without the use of pseudo-bulk replicates.}
 
-\item{plotSummary}{A character vector containing the features to be potted. Possible values include "bulkTrack" (the ATAC-seq signal), "featureTrack" (i.e. the peak bed regions), and "geneTrack" (line diagrams of genes with introns and exons shown. Blue-colored genes are on the minus strand and red-colored genes are on the plus strand).}
+\item{plotSummary}{A character vector containing the features to be potted. Possible values include "bulkTrack" (the ATAC-seq signal), "featureTrack" (i.e. the peak regions), and "geneTrack" (line diagrams of genes with introns and exons shown. Blue-colored genes are on the minus strand and red-colored genes are on the plus strand).}
 
-\item{sizes}{A numeric vector containing 3 values that indicate the sizes of the individual components passed in \code{plotSummary}. The order must be the same as \code{plotSummary}.}
+\item{sizes}{A numeric vector containing up to 3 values that indicate the sizes of the individual components passed to \code{plotSummary}. The order must be the same as \code{plotSummary}.}
 
-\item{features}{A \code{GRanges} object containing the "features" to be plotted (This should be thought of as a bed track. i.e. the set of peaks obtained using \code{getPeakSet(ArchRProj))}.}
+\item{features}{A \code{GRanges} object containing the "features" to be plotted via the "featureTrack". This should be thought of as a bed track. i.e. the set of peaks obtained using \code{getPeakSet(ArchRProj))}.}
 
-\item{geneSymbol}{If "region" is not supplied, plotting can be centered at the transcription start site corresponding to the gene symbol(s) passed here.}
+\item{geneSymbol}{If \code{region} is not supplied, plotting can be centered at the transcription start site corresponding to the gene symbol(s) passed here.}
 
 \item{upstream}{The number of basepairs upstream of the transcription start site of \code{geneSymbol} to extend the plotting window. If \code{region} is supplied, this argument is ignored.}
 
@@ -39,11 +39,13 @@ ArchRRegionTrack(ArchRProj = NULL, region = NULL,
 
 \item{tileSize}{The numeric width of the tile/bin in basepairs for plotting ATAC-seq signal tracks. All insertions in a single bin will be summed.}
 
-\item{normMethod}{The name of the column in \code{cellColData} object by which normalization should be performed. The recommended and default value is "ReadsInTSS" which simultaneously normalizes tracks based on sequencing depth and sample data quality.}
+\item{minCells}{The minimum number of cells contained within a cell group to allow for this cell group to be plotted. This argument can be used to exclude pseudo-bulk replicates generated from low numbers of cells.}
+
+\item{normMethod}{The name of the column in \code{cellColData} by which normalization should be performed. The recommended and default value is "ReadsInTSS" which simultaneously normalizes tracks based on sequencing depth and sample data quality.}
 
 \item{threads}{The number of threads to use for parallel execution.}
 
-\item{ylim}{The numeric quantile y-axis limit to be used for for "bulkTrack" plotting. If not provided, the y-axis limit will be c(0, 0.999).}
+\item{ylim}{QQQ IS THIS TRUE? The numeric quantile y-axis limit to be used for for "bulkTrack" plotting. If not provided, the y-axis limit will be c(0, 0.999).}
 
 \item{baseSize}{The numeric font size to be used in the plot. This applies to all plot labels.}
 
@@ -51,11 +53,11 @@ ArchRRegionTrack(ArchRProj = NULL, region = NULL,
 
 \item{tickWidth}{The numeric line width to be used for axis tick marks.}
 
-\item{facetbaseSize}{The numeric font size to be used in the facets (gray boxes) of the plot.}
+\item{facetbaseSize}{The numeric font size to be used in the facets (gray boxes used to provide track labels) of the plot.}
 
-\item{geneAnno}{The \code{geneAnnotation} object to be used for plotting the "geneTrack" object. See createGeneAnnotation() for more info.}
+\item{geneAnno}{QQQ GENE ANNO VS GENE ANNOTATION NEEDS TO BE STANDARDIZED The \code{geneAnnotation} object to be used for plotting the "geneTrack" object. See createGeneAnnotation() for more info.}
 
-\item{title}{The title to add at the top of the plot next to the plot genomic coordinates.}
+\item{title}{The title to add at the top of the plot next to the plot's genomic coordinates.}
 
 \item{...}{additional args}
 }
diff --git a/man/addArchRThreads.Rd b/man/addArchRThreads.Rd
index b33647c1..d04460d0 100644
--- a/man/addArchRThreads.Rd
+++ b/man/addArchRThreads.Rd
@@ -2,13 +2,13 @@
 % Please edit documentation in R/ArchRProjectMethods.R
 \name{addArchRThreads}
 \alias{addArchRThreads}
-\title{Add global number of threads for default parallel computing.}
+\title{Add a globally-applied number of threads to use for parallel computing.}
 \usage{
 addArchRThreads(threads = floor(parallel::detectCores()/2))
 }
 \arguments{
-\item{threads}{default number of threads to be used for parallel execution in ArchR functions by default.}
+\item{threads}{The default number of threads to be used for parallel execution across all ArchR functions. This value is stored as a global environment variable, not part of the \code{ArchRProject}. This can be overwritten on a per-function basis using the given function's \code{threads} parameter.}
 }
 \description{
-This function will set the global number of threads to be used for ArchR functions.
+This function will set the number of threads to be used for parallel computing across all ArchR functions.
 }
diff --git a/man/addCNVMatrix.Rd b/man/addCNVMatrix.Rd
index d63a9bc2..63e60b34 100644
--- a/man/addCNVMatrix.Rd
+++ b/man/addCNVMatrix.Rd
@@ -7,7 +7,8 @@
 addCNVMatrix(input, chromSizes = getChromSizes(input),
   blacklist = getBlacklist(input), genome = getGenome(input),
   windowSize = 1e+07, stepSize = 2e+06, excludeChr = c("chrM",
-  "chrY"), threads = 1, parallelParam = NULL, force = FALSE, ...)
+  "chrY"), threads = getArchRThreads(), parallelParam = NULL,
+  force = FALSE, ...)
 }
 \arguments{
 \item{input}{An \code{ArchRProject} object or character vector of ArrowFiles.}
diff --git a/man/addCellColData.Rd b/man/addCellColData.Rd
index df1d1911..24083b63 100644
--- a/man/addCellColData.Rd
+++ b/man/addCellColData.Rd
@@ -12,7 +12,7 @@ addCellColData(ArchRProj, data = NULL, name = NULL,
 
 \item{data}{The data to add to \code{cellColData}.}
 
-\item{name}{The column header name to be used for this new data in \code{cellColData}. If a column with this name already exists, you may set \code{force} equal to TRUE to overwrite the data in this column.}
+\item{name}{The column header name to be used for this new data in \code{cellColData}. If a column with this name already exists, you may set \code{force} equal to \code{TRUE} to overwrite the data in this column.}
 
 \item{cells}{The names of the cells corresponding to \code{data}. Typically new data is added to all cells but you may use this argument to only add data to a subset of cells. Cells where \code{data} is not added are set to \code{NA}.}
 
diff --git a/man/addClusters.Rd b/man/addClusters.Rd
index ff49003f..93582805 100644
--- a/man/addClusters.Rd
+++ b/man/addClusters.Rd
@@ -21,7 +21,7 @@ addClusters(input = NULL, reducedDims = "IterativeLSI",
 
 \item{seed}{A number to be used as the seed for random number generation required in cluster determination. It is recommended to keep track of the seed used so that you can reproduce results downstream.}
 
-\item{method}{A string indicated the clustering method to be used. Supported methods are "Seurat" and "Scran".}
+\item{method}{A string indicating the clustering method to be used. Supported methods are "Seurat" and "Scran".}
 
 \item{dimsToUse}{A vector containing the dimensions from the \code{reducedDims} object to use in clustering.}
 
diff --git a/man/addCoAccessibility.Rd b/man/addCoAccessibility.Rd
index 941157e8..569baf71 100644
--- a/man/addCoAccessibility.Rd
+++ b/man/addCoAccessibility.Rd
@@ -7,12 +7,12 @@
 addCoAccessibility(ArchRProj, reducedDims = "IterativeLSI", k = 100,
   knnIteration = 5000, overlapCutoff = 0.8, maxDist = 250000,
   scaleTo = 10^4, log2Norm = TRUE, seed = 1, knnMethod = "nabor",
-  threads = 1, ...)
+  threads = getArchRThreads(), ...)
 }
 \arguments{
 \item{ArchRProj}{An \code{ArchRProject} object.}
 
-\item{reducedDims}{The name of the \code{reducedDims} object (i.e. IterativeLSI) to retrieve from the designated \code{ArchRProject}.}
+\item{reducedDims}{The name of the \code{reducedDims} object (i.e. "IterativeLSI") to retrieve from the designated \code{ArchRProject}.}
 
 \item{k}{The number of k-nearest neighbors to use for creating single cell groups for correlation.}
 
diff --git a/man/addDeviationsMatrix.Rd b/man/addDeviationsMatrix.Rd
index 23062259..8bb9abec 100644
--- a/man/addDeviationsMatrix.Rd
+++ b/man/addDeviationsMatrix.Rd
@@ -6,8 +6,8 @@
 \usage{
 addDeviationsMatrix(ArchRProj, peakAnnotation = NULL, matches = NULL,
   bgdPeaks = getBgdPeaks(ArchRProj), matrixName = NULL, out = c("z",
-  "deviations"), binarize = FALSE, threads = 1, parallelParam = NULL,
-  force = FALSE, ...)
+  "deviations"), binarize = FALSE, threads = getArchRThreads(),
+  parallelParam = NULL, force = FALSE, ...)
 }
 \arguments{
 \item{ArchRProj}{An \code{ArchRProject} object.}
diff --git a/man/addDoubletScores.Rd b/man/addDoubletScores.Rd
index d87ec448..120a4566 100644
--- a/man/addDoubletScores.Rd
+++ b/man/addDoubletScores.Rd
@@ -8,8 +8,8 @@ addDoubletScores(input, useMatrix = "TileMatrix", k = 10,
   nTrials = 5, dimsToUse = 1:25, corCutOff = 0.75,
   knnMethod = "UMAP", UMAPParams = list(),
   LSIParams = list(sampleCells = NULL), outDir = "QualityControl",
-  threads = 1, parallelParam = NULL, verboseHeader = TRUE,
-  verboseAll = FALSE, ...)
+  threads = getArchRThreads(), parallelParam = NULL,
+  verboseHeader = TRUE, verboseAll = FALSE, ...)
 }
 \arguments{
 \item{input}{An \code{ArchRProject} object or a character vector containing the names of ArrowFiles to be used.}
diff --git a/man/addEmbedding.Rd b/man/addEmbedding.Rd
index 1bdf893f..e7341ace 100644
--- a/man/addEmbedding.Rd
+++ b/man/addEmbedding.Rd
@@ -7,7 +7,7 @@
 addEmbedding(ArchRProj = NULL, reducedDims = "IterativeLSI",
   embedding = "UMAP", embeddingOut = NULL, dimsToUse = NULL,
   corCutOff = 0.75, saveModel = TRUE, seed = 1, force = FALSE,
-  threads = 1, embeddingParams = list(), ...)
+  threads = getArchRThreads(), embeddingParams = list(), ...)
 }
 \arguments{
 \item{ArchRProj}{An \code{ArchRProject} object.}
diff --git a/man/addFeatureMatrix.Rd b/man/addFeatureMatrix.Rd
index dc023aa6..e1579a9d 100644
--- a/man/addFeatureMatrix.Rd
+++ b/man/addFeatureMatrix.Rd
@@ -5,7 +5,7 @@
 \title{Add a feature matrix to an ArchRProject or a set of ArrowFiles}
 \usage{
 addFeatureMatrix(input, features = NULL, matrixName = "FeatureMatrix",
-  ceiling = Inf, binarize = FALSE, threads = 1,
+  ceiling = Inf, binarize = FALSE, threads = getArchRThreads(),
   parallelParam = NULL, force = FALSE, ...)
 }
 \arguments{
diff --git a/man/addGeneScoreMatrix.Rd b/man/addGeneScoreMatrix.Rd
index bd2492a0..b57528d4 100644
--- a/man/addGeneScoreMatrix.Rd
+++ b/man/addGeneScoreMatrix.Rd
@@ -11,8 +11,8 @@ addGeneScoreMatrix(input = NULL, genes = ifelse(inherits(input,
   downstream = c(5000, 1e+05), tileSize = 500, ceiling = 4,
   useGeneBoundaries = TRUE, scaleTo = 10000, excludeChr = c("chrY",
   "chrM"), blacklist = ifelse(inherits(input, "ArchRProject"),
-  getBlacklist(input), NULL), threads = 1, parallelParam = NULL,
-  force = FALSE, ...)
+  getBlacklist(input), NULL), threads = getArchRThreads(),
+  parallelParam = NULL, force = FALSE, ...)
 }
 \arguments{
 \item{input}{An \code{ArchRProject} object or character vector of ArrowFiles.}
diff --git a/man/addGroupCoverages.Rd b/man/addGroupCoverages.Rd
index 7ad533b3..49f81fcf 100644
--- a/man/addGroupCoverages.Rd
+++ b/man/addGroupCoverages.Rd
@@ -7,7 +7,7 @@
 addGroupCoverages(ArchRProj = NULL, groupBy = "Clusters",
   useLabels = TRUE, minCells = 40, maxCells = 500,
   maxFragments = 25 * 10^6, minReplicates = 2, maxReplicates = 5,
-  sampleRatio = 0.8, kmerLength = 6, threads = 1,
+  sampleRatio = 0.8, kmerLength = 6, threads = getArchRThreads(),
   parallelParam = "mclapply", force = FALSE, verboseHeader = TRUE,
   verboseAll = FALSE, ...)
 }
diff --git a/man/addIterativeLSI.Rd b/man/addIterativeLSI.Rd
index de23803a..ebc9ec1e 100644
--- a/man/addIterativeLSI.Rd
+++ b/man/addIterativeLSI.Rd
@@ -12,8 +12,8 @@ addIterativeLSI(ArchRProj = NULL, useMatrix = "TileMatrix",
   totalFeatures = 5e+05, filterQuantile = 0.99,
   saveIterations = TRUE, outDir = getOutputDirectory(ArchRProj),
   clusterParams = list(), runHarmony = FALSE, harmonyParams = list(),
-  threads = 1, seed = 1, verboseHeader = TRUE, verboseAll = FALSE,
-  force = FALSE, ...)
+  threads = getArchRThreads(), seed = 1, verboseHeader = TRUE,
+  verboseAll = FALSE, force = FALSE, ...)
 }
 \arguments{
 \item{ArchRProj}{An \code{ArchRProject} object.}
diff --git a/man/addPeakMatrix.Rd b/man/addPeakMatrix.Rd
index aeb986f8..b9b6aa00 100644
--- a/man/addPeakMatrix.Rd
+++ b/man/addPeakMatrix.Rd
@@ -5,7 +5,8 @@
 \title{Add PeakMatrix to Arrows in ArchRProject}
 \usage{
 addPeakMatrix(ArchRProj, ceiling = 4, binarize = FALSE,
-  parallelParam = NULL, threads = 1, force = FALSE, ...)
+  parallelParam = NULL, threads = getArchRThreads(), force = FALSE,
+  ...)
 }
 \arguments{
 \item{ArchRProj}{An \code{ArchRProject} object.}
diff --git a/man/addProjectSummary.Rd b/man/addProjectSummary.Rd
index 1d3bf45a..eece6b78 100644
--- a/man/addProjectSummary.Rd
+++ b/man/addProjectSummary.Rd
@@ -2,7 +2,7 @@
 % Please edit documentation in R/ArchRProjectMethods.R
 \name{addProjectSummary}
 \alias{addProjectSummary}
-\title{Add projectSummary tp ArchRProject}
+\title{Add projectSummary to an ArchRProject}
 \usage{
 addProjectSummary(ArchRProj, name, summary, ...)
 }
@@ -16,5 +16,5 @@ addProjectSummary(ArchRProj, name, summary, ...)
 \item{...}{additional args}
 }
 \description{
-This function adds info to the projectSummary from an ArchRProject
+This function adds info to the projectSummary of an ArchRProject
 }
diff --git a/man/addReproduciblePeakSet.Rd b/man/addReproduciblePeakSet.Rd
index cde29756..52ec16a5 100644
--- a/man/addReproduciblePeakSet.Rd
+++ b/man/addReproduciblePeakSet.Rd
@@ -11,9 +11,9 @@ addReproduciblePeakSet(ArchRProj = NULL, groupBy = "Clusters",
   extsize = 150, method = "q", cutOff = 0.1, extendSummits = 250,
   promoterDist = 500, genomeAnno = getGenomeAnnotation(ArchRProj),
   geneAnno = getGeneAnnotation(ArchRProj),
-  additionalParams = "--nomodel --nolambda", threads = 1,
-  parallelParam = "mclapply", force = FALSE, verboseHeader = TRUE,
-  verboseAll = FALSE, ...)
+  additionalParams = "--nomodel --nolambda",
+  threads = getArchRThreads(), parallelParam = "mclapply",
+  force = FALSE, verboseHeader = TRUE, verboseAll = FALSE, ...)
 }
 \arguments{
 \item{ArchRProj}{An \code{ArchRProject} object.}
diff --git a/man/addSampleColData.Rd b/man/addSampleColData.Rd
index 94d45c08..f5383ba1 100644
--- a/man/addSampleColData.Rd
+++ b/man/addSampleColData.Rd
@@ -2,7 +2,7 @@
 % Please edit documentation in R/ArchRProjectMethods.R
 \name{addSampleColData}
 \alias{addSampleColData}
-\title{Add information to sampleColData to an ArchRProject}
+\title{Add information to sampleColData in an ArchRProject}
 \usage{
 addSampleColData(ArchRProj, data = NULL, name = NULL, samples = NULL,
   force = FALSE)
@@ -10,9 +10,9 @@ addSampleColData(ArchRProj, data = NULL, name = NULL, samples = NULL,
 \arguments{
 \item{ArchRProj}{An \code{ArchRProject} object.}
 
-\item{data}{The data to add to \code{sampleColData}.}
+\item{data}{The data as a vector to add to \code{sampleColData}.}
 
-\item{name}{The column header name to be used for this new data in \code{sampleColData}. If a column with this name already exists, you may set \code{force} equal to TRUE to overwrite the data in this column.}
+\item{name}{The column header name to be used for this new data in \code{sampleColData}. If a column with this name already exists, you may set \code{force} equal to \code{TRUE} to overwrite the data in this column.}
 
 \item{samples}{The names of the samples corresponding to \code{data}. Typically new data is added to all samples but you may use this argument to only add data to a subset of samples. Samples where \code{data} is not added are set to \code{NA}.}
 
@@ -21,5 +21,5 @@ addSampleColData(ArchRProj, data = NULL, name = NULL, samples = NULL,
 \item{...}{additional args}
 }
 \description{
-This function adds new data to sampleColData in ArchRProject.
+This function adds new data to sampleColData in an ArchRProject.
 }
diff --git a/man/addTileMatrix.Rd b/man/addTileMatrix.Rd
index 17ce701a..2bcbbadc 100644
--- a/man/addTileMatrix.Rd
+++ b/man/addTileMatrix.Rd
@@ -8,8 +8,8 @@ addTileMatrix(input = NULL, chromSizes = ifelse(inherits(input,
   "ArchRProject"), chromSizes(input), NULL),
   blacklist = ifelse(inherits(input, "ArchRProject"),
   getBlacklist(input), NULL), tileSize = 500, binarize = TRUE,
-  excludeChr = c("chrM", "chrY"), threads = 1, parallelParam = NULL,
-  force = FALSE, ...)
+  excludeChr = c("chrM", "chrY"), threads = getArchRThreads(),
+  parallelParam = NULL, force = FALSE, ...)
 }
 \arguments{
 \item{input}{An \code{ArchRProject} object or character vector of ArrowFiles.}
diff --git a/man/createArrowFiles.Rd b/man/createArrowFiles.Rd
index 9c110984..b7fe61b3 100644
--- a/man/createArrowFiles.Rd
+++ b/man/createArrowFiles.Rd
@@ -13,8 +13,8 @@ createArrowFiles(inputFiles = NULL, sampleNames = NULL,
   gsubExpression = NULL, bamFlag = NULL, offsetPlus = 4,
   offsetMinus = -5, addTileMat = TRUE, TileMatParams = list(),
   addGeneScoreMat = TRUE, GeneScoreMatParams = list(), force = FALSE,
-  threads = 1, parallelParam = NULL, verboseHeader = TRUE,
-  verboseAll = FALSE, ...)
+  threads = getArchRThreads(), parallelParam = NULL,
+  verboseHeader = TRUE, verboseAll = FALSE, ...)
 }
 \arguments{
 \item{inputFiles}{The names of the input files to use to generate the arrow files. These files can be in any of the following formats: scATAC tabix fragment files or a bam file).}
@@ -63,7 +63,7 @@ createArrowFiles(inputFiles = NULL, sampleNames = NULL,
 
 \item{addGeneScoreMat}{A boolean value indicating whether to add a Gene-Score Matrix to each Arrow file. A Gene-Score Matrix uses ATAC-seq signal proximal to the TSS to estimate gene activity.}
 
-\item{GeneScoreMatParams}{A list of parameters to pass to the \code{addGeneScoreMatrix()} function. See \code{ArchR::addGeneScoreMatrix()} for options.}
+\item{GeneScoreMatParams}{A list of parameters to pass to the \code{\link[=addGeneScoreMatrix]{addGeneScoreMatrix()}} function. See \code{ArchR::addGeneScoreMatrix()} for options.}
 
 \item{force}{A boolean value indicating whether to force arrow files to be overwritten if they already exist in \code{outDir}.}
 
diff --git a/man/createGeneAnnnotation.Rd b/man/createGeneAnnnotation.Rd
index 7439e495..bb546d91 100644
--- a/man/createGeneAnnnotation.Rd
+++ b/man/createGeneAnnnotation.Rd
@@ -2,24 +2,24 @@
 % Please edit documentation in R/ArchRProjectMethods.R
 \name{createGeneAnnnotation}
 \alias{createGeneAnnnotation}
-\title{Create Gene Annotation for ArchR}
+\title{Create a gene annotation object for ArchR}
 \usage{
 createGeneAnnnotation(genome = NULL, TxDb = NULL, OrgDb = NULL,
   genes = NULL, exons = NULL, TSS = NULL)
 }
 \arguments{
-\item{genome}{A string that specifies the genome (ie hg38, hg19, mm10, mm9).}
+\item{genome}{A string that specifies the genome (ie "hg38", "hg19", "mm10", "mm9"). If \code{genome} is not supplied, \code{TxDb} and \code{OrgDb} are required. If genome is supplied, \code{TxDb} and \code{OrgDb} will be ignored.}
 
-\item{TxDb}{A transcript database from Bioconductor which contains information for gene/transcript coordinates.}
+\item{TxDb}{QQQ A \code{TxDb} object (transcript database) from Bioconductor which contains information for gene/transcript coordinates. For example, from \code{txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene}.}
 
-\item{OrgDb}{An organism database from Bioconductor which contains information for gene/transcript symbols from ids.}
+\item{OrgDb}{QQQ An \code{OrgDb} object (organism database) from Bioconductor which contains information for gene/transcript symbols from ids. For example, from QQQ.}
 
-\item{genes}{A GRanges of gene coordinates (start to end). Needs to have a symbols column matching the exons symbols column.}
+\item{genes}{A \code{GRanges} object containing gene coordinates (start to end). Must have a symbols column matching the symbols column of \code{exons}.}
 
-\item{exons}{A GRanges of gene exon coordinates. Needs to have a symbols column matching the genes symbols column}
+\item{exons}{A \code{GRanges} object containing gene exon coordinates. Must have a symbols column matching the symbols column of \code{genes}.}
 
-\item{TSS}{A GRanges of transcription start sites (stranded) for computing TSS enrichment scores downstream.}
+\item{TSS}{A \code{GRanges} object containing standed transcription start site coordinates for computing TSS enrichment scores downstream.}
 }
 \description{
-This function will create a gene annotation that can be used for createArrowFiles, ArchRProject, etc.
+This function will create a gene annotation object that can be used for creating ArrowFiles or an ArchRProject, etc.
 }
diff --git a/man/createGenomeAnnotation.Rd b/man/createGenomeAnnotation.Rd
index b4b6c37f..018dfe33 100644
--- a/man/createGenomeAnnotation.Rd
+++ b/man/createGenomeAnnotation.Rd
@@ -2,20 +2,20 @@
 % Please edit documentation in R/ArchRProjectMethods.R
 \name{createGenomeAnnotation}
 \alias{createGenomeAnnotation}
-\title{Create Genome Annotation for ArchR}
+\title{Create a genome annotation object for ArchR}
 \usage{
 createGenomeAnnotation(genome = NULL, chromSizes = NULL,
   blacklist = NULL, filter = TRUE)
 }
 \arguments{
-\item{genome}{A string that points to a BSgenome or a BSgenome object (ie hg38, BSgenome.Hsapiens.UCSC.hg38).}
+\item{genome}{Either (i) a string that is a valid \code{BSgenome} or (ii) a \code{BSgenome} object (ie "hg38" or "BSgenome.Hsapiens.UCSC.hg38").}
 
-\item{chromSizes}{A GRanges of chromosome start and end coordinates.}
+\item{chromSizes}{A \code{GRanges} object containing chromosome start and end coordinates.}
 
-\item{blacklist}{A GRanges of regions that should be excluded from analyses due to unwanted biases.}
+\item{blacklist}{A \code{GRanges} object containing regions that should be excluded from analyses due to unwanted biases.}
 
-\item{filter}{A boolean indicating whether non-normal chromosome scaffolds should be excluded.}
+\item{filter}{QQQ A boolean value indicating whether non-standard chromosome scaffolds should be excluded. These "non-standard" chromosomes are defined by QQQ.}
 }
 \description{
-This function will create a genome annotation that can be used for createArrowFiles, ArchRProject, etc.
+This function will create a genome annotation object that can be used for creating ArrowFiles or an ArchRProject, etc.
 }
diff --git a/man/getArchRThreads.Rd b/man/getArchRThreads.Rd
index 22884b27..22fabcde 100644
--- a/man/getArchRThreads.Rd
+++ b/man/getArchRThreads.Rd
@@ -2,10 +2,10 @@
 % Please edit documentation in R/ArchRProjectMethods.R
 \name{getArchRThreads}
 \alias{getArchRThreads}
-\title{Get global number of threads for default parallel computing.}
+\title{Get globally-applied number of threads to use for parallel computing.}
 \usage{
 getArchRThreads()
 }
 \description{
-This function will get the global number of threads to be used for ArchR functions.
+This function will get the number of threads to be used for parallel execution across all ArchR functions.
 }
diff --git a/man/getBlacklist.Rd b/man/getBlacklist.Rd
index d8afe4fa..34ee4946 100644
--- a/man/getBlacklist.Rd
+++ b/man/getBlacklist.Rd
@@ -2,7 +2,7 @@
 % Please edit documentation in R/ArchRProjectMethods.R
 \name{getBlacklist}
 \alias{getBlacklist}
-\title{Get blacklist from an ArchRProject}
+\title{Get the blacklist from an ArchRProject}
 \usage{
 getBlacklist(ArchRProj, ...)
 }
@@ -12,5 +12,5 @@ getBlacklist(ArchRProj, ...)
 \item{...}{additional args}
 }
 \description{
-This function gets the blacklist (the regions to be excluded from analysis) as a GRanges from the genomeAnnotation of a given ArchRProject.
+This function gets the blacklist (the regions to be excluded from analysis) as a GRanges object from the genomeAnnotation of a given ArchRProject.
 }
diff --git a/man/getChromSizes.Rd b/man/getChromSizes.Rd
index d84a714c..72377406 100644
--- a/man/getChromSizes.Rd
+++ b/man/getChromSizes.Rd
@@ -12,5 +12,5 @@ getChromSizes(ArchRProj, ...)
 \item{...}{additional args}
 }
 \description{
-This function gets the chromosome lengths as a GRanges onject from the genomeAnnotation of a given ArchRProject.
+This function gets the chromosome lengths as a GRanges object from the genomeAnnotation of a given ArchRProject.
 }
diff --git a/man/getEmbedding.Rd b/man/getEmbedding.Rd
index 376dbf1a..882d254c 100644
--- a/man/getEmbedding.Rd
+++ b/man/getEmbedding.Rd
@@ -9,7 +9,7 @@ getEmbedding(ArchRProj, embedding = "UMAP", returnDF = TRUE, ...)
 \arguments{
 \item{ArchRProj}{An \code{ArchRProject} object.}
 
-\item{embedding}{The name of the \code{embeddings} object (i.e. UMAP, TSNE see embeddingOut of addEmbeddings) to retrieve from the designated \code{ArchRProject}.}
+\item{embedding}{The name of the \code{embeddings} object (i.e. UMAP, TSNE see \code{embeddingOut} of the \code{addEmbeddings()} function) to retrieve from the designated \code{ArchRProject}.}
 
 \item{returnDF}{A boolean value indicating whether to return the embedding object as a \code{data.frame}. Otherwise, it will return the full embedding object.}
 
diff --git a/man/getExons.Rd b/man/getExons.Rd
index 1491da95..e2ac5285 100644
--- a/man/getExons.Rd
+++ b/man/getExons.Rd
@@ -14,5 +14,5 @@ getExons(ArchRProj, symbols = NULL, ...)
 \item{...}{additional args}
 }
 \description{
-This function gets the exons coordinates as a GRanges from the geneAnnotation of a given ArchRProject.
+This function gets the exons coordinates as a GRanges object from the geneAnnotation of a given ArchRProject.
 }
diff --git a/man/getFeatures.Rd b/man/getFeatures.Rd
index 00052ddf..af78892c 100644
--- a/man/getFeatures.Rd
+++ b/man/getFeatures.Rd
@@ -12,9 +12,9 @@ getFeatures(ArchRProj, useMatrix = "GeneScoreMatrix", select = NULL,
 
 \item{useMatrix}{The name of the data matrix as stored in the ArrowFiles of the \code{ArchRProject}. Options include "TileMatrix", "GeneScoreMatrix", etc.}
 
-\item{select}{A string specifying a specific featureName (or rowname) found with grep}
+\item{select}{A string specifying a specific feature name (or rowname) to be found with \code{grep}.}
 
-\item{ignore.case}{A boolean value indicating whether or not to ignore the case (upper-case / lower-case) when searching via grep for the string passed to \code{select}.}
+\item{ignore.case}{A boolean value indicating whether to ignore the case (upper-case / lower-case) when searching via grep for the string passed to \code{select}.}
 
 \item{...}{additional args}
 }
diff --git a/man/getGeneAnnotation.Rd b/man/getGeneAnnotation.Rd
index 74890afc..39ebd440 100644
--- a/man/getGeneAnnotation.Rd
+++ b/man/getGeneAnnotation.Rd
@@ -12,5 +12,5 @@ getGeneAnnotation(ArchRProj, ...)
 \item{...}{additional args}
 }
 \description{
-This function gets the geneAnnotation (see createGeneAnnotation) from a given ArchRProject
+This function gets the geneAnnotation from a given ArchRProject
 }
diff --git a/man/getGenes.Rd b/man/getGenes.Rd
index 048f00f9..ca2d276a 100644
--- a/man/getGenes.Rd
+++ b/man/getGenes.Rd
@@ -14,5 +14,5 @@ getGenes(ArchRProj, symbols = NULL, ...)
 \item{...}{additional args}
 }
 \description{
-This function gets the genes start to end coordinates as a GRanges from the geneAnnotation of a given ArchRProject.
+This function gets the genes start and end coordinates as a GRanges object from the geneAnnotation of a given ArchRProject.
 }
diff --git a/man/getGenomeAnnotation.Rd b/man/getGenomeAnnotation.Rd
index 5d212a5f..0cec92fc 100644
--- a/man/getGenomeAnnotation.Rd
+++ b/man/getGenomeAnnotation.Rd
@@ -2,7 +2,7 @@
 % Please edit documentation in R/ArchRProjectMethods.R
 \name{getGenomeAnnotation}
 \alias{getGenomeAnnotation}
-\title{Get genomeAnnotation from an ArchRProject}
+\title{Get the genomeAnnotation from an ArchRProject}
 \usage{
 getGenomeAnnotation(ArchRProj, ...)
 }
@@ -12,5 +12,5 @@ getGenomeAnnotation(ArchRProj, ...)
 \item{...}{additional args}
 }
 \description{
-This function gets the genomeAnnotation (see createGenomeAnnotation) from a given ArchRProject.
+This function gets the genomeAnnotation from a given ArchRProject.
 }
diff --git a/man/getPeakSet.Rd b/man/getPeakSet.Rd
index b63489c5..3f2d9ae0 100644
--- a/man/getPeakSet.Rd
+++ b/man/getPeakSet.Rd
@@ -7,7 +7,7 @@
 getPeakSet(ArchRProj, ...)
 }
 \arguments{
-\item{ArchRProj}{An ArchRProject object.}
+\item{ArchRProj}{An \code{ArchRProject} object.}
 
 \item{...}{additional args}
 }
diff --git a/man/getProjectSummary.Rd b/man/getProjectSummary.Rd
index f82a7f50..00f4cc74 100644
--- a/man/getProjectSummary.Rd
+++ b/man/getProjectSummary.Rd
@@ -2,7 +2,7 @@
 % Please edit documentation in R/ArchRProjectMethods.R
 \name{getProjectSummary}
 \alias{getProjectSummary}
-\title{Get projectSummary from ArchRProject}
+\title{Get projectSummary from an ArchRProject}
 \usage{
 getProjectSummary(ArchRProj, returnSummary = FALSE, ...)
 }
diff --git a/man/getReducedDims.Rd b/man/getReducedDims.Rd
index 5d27876e..565dba64 100644
--- a/man/getReducedDims.Rd
+++ b/man/getReducedDims.Rd
@@ -10,13 +10,13 @@ getReducedDims(ArchRProj, reducedDims = "IterativeLSI",
 \arguments{
 \item{ArchRProj}{An \code{ArchRProject} object.}
 
-\item{reducedDims}{The name of the \code{reducedDims} object (i.e. IterativeLSI) to retrieve from the designated \code{ArchRProject}.}
+\item{reducedDims}{The name of the \code{reducedDims} object (i.e. "IterativeLSI") to retrieve from the designated \code{ArchRProject}.}
 
 \item{returnMatrix}{If set to "mat" or "matrix", the function will return the \code{reducedDims} object as a matrix with entries for each individual cell. Otherwise, it will return the full \code{reducedDims} object.}
 
 \item{dimsToUse}{A vector containing the dimensions (i.e. 1:25) to return from the \code{reducedDims} object.}
 
-\item{corCutOff}{A numeric cutoff for the correlation of each dimension to the sequencing depth. If the dimension has a correlation to sequencing depth that is greater than the corCutOff, it will be excluded.}
+\item{corCutOff}{A numeric cutoff for the correlation of each dimension to the sequencing depth. If the dimension has a correlation to sequencing depth that is greater than the \code{corCutOff}, it will be excluded.}
 
 \item{...}{additional args}
 }
diff --git a/man/getSampleColData.Rd b/man/getSampleColData.Rd
index 3cb3ea2c..c3c9a035 100644
--- a/man/getSampleColData.Rd
+++ b/man/getSampleColData.Rd
@@ -9,12 +9,12 @@ getSampleColData(ArchRProj, select = NULL, drop = FALSE, ...)
 \arguments{
 \item{ArchRProj}{An \code{ArchRProject} object.}
 
-\item{select}{A character vector containing the column names to select from sampleColData.}
+\item{select}{A character vector containing the column names to select from \code{sampleColData}.}
 
 \item{drop}{A boolean value that indicates whether to drop the \code{dataframe} structure and convert to a vector if selecting only one column.}
 
 \item{...}{additional args}
 }
 \description{
-This function gets the \code{sampleColData} from a given \code{ArchRProject}.
+This function gets the sampleColData from a given ArchRProject.
 }
diff --git a/man/getTrajectory.Rd b/man/getTrajectory.Rd
index 6e5f1155..d125c1c9 100644
--- a/man/getTrajectory.Rd
+++ b/man/getTrajectory.Rd
@@ -6,7 +6,7 @@
 \usage{
 getTrajectory(ArchRProj, name = "Trajectory",
   useMatrix = "GeneScoreMatrix", varCutOff = 0.1,
-  maxFeatures = 25000, groupEvery = 2, threads = 1,
+  maxFeatures = 25000, groupEvery = 2, threads = getArchRThreads(),
   scaleTo = 10000, log2Norm = TRUE, smooth = TRUE,
   smoothFormula = "y ~ s(x, bs = 'cs')", ...)
 }
diff --git a/man/getValidBarcodes.Rd b/man/getValidBarcodes.Rd
index aa140260..66cb59b4 100644
--- a/man/getValidBarcodes.Rd
+++ b/man/getValidBarcodes.Rd
@@ -7,7 +7,7 @@
 getValidBarcodes(csvFiles, sampleNames, ...)
 }
 \arguments{
-\item{csvFiles}{A character vector of file names to be read in for identification of valid cell barcodes.}
+\item{csvFiles}{A character vector of names from 10x CSV files to be read in for identification of valid cell barcodes.}
 
 \item{sampleNames}{A character vector containing the sample names to be associated with each individual entry in \code{csvFiles}.}
 
diff --git a/man/markerFeatures.Rd b/man/markerFeatures.Rd
index fc79c60e..71441eb5 100644
--- a/man/markerFeatures.Rd
+++ b/man/markerFeatures.Rd
@@ -8,9 +8,9 @@ markerFeatures(ArchRProj = NULL, groupBy = "Clusters",
   useGroups = NULL, bgdGroups = NULL, useMatrix = "GeneScoreMatrix",
   bias = c("TSSEnrichment", "log10(nFrags)"), normBy = NULL,
   testMethod = "wilcoxon", maxCells = 500, scaleTo = 10^4,
-  threads = 1, k = 100, bufferRatio = 0.8, binarize = FALSE,
-  useSeqnames = NULL, method = "ArchR", verboseHeader = TRUE,
-  verboseAll = FALSE, ...)
+  threads = getArchRThreads(), k = 100, bufferRatio = 0.8,
+  binarize = FALSE, useSeqnames = NULL, method = "ArchR",
+  verboseHeader = TRUE, verboseAll = FALSE, ...)
 }
 \arguments{
 \item{ArchRProj}{An \code{ArchRProject} object.}
diff --git a/man/nCells.Rd b/man/nCells.Rd
index 47eaea3b..99b2ea35 100644
--- a/man/nCells.Rd
+++ b/man/nCells.Rd
@@ -12,5 +12,5 @@ nCells(input, ...)
 \item{...}{additional args}
 }
 \description{
-This function gets number of cells in ArchRProject/ArrowFile
+This function gets number of cells from an ArchRProject or ArrowFile
 }
diff --git a/man/plotFootprints.Rd b/man/plotFootprints.Rd
index 86f95bcc..875ee704 100644
--- a/man/plotFootprints.Rd
+++ b/man/plotFootprints.Rd
@@ -9,8 +9,8 @@ plotFootprints(ArchRProj = NULL, positions = NULL,
   useGroups = NULL, pal = NULL, flank = 250, flankNorm = 50,
   smoothWindow = 10, minCells = 25, nTop = NULL,
   normMethod = "none", inputSE = NULL, height = 6, width = 4,
-  addDOC = TRUE, useSink = TRUE, threads = 1, verboseHeader = TRUE,
-  verboseAll = FALSE, ...)
+  addDOC = TRUE, useSink = TRUE, threads = getArchRThreads(),
+  verboseHeader = TRUE, verboseAll = FALSE, ...)
 }
 \arguments{
 \item{ArchRProj}{An \code{ArchRProject} object}
diff --git a/man/plotPDF.Rd b/man/plotPDF.Rd
index 77b4849a..378c2dca 100644
--- a/man/plotPDF.Rd
+++ b/man/plotPDF.Rd
@@ -17,16 +17,16 @@ plotPDF(..., name = "Plot", width = 6, height = 6,
 
 \item{height}{The height in inches to be used for the output PDF.}
 
-\item{ArchRProj}{An \code{ArchRProject} object to be used for getting plotDirectory in outputDirectory.}
+\item{ArchRProj}{QQQ WHAT IS PLOT DIRECTORY? An \code{ArchRProject} object to be used for getting plotDirectory in outputDirectory.}
 
-\item{addDOC}{A boolean variable that determines whether to add the date of creation to end of the PDF file name. This is useful for preventing overwritting of old plots.}
+\item{addDOC}{A boolean variable that determines whether to add the date of creation to the end of the PDF file name. This is useful for preventing overwritting of old plots.}
 
 \item{useDingbats}{A boolean variable that determines wheter to use dingbats characters for plotting points.}
 
 \item{plotList}{A \code{list} of plots to be printed to the output PDF file. Each element of \code{plotList} should be a printable plot formatted object (ggplot2, plot, heatmap, etc).}
 
-\item{useSink}{use sink to hide messages from plotting}
+\item{useSink}{QQQ A boolean value indicating whether sink should be used to hide output messages that result from plotting.}
 }
 \description{
-This function will save a plot or set of plots as a PDF file in the output directory of a given ArchRProject.
+This function will save a plot or set of plots as a PDF file in the outputDirectory of a given ArchRProject.
 }