diff --git a/DESCRIPTION b/DESCRIPTION
index cb590de..1867c06 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: chromVAR
 Type: Package
 Title: Chromatin Variation Across Regions
-Version: 1.5.0
+Version: 1.35.1
 Authors@R: c(
     person("Alicia", "Schep", email = "aschep@gmail.com", role = c("aut","cre")),
     person("Jason", "Buenrostro", role = "ctb"),
@@ -15,13 +15,14 @@ Description: Determine variation in chromatin accessibility across sets of
 License: MIT + file LICENSE
 Imports:
     IRanges,
-    GenomeInfoDb,
+    Seqinfo,
     GenomicRanges,
     ggplot2,
     nabor,
     BiocParallel,
     BiocGenerics,
     Biostrings,
+    pwalign,
     TFBSTools,
     Rsamtools,
     S4Vectors,
@@ -54,6 +55,6 @@ Suggests:
 biocViews: SingleCell, Sequencing, GeneRegulation, ImmunoOncology
 LazyData: TRUE
 LinkingTo: Rcpp, RcppArmadillo
-SystemRequirements: C++11
+SystemRequirements: C++14
 VignetteBuilder: knitr
-RoxygenNote: 6.0.1
+RoxygenNote: 7.3.2
diff --git a/NAMESPACE b/NAMESPACE
index 2a59c99..5935eb2 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -70,14 +70,10 @@ importClassesFrom(SummarizedExperiment,SummarizedExperiment)
 importFrom(BSgenome,getBSgenome)
 importFrom(BiocGenerics,relist)
 importFrom(BiocParallel,bplapply)
-importFrom(Biostrings,nucleotideSubstitutionMatrix)
-importFrom(Biostrings,stringDist)
+importFrom(pwalign,nucleotideSubstitutionMatrix)
+importFrom(pwalign,stringDist)
 importFrom(DT,datatable)
 importFrom(DT,formatSignif)
-importFrom(GenomeInfoDb,"seqlevels<-")
-importFrom(GenomeInfoDb,seqlevels)
-importFrom(GenomeInfoDb,seqnames)
-importFrom(GenomeInfoDb,sortSeqlevels)
 importFrom(IRanges,IRanges)
 importFrom(IRanges,PartitioningByEnd)
 importFrom(IRanges,overlapsAny)
@@ -91,6 +87,10 @@ importFrom(S4Vectors,elementNROWS)
 importFrom(S4Vectors,isSorted)
 importFrom(S4Vectors,queryHits)
 importFrom(S4Vectors,subjectHits)
+importFrom(Seqinfo,"seqlevels<-")
+importFrom(Seqinfo,seqlevels)
+importFrom(Seqinfo,seqnames)
+importFrom(Seqinfo,sortSeqlevels)
 importFrom(TFBSTools,PWMatrix)
 importFrom(TFBSTools,PWMatrixList)
 importFrom(TFBSTools,bg)
diff --git a/R/background_peaks.R b/R/background_peaks.R
index 53d837d..463de24 100644
--- a/R/background_peaks.R
+++ b/R/background_peaks.R
@@ -22,7 +22,7 @@ setGeneric("addGCBias", function(object, ...) standardGeneric("addGCBias"))
 #' @export
 setMethod(addGCBias, c(object = "RangedSummarizedExperiment"), 
           function(object, 
-                   genome = GenomeInfoDb::genome(object)) {
+                   genome = Seqinfo::genome(object)) {
             genome <- validate_genome_input(genome)
             peaks <- rowRanges(object)
             seqs <- getSeq(genome, peaks)
@@ -38,7 +38,7 @@ setMethod(addGCBias, c(object = "RangedSummarizedExperiment"),
 #' @export
 setMethod(addGCBias, c(object = "SummarizedExperiment"), 
           function(object, peaks, 
-                   genome = GenomeInfoDb::genome(peaks)) {
+                   genome = Seqinfo::genome(peaks)) {
             genome <- validate_genome_input(genome)
             seqs <- getSeq(genome, peaks)
             nucfreqs <- letterFrequency(seqs, c("A", "C", "G", "T"))
diff --git a/R/chromVAR.R b/R/chromVAR.R
index 1bf6033..0e213f3 100644
--- a/R/chromVAR.R
+++ b/R/chromVAR.R
@@ -21,7 +21,7 @@
 #' txtProgressBar
 #' @importFrom Rcpp sourceCpp
 #' @importFrom S4Vectors queryHits subjectHits DataFrame elementNROWS isSorted
-#' @importFrom GenomeInfoDb seqlevels seqlevels<- sortSeqlevels seqnames
+#' @importFrom Seqinfo seqlevels seqlevels<- sortSeqlevels seqnames
 #' @importFrom Rsamtools ScanBamParam scanBamFlag scanBam countBam
 #' @importFrom IRanges IRanges overlapsAny
 #' @importFrom BiocParallel bplapply
diff --git a/R/kmers.R b/R/kmers.R
index 02cec1d..21a7e08 100644
--- a/R/kmers.R
+++ b/R/kmers.R
@@ -56,7 +56,7 @@ deviationsCovariability <- function(object) {
   return(normed_covs)
 }
 
-#' @importFrom Biostrings nucleotideSubstitutionMatrix stringDist
+#' @importFrom pwalign nucleotideSubstitutionMatrix stringDist
 get_kmer_dist <- function(kmers) {
   stopifnot(all_equal(nchar(kmers)))
   out <- as.matrix(stringDist(kmers, 
diff --git a/R/match_kmers.R b/R/match_kmers.R
index c4cd714..b5d1d96 100644
--- a/R/match_kmers.R
+++ b/R/match_kmers.R
@@ -153,7 +153,7 @@ setMethod("matchKmers", signature(k = "character", subject = "DNAString"),
 setMethod("matchKmers", signature(k = "character", subject = "GenomicRanges"),
           function(k,
                    subject, 
-                   genome = GenomeInfoDb::genome(subject),
+                   genome = Seqinfo::genome(subject),
                    out = c("matches", "positions")) {
             out <- match.arg(out)
             GenomicRanges::strand(subject) <- "+"
diff --git a/R/motifs.R b/R/motifs.R
index e173dc2..348731e 100644
--- a/R/motifs.R
+++ b/R/motifs.R
@@ -1,28 +1,33 @@
 #' getJasparMotifs
 #'
 #' Function to get motifs from JASPAR database
-#' @param species Which species?  use eithe jaspar code or latin name. 
+#' @param species Which species?  use eithe jaspar code or latin name.
 #' default is 'Homo sapiens'
 #' @param collection Which collection to use?  default is 'CORE'
-#' @param ... additional arguments to opts for 
+#' @param jaspar_db Which JASPAR database? default is `JASPAR2016::JASPAR2016`
+#' @param ... additional arguments to opts for
 #' \code{\link[TFBSTools]{getMatrixSet}}
 #' @details Simply a wrapper function for \code{\link[TFBSTools]{getMatrixSet}}
 #'  that calls JASPAR2016 database using \code{\link[JASPAR2016]{JASPAR2016}}
 #' @return \code{\link[TFBSTools]{PFMatrixList}}
 #' @export
-#' @examples 
-#' 
+#' @examples
+#'
 #' motifs <- getJasparMotifs()
-#' 
-#' 
-getJasparMotifs <- function(species = "Homo sapiens", 
-                              collection = "CORE", ...) {
+#'
+#' # use the JASPAR2020 database
+#' motifs <- getJasparMotifs(jaspar_db = JASPAR2020::JASPAR2020)
+#'
+getJasparMotifs <- function(species = "Homo sapiens",
+                            collection = "CORE",
+                            jaspar_db = JASPAR2016::JASPAR2016,
+                            ...) {
   opts <- list()
   opts["species"] <- species
   opts["collection"] <- collection
   opts <- c(opts, list(...))
-  out <- TFBSTools::getMatrixSet(JASPAR2016::JASPAR2016, opts)
-  if (!isTRUE(all.equal(TFBSTools::name(out), names(out)))) 
+  out <- TFBSTools::getMatrixSet(jaspar_db, opts)
+  if (!isTRUE(all.equal(TFBSTools::name(out), names(out))))
     names(out) <- paste(names(out), TFBSTools::name(out), sep = "_")
   return(out)
 }
diff --git a/data-raw/example_counts.R b/data-raw/example_counts.R
index ffbbcff..a1685e5 100644
--- a/data-raw/example_counts.R
+++ b/data-raw/example_counts.R
@@ -17,7 +17,7 @@ cleanup_peaks <- function(peaks){
   non_mito_peaks = which(!blacklisted)
   peaks <- peaks[non_mito_peaks]
   
-  seqlengths(peaks) <- GenomeInfoDb::seqlengths(BSgenome.Hsapiens.UCSC.hg19::BSgenome.Hsapiens.UCSC.hg19)[GenomeInfoDb::seqlevels(peaks)]
+  seqlengths(peaks) <- Seqinfo::seqlengths(BSgenome.Hsapiens.UCSC.hg19::BSgenome.Hsapiens.UCSC.hg19)[Seqinfo::seqlevels(peaks)]
   within_boundaries = which(GenomicRanges::trim(peaks) == peaks)
   peaks <- peaks[within_boundaries]
   return(peaks)
diff --git a/data/example_counts.rda b/data/example_counts.rda
index eaec5dc..03c222a 100644
Binary files a/data/example_counts.rda and b/data/example_counts.rda differ
diff --git a/data/mini_counts.rda b/data/mini_counts.rda
index 63ed7a5..a4737e1 100644
Binary files a/data/mini_counts.rda and b/data/mini_counts.rda differ
diff --git a/data/mini_dev.rda b/data/mini_dev.rda
index b8f058d..fa6d94c 100644
Binary files a/data/mini_dev.rda and b/data/mini_dev.rda differ
diff --git a/data/mini_ix.rda b/data/mini_ix.rda
index 6999133..72d5414 100644
Binary files a/data/mini_ix.rda and b/data/mini_ix.rda differ
diff --git a/man/addGCBias.Rd b/man/addGCBias.Rd
index b2e3ca6..c202d3c 100644
--- a/man/addGCBias.Rd
+++ b/man/addGCBias.Rd
@@ -1,6 +1,5 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/background_peaks.R
-\docType{methods}
 \name{addGCBias}
 \alias{addGCBias}
 \alias{addGCBias,RangedSummarizedExperiment-method}
@@ -9,11 +8,9 @@
 \usage{
 addGCBias(object, ...)
 
-\S4method{addGCBias}{RangedSummarizedExperiment}(object,
-  genome = GenomeInfoDb::genome(object))
+\S4method{addGCBias}{RangedSummarizedExperiment}(object, genome = Seqinfo::genome(object))
 
-\S4method{addGCBias}{SummarizedExperiment}(object, peaks,
-  genome = GenomeInfoDb::genome(peaks))
+\S4method{addGCBias}{SummarizedExperiment}(object, peaks, genome = Seqinfo::genome(peaks))
 }
 \arguments{
 \item{object}{(Ranged)SummarizedExperiment}
@@ -34,11 +31,11 @@ Computes GC content for peaks
 }
 \section{Methods (by class)}{
 \itemize{
-\item \code{RangedSummarizedExperiment}: method for RangedSummarizedExperiment
+\item \code{addGCBias(RangedSummarizedExperiment)}: method for RangedSummarizedExperiment
 
-\item \code{SummarizedExperiment}: method for SummarizedExperiment
-}}
+\item \code{addGCBias(SummarizedExperiment)}: method for SummarizedExperiment
 
+}}
 \examples{
 
 data(example_counts, package = "chromVAR")
diff --git a/man/annotationMatches.Rd b/man/annotationMatches.Rd
index 470cfb1..649d619 100644
--- a/man/annotationMatches.Rd
+++ b/man/annotationMatches.Rd
@@ -1,12 +1,10 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/get_annotations.R
-\docType{methods}
 \name{annotationMatches}
 \alias{annotationMatches}
 \alias{annotationMatches,SummarizedExperiment-method}
 \alias{annoation_matches<-,SummarizedExperiment-method}
 \alias{annotationMatches<-}
-\alias{annotationMatches,SummarizedExperiment-method}
 \alias{annotationMatches<-,SummarizedExperiment-method}
 \title{annotationMatches}
 \usage{
diff --git a/man/cbind-chromVARDeviations-method.Rd b/man/cbind-chromVARDeviations-method.Rd
index 97bcc64..dc8c8bd 100644
--- a/man/cbind-chromVARDeviations-method.Rd
+++ b/man/cbind-chromVARDeviations-method.Rd
@@ -1,6 +1,5 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/compute_deviations.R
-\docType{methods}
 \name{cbind,chromVARDeviations-method}
 \alias{cbind,chromVARDeviations-method}
 \title{cbind method for chromVARDeviations}
diff --git a/man/chromVAR.Rd b/man/chromVAR.Rd
index 762740d..27b6ac2 100644
--- a/man/chromVAR.Rd
+++ b/man/chromVAR.Rd
@@ -2,11 +2,23 @@
 % Please edit documentation in R/chromVAR.R
 \docType{package}
 \name{chromVAR}
-\alias{chromVAR}
 \alias{chromVAR-package}
+\alias{chromVAR}
 \title{chromVAR: A package for computing variability across sets of peaks.}
 \description{
 Determine variation in chromatin accessibility across sets of
 annotations or peaks. Designed primarily for single-cell or sparse chromatin
 accessibility, e.g. from scATAC-seq or sparse ATAC or DNAse-seq experiments.
 }
+\author{
+\strong{Maintainer}: Alicia Schep \email{aschep@gmail.com}
+
+Other contributors:
+\itemize{
+  \item Jason Buenrostro [contributor]
+  \item Caleb Lareau [contributor]
+  \item William Greenleaf [thesis advisor]
+  \item Stanford University [copyright holder]
+}
+
+}
diff --git a/man/computeDeviations.Rd b/man/computeDeviations.Rd
index f45c3c1..72b5791 100644
--- a/man/computeDeviations.Rd
+++ b/man/computeDeviations.Rd
@@ -1,6 +1,5 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/compute_deviations.R
-\docType{methods}
 \name{computeDeviations}
 \alias{computeDeviations}
 \alias{computeDeviations,SummarizedExperiment,SummarizedExperiment-method}
@@ -15,33 +14,61 @@
 \usage{
 computeDeviations(object, annotations, ...)
 
-\S4method{computeDeviations}{SummarizedExperiment,SummarizedExperiment}(object,
-  annotations, background_peaks = getBackgroundPeaks(object),
-  expectation = computeExpectations(object))
-
-\S4method{computeDeviations}{SummarizedExperiment,MatrixOrmatrix}(object,
-  annotations, background_peaks = getBackgroundPeaks(object),
-  expectation = computeExpectations(object))
-
-\S4method{computeDeviations}{SummarizedExperiment,list}(object, annotations,
+\S4method{computeDeviations}{SummarizedExperiment,SummarizedExperiment}(
+  object,
+  annotations,
   background_peaks = getBackgroundPeaks(object),
-  expectation = computeExpectations(object))
-
-\S4method{computeDeviations}{SummarizedExperiment,missingOrNULL}(object,
-  annotations, background_peaks = getBackgroundPeaks(object),
-  expectation = computeExpectations(object))
+  expectation = computeExpectations(object)
+)
 
-\S4method{computeDeviations}{MatrixOrmatrix,SummarizedExperiment}(object,
-  annotations, background_peaks, expectation = computeExpectations(object))
-
-\S4method{computeDeviations}{MatrixOrmatrix,MatrixOrmatrix}(object, annotations,
-  background_peaks, expectation = computeExpectations(object))
+\S4method{computeDeviations}{SummarizedExperiment,MatrixOrmatrix}(
+  object,
+  annotations,
+  background_peaks = getBackgroundPeaks(object),
+  expectation = computeExpectations(object)
+)
 
-\S4method{computeDeviations}{MatrixOrmatrix,list}(object, annotations,
-  background_peaks, expectation = computeExpectations(object))
+\S4method{computeDeviations}{SummarizedExperiment,list}(
+  object,
+  annotations,
+  background_peaks = getBackgroundPeaks(object),
+  expectation = computeExpectations(object)
+)
 
-\S4method{computeDeviations}{MatrixOrmatrix,missingOrNULL}(object, annotations,
-  background_peaks, expectation = computeExpectations(object))
+\S4method{computeDeviations}{SummarizedExperiment,missingOrNULL}(
+  object,
+  annotations,
+  background_peaks = getBackgroundPeaks(object),
+  expectation = computeExpectations(object)
+)
+
+\S4method{computeDeviations}{MatrixOrmatrix,SummarizedExperiment}(
+  object,
+  annotations,
+  background_peaks,
+  expectation = computeExpectations(object)
+)
+
+\S4method{computeDeviations}{MatrixOrmatrix,MatrixOrmatrix}(
+  object,
+  annotations,
+  background_peaks,
+  expectation = computeExpectations(object)
+)
+
+\S4method{computeDeviations}{MatrixOrmatrix,list}(
+  object,
+  annotations,
+  background_peaks,
+  expectation = computeExpectations(object)
+)
+
+\S4method{computeDeviations}{MatrixOrmatrix,missingOrNULL}(
+  object,
+  annotations,
+  background_peaks,
+  expectation = computeExpectations(object)
+)
 }
 \arguments{
 \item{object}{chromVARCounts object}
@@ -69,29 +96,32 @@ multiprocessing using \code{\link[BiocParallel]{bplapply}}
 }
 \section{Methods (by class)}{
 \itemize{
-\item \code{object = SummarizedExperiment,annotations = SummarizedExperiment}: object and annotations are SummarizedExperiment
+\item \code{computeDeviations(
+  object = SummarizedExperiment,
+  annotations = SummarizedExperiment
+)}: object and annotations are SummarizedExperiment
 
-\item \code{object = SummarizedExperiment,annotations = MatrixOrmatrix}: object is SummarizedExperiment,
+\item \code{computeDeviations(object = SummarizedExperiment, annotations = MatrixOrmatrix)}: object is SummarizedExperiment,
 annotations are Matrix
 
-\item \code{object = SummarizedExperiment,annotations = list}: object is SummarizedExperiment,
+\item \code{computeDeviations(object = SummarizedExperiment, annotations = list)}: object is SummarizedExperiment,
 annotations are list
 
-\item \code{object = SummarizedExperiment,annotations = missingOrNULL}: object is SummarizedExperiment,
+\item \code{computeDeviations(object = SummarizedExperiment, annotations = missingOrNULL)}: object is SummarizedExperiment,
 annotations are missing
 
-\item \code{object = MatrixOrmatrix,annotations = SummarizedExperiment}: object and annotations are SummarizedExperiment
+\item \code{computeDeviations(object = MatrixOrmatrix, annotations = SummarizedExperiment)}: object and annotations are SummarizedExperiment
 
-\item \code{object = MatrixOrmatrix,annotations = MatrixOrmatrix}: object is SummarizedExperiment,
+\item \code{computeDeviations(object = MatrixOrmatrix, annotations = MatrixOrmatrix)}: object is SummarizedExperiment,
 annotations are Matrix
 
-\item \code{object = MatrixOrmatrix,annotations = list}: object is SummarizedExperiment,
+\item \code{computeDeviations(object = MatrixOrmatrix, annotations = list)}: object is SummarizedExperiment,
 annotations are list
 
-\item \code{object = MatrixOrmatrix,annotations = missingOrNULL}: object is SummarizedExperiment,
+\item \code{computeDeviations(object = MatrixOrmatrix, annotations = missingOrNULL)}: object is SummarizedExperiment,
 annotations are missing
-}}
 
+}}
 \examples{
 # Register BiocParallel
 BiocParallel::register(BiocParallel::SerialParam())
diff --git a/man/computeExpectations.Rd b/man/computeExpectations.Rd
index d98e4e8..b54b7a1 100644
--- a/man/computeExpectations.Rd
+++ b/man/computeExpectations.Rd
@@ -1,6 +1,5 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/compute_deviations.R
-\docType{methods}
 \name{computeExpectations}
 \alias{computeExpectations}
 \alias{computeExpectations,MatrixOrmatrix-method}
@@ -9,11 +8,9 @@
 \usage{
 computeExpectations(object, ...)
 
-\S4method{computeExpectations}{MatrixOrmatrix}(object, norm = FALSE,
-  group = NULL)
+\S4method{computeExpectations}{MatrixOrmatrix}(object, norm = FALSE, group = NULL)
 
-\S4method{computeExpectations}{SummarizedExperiment}(object, norm = FALSE,
-  group = NULL)
+\S4method{computeExpectations}{SummarizedExperiment}(object, norm = FALSE, group = NULL)
 }
 \arguments{
 \item{object}{SummarizedExperiment}
@@ -49,12 +46,12 @@ By default, this function will compute the expected fraction of
 }
 \section{Methods (by class)}{
 \itemize{
-\item \code{MatrixOrmatrix}: method for Matrix or matrix
+\item \code{computeExpectations(MatrixOrmatrix)}: method for Matrix or matrix
 
-\item \code{SummarizedExperiment}: method for SummarizedExperiment with counts
+\item \code{computeExpectations(SummarizedExperiment)}: method for SummarizedExperiment with counts
 slot
-}}
 
+}}
 \examples{
 
 # First get some data
diff --git a/man/computeVariability.Rd b/man/computeVariability.Rd
index 853cb1c..e303676 100644
--- a/man/computeVariability.Rd
+++ b/man/computeVariability.Rd
@@ -4,8 +4,13 @@
 \alias{computeVariability}
 \title{computeVariability}
 \usage{
-computeVariability(object, bootstrap_error = TRUE, bootstrap_samples = 1000,
-  bootstrap_quantiles = c(0.025, 0.975), na.rm = TRUE)
+computeVariability(
+  object,
+  bootstrap_error = TRUE,
+  bootstrap_samples = 1000,
+  bootstrap_quantiles = c(0.025, 0.975),
+  na.rm = TRUE
+)
 }
 \arguments{
 \item{object}{output from \code{\link{computeDeviations}}}
diff --git a/man/deviationScores.Rd b/man/deviationScores.Rd
index fa2fdf6..f237675 100644
--- a/man/deviationScores.Rd
+++ b/man/deviationScores.Rd
@@ -1,10 +1,8 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/compute_deviations.R
-\docType{methods}
 \name{deviationScores}
 \alias{deviationScores}
 \alias{deviationScores,chromVARDeviations-method}
-\alias{deviationScores,chromVARDeviations-method}
 \title{deviationScores}
 \usage{
 deviationScores(object)
diff --git a/man/deviations.Rd b/man/deviations.Rd
index 32ad3d3..ce2f4f5 100644
--- a/man/deviations.Rd
+++ b/man/deviations.Rd
@@ -1,10 +1,8 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/compute_deviations.R
-\docType{methods}
 \name{deviations}
 \alias{deviations}
 \alias{deviations,chromVARDeviations-method}
-\alias{deviations,chromVARDeviations-method}
 \title{deviations}
 \usage{
 deviations(object)
diff --git a/man/deviationsTsne.Rd b/man/deviationsTsne.Rd
index 1c17710..66ef41c 100644
--- a/man/deviationsTsne.Rd
+++ b/man/deviationsTsne.Rd
@@ -4,9 +4,15 @@
 \alias{deviationsTsne}
 \title{deviationsTsne}
 \usage{
-deviationsTsne(object, threshold = 1.5, perplexity = if (what == "samples")
-  30 else 8, max_iter = 1000, theta = 0.5, what = c("samples",
-  "annotations"), shiny = FALSE)
+deviationsTsne(
+  object,
+  threshold = 1.5,
+  perplexity = if (what == "samples") 30 else 8,
+  max_iter = 1000,
+  theta = 0.5,
+  what = c("samples", "annotations"),
+  shiny = FALSE
+)
 }
 \arguments{
 \item{object}{deviations result}
diff --git a/man/differentialDeviations.Rd b/man/differentialDeviations.Rd
index b2e6ccf..58489ba 100644
--- a/man/differentialDeviations.Rd
+++ b/man/differentialDeviations.Rd
@@ -4,8 +4,12 @@
 \alias{differentialDeviations}
 \title{differentialDeviations}
 \usage{
-differentialDeviations(object, groups, alternative = c("two.sided", "less",
-  "greater"), parametric = TRUE)
+differentialDeviations(
+  object,
+  groups,
+  alternative = c("two.sided", "less", "greater"),
+  parametric = TRUE
+)
 }
 \arguments{
 \item{object}{chromVARDeviations object}
diff --git a/man/filterPeaks.Rd b/man/filterPeaks.Rd
index 0c15562..629ddc7 100644
--- a/man/filterPeaks.Rd
+++ b/man/filterPeaks.Rd
@@ -4,8 +4,12 @@
 \alias{filterPeaks}
 \title{filterPeaks}
 \usage{
-filterPeaks(object, min_fragments_per_peak = 1, non_overlapping = TRUE,
-  ix_return = FALSE)
+filterPeaks(
+  object,
+  min_fragments_per_peak = 1,
+  non_overlapping = TRUE,
+  ix_return = FALSE
+)
 }
 \arguments{
 \item{object}{SummarizedExperiment with matrix of fragment counts per peak
diff --git a/man/filterSamples.Rd b/man/filterSamples.Rd
index 867a69b..bb30ece 100644
--- a/man/filterSamples.Rd
+++ b/man/filterSamples.Rd
@@ -4,8 +4,13 @@
 \alias{filterSamples}
 \title{filterSamples}
 \usage{
-filterSamples(object, min_in_peaks = NULL, min_depth = NULL,
-  shiny = interactive(), ix_return = FALSE)
+filterSamples(
+  object,
+  min_in_peaks = NULL,
+  min_depth = NULL,
+  shiny = interactive(),
+  ix_return = FALSE
+)
 }
 \arguments{
 \item{object}{SummarizedExperiment with matrix of fragment counts per peak
diff --git a/man/filterSamplesPlot.Rd b/man/filterSamplesPlot.Rd
index 56a5d7f..5c6a5c1 100644
--- a/man/filterSamplesPlot.Rd
+++ b/man/filterSamplesPlot.Rd
@@ -4,8 +4,12 @@
 \alias{filterSamplesPlot}
 \title{filterSamplesPlot}
 \usage{
-filterSamplesPlot(object, min_in_peaks = NULL, min_depth = NULL,
-  use_plotly = interactive())
+filterSamplesPlot(
+  object,
+  min_in_peaks = NULL,
+  min_depth = NULL,
+  use_plotly = interactive()
+)
 }
 \arguments{
 \item{object}{SummarizedExperiment with matrix of fragment counts per peak 
diff --git a/man/getAnnotationCorrelation.Rd b/man/getAnnotationCorrelation.Rd
index 996eb53..cb6f7a3 100644
--- a/man/getAnnotationCorrelation.Rd
+++ b/man/getAnnotationCorrelation.Rd
@@ -1,6 +1,5 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/variability_synergy.R
-\docType{methods}
 \name{getAnnotationCorrelation}
 \alias{getAnnotationCorrelation}
 \alias{getAnnotationCorrelation,SummarizedExperiment,SummarizedExperiment-method}
@@ -13,32 +12,53 @@
 \usage{
 getAnnotationCorrelation(object, annotations, ...)
 
-
-  \S4method{getAnnotationCorrelation}{SummarizedExperiment,SummarizedExperiment}(object,
-  annotations, background_peaks = getBackgroundPeaks(object),
-  expectation = computeExpectations(object), variabilities = NULL)
-
-
-  \S4method{getAnnotationCorrelation}{SummarizedExperiment,MatrixOrmatrix}(object,
-  annotations, background_peaks = getBackgroundPeaks(object),
-  expectation = computeExpectations(object), variabilities = NULL)
-
-\S4method{getAnnotationCorrelation}{SummarizedExperiment,list}(object,
-  annotations, background_peaks = getBackgroundPeaks(object),
-  expectation = computeExpectations(object), variabilities = NULL)
-
-
-  \S4method{getAnnotationCorrelation}{MatrixOrmatrix,SummarizedExperiment}(object,
-  annotations, background_peaks, expectation = computeExpectations(object),
-  variabilities = NULL)
-
-\S4method{getAnnotationCorrelation}{MatrixOrmatrix,MatrixOrmatrix}(object,
-  annotations, background_peaks, expectation = computeExpectations(object),
-  variabilities = NULL)
-
-\S4method{getAnnotationCorrelation}{MatrixOrmatrix,list}(object, annotations,
-  background_peaks, expectation = computeExpectations(object),
-  variabilities = NULL)
+\S4method{getAnnotationCorrelation}{SummarizedExperiment,SummarizedExperiment}(
+  object,
+  annotations,
+  background_peaks = getBackgroundPeaks(object),
+  expectation = computeExpectations(object),
+  variabilities = NULL
+)
+
+\S4method{getAnnotationCorrelation}{SummarizedExperiment,MatrixOrmatrix}(
+  object,
+  annotations,
+  background_peaks = getBackgroundPeaks(object),
+  expectation = computeExpectations(object),
+  variabilities = NULL
+)
+
+\S4method{getAnnotationCorrelation}{SummarizedExperiment,list}(
+  object,
+  annotations,
+  background_peaks = getBackgroundPeaks(object),
+  expectation = computeExpectations(object),
+  variabilities = NULL
+)
+
+\S4method{getAnnotationCorrelation}{MatrixOrmatrix,SummarizedExperiment}(
+  object,
+  annotations,
+  background_peaks,
+  expectation = computeExpectations(object),
+  variabilities = NULL
+)
+
+\S4method{getAnnotationCorrelation}{MatrixOrmatrix,MatrixOrmatrix}(
+  object,
+  annotations,
+  background_peaks,
+  expectation = computeExpectations(object),
+  variabilities = NULL
+)
+
+\S4method{getAnnotationCorrelation}{MatrixOrmatrix,list}(
+  object,
+  annotations,
+  background_peaks,
+  expectation = computeExpectations(object),
+  variabilities = NULL
+)
 }
 \arguments{
 \item{object}{result from computeDeviations}
@@ -67,22 +87,31 @@ should only be run on small number of motifs/kmers/peaksets
 }
 \section{Methods (by class)}{
 \itemize{
-\item \code{object = SummarizedExperiment,annotations = SummarizedExperiment}: object and annotations are 
+\item \code{getAnnotationCorrelation(
+  object = SummarizedExperiment,
+  annotations = SummarizedExperiment
+)}: object and annotations are 
 SummarizedExperiment
 
-\item \code{object = SummarizedExperiment,annotations = MatrixOrmatrix}: object is SummarizedExperiment, 
+\item \code{getAnnotationCorrelation(
+  object = SummarizedExperiment,
+  annotations = MatrixOrmatrix
+)}: object is SummarizedExperiment, 
 annotations are Matrix
 
-\item \code{object = SummarizedExperiment,annotations = list}: object is SummarizedExperiment, 
+\item \code{getAnnotationCorrelation(object = SummarizedExperiment, annotations = list)}: object is SummarizedExperiment, 
 annotations are list
 
-\item \code{object = MatrixOrmatrix,annotations = SummarizedExperiment}: object and annotations are 
+\item \code{getAnnotationCorrelation(
+  object = MatrixOrmatrix,
+  annotations = SummarizedExperiment
+)}: object and annotations are 
 SummarizedExperiment
 
-\item \code{object = MatrixOrmatrix,annotations = MatrixOrmatrix}: object is SummarizedExperiment, 
+\item \code{getAnnotationCorrelation(object = MatrixOrmatrix, annotations = MatrixOrmatrix)}: object is SummarizedExperiment, 
 annotations are Matrix
 
-\item \code{object = MatrixOrmatrix,annotations = list}: object is SummarizedExperiment, 
+\item \code{getAnnotationCorrelation(object = MatrixOrmatrix, annotations = list)}: object is SummarizedExperiment, 
 annotations are list
-}}
 
+}}
diff --git a/man/getAnnotationSynergy.Rd b/man/getAnnotationSynergy.Rd
index 9e7d55e..97bd33c 100644
--- a/man/getAnnotationSynergy.Rd
+++ b/man/getAnnotationSynergy.Rd
@@ -1,6 +1,5 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/variability_synergy.R
-\docType{methods}
 \name{getAnnotationSynergy}
 \alias{getAnnotationSynergy}
 \alias{getAnnotationSynergy,SummarizedExperiment,SummarizedExperiment-method}
@@ -13,33 +12,59 @@
 \usage{
 getAnnotationSynergy(object, annotations, ...)
 
-
-  \S4method{getAnnotationSynergy}{SummarizedExperiment,SummarizedExperiment}(object,
-  annotations, background_peaks = getBackgroundPeaks(object),
-  expectation = computeExpectations(object), variabilities = NULL,
-  nbg = 25)
-
-\S4method{getAnnotationSynergy}{SummarizedExperiment,MatrixOrmatrix}(object,
-  annotations, background_peaks = getBackgroundPeaks(object),
-  expectation = computeExpectations(object), variabilities = NULL,
-  nbg = 25)
-
-\S4method{getAnnotationSynergy}{SummarizedExperiment,list}(object, annotations,
+\S4method{getAnnotationSynergy}{SummarizedExperiment,SummarizedExperiment}(
+  object,
+  annotations,
   background_peaks = getBackgroundPeaks(object),
-  expectation = computeExpectations(object), variabilities = NULL,
-  nbg = 25)
-
-\S4method{getAnnotationSynergy}{MatrixOrmatrix,SummarizedExperiment}(object,
-  annotations, background_peaks, expectation = computeExpectations(object),
-  variabilities = NULL, nbg = 25)
-
-\S4method{getAnnotationSynergy}{MatrixOrmatrix,MatrixOrmatrix}(object,
-  annotations, background_peaks, expectation = computeExpectations(object),
-  variabilities = NULL, nbg = 25)
-
-\S4method{getAnnotationSynergy}{MatrixOrmatrix,list}(object, annotations,
-  background_peaks, expectation = computeExpectations(object),
-  variabilities = NULL, nbg = 25)
+  expectation = computeExpectations(object),
+  variabilities = NULL,
+  nbg = 25
+)
+
+\S4method{getAnnotationSynergy}{SummarizedExperiment,MatrixOrmatrix}(
+  object,
+  annotations,
+  background_peaks = getBackgroundPeaks(object),
+  expectation = computeExpectations(object),
+  variabilities = NULL,
+  nbg = 25
+)
+
+\S4method{getAnnotationSynergy}{SummarizedExperiment,list}(
+  object,
+  annotations,
+  background_peaks = getBackgroundPeaks(object),
+  expectation = computeExpectations(object),
+  variabilities = NULL,
+  nbg = 25
+)
+
+\S4method{getAnnotationSynergy}{MatrixOrmatrix,SummarizedExperiment}(
+  object,
+  annotations,
+  background_peaks,
+  expectation = computeExpectations(object),
+  variabilities = NULL,
+  nbg = 25
+)
+
+\S4method{getAnnotationSynergy}{MatrixOrmatrix,MatrixOrmatrix}(
+  object,
+  annotations,
+  background_peaks,
+  expectation = computeExpectations(object),
+  variabilities = NULL,
+  nbg = 25
+)
+
+\S4method{getAnnotationSynergy}{MatrixOrmatrix,list}(
+  object,
+  annotations,
+  background_peaks,
+  expectation = computeExpectations(object),
+  variabilities = NULL,
+  nbg = 25
+)
 }
 \arguments{
 \item{object}{result from computeDeviations}
@@ -69,22 +94,31 @@ should only be run on small number of motifs/kmers/peaksets
 }
 \section{Methods (by class)}{
 \itemize{
-\item \code{object = SummarizedExperiment,annotations = SummarizedExperiment}: object and annotations are 
+\item \code{getAnnotationSynergy(
+  object = SummarizedExperiment,
+  annotations = SummarizedExperiment
+)}: object and annotations are 
 SummarizedExperiment
 
-\item \code{object = SummarizedExperiment,annotations = MatrixOrmatrix}: object is SummarizedExperiment, 
+\item \code{getAnnotationSynergy(
+  object = SummarizedExperiment,
+  annotations = MatrixOrmatrix
+)}: object is SummarizedExperiment, 
 annotations are Matrix
 
-\item \code{object = SummarizedExperiment,annotations = list}: object is SummarizedExperiment, 
+\item \code{getAnnotationSynergy(object = SummarizedExperiment, annotations = list)}: object is SummarizedExperiment, 
 annotations are list
 
-\item \code{object = MatrixOrmatrix,annotations = SummarizedExperiment}: object and annotations are 
+\item \code{getAnnotationSynergy(
+  object = MatrixOrmatrix,
+  annotations = SummarizedExperiment
+)}: object and annotations are 
 SummarizedExperiment
 
-\item \code{object = MatrixOrmatrix,annotations = MatrixOrmatrix}: object is SummarizedExperiment, 
+\item \code{getAnnotationSynergy(object = MatrixOrmatrix, annotations = MatrixOrmatrix)}: object is SummarizedExperiment, 
 annotations are Matrix
 
-\item \code{object = MatrixOrmatrix,annotations = list}: object is SummarizedExperiment, 
+\item \code{getAnnotationSynergy(object = MatrixOrmatrix, annotations = list)}: object is SummarizedExperiment, 
 annotations are list
-}}
 
+}}
diff --git a/man/getAnnotations.Rd b/man/getAnnotations.Rd
index 6f7c223..278485f 100644
--- a/man/getAnnotations.Rd
+++ b/man/getAnnotations.Rd
@@ -1,6 +1,5 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/get_annotations.R
-\docType{methods}
 \name{getAnnotations}
 \alias{getAnnotations}
 \alias{getAnnotations,GRangesList-method}
@@ -20,8 +19,7 @@ getAnnotations(annotations, ...)
 
 \S4method{getAnnotations}{list}(annotations, npeaks = NULL, ...)
 
-\S4method{getAnnotations}{character}(annotations, rowRanges, column = NULL,
-  ...)
+\S4method{getAnnotations}{character}(annotations, rowRanges, column = NULL, ...)
 }
 \arguments{
 \item{annotations}{matrix, Matrix, or data.frame of fragment counts,
@@ -44,17 +42,17 @@ getAnnotations
 }
 \section{Methods (by class)}{
 \itemize{
-\item \code{GRangesList}: get annotation matrix from GRangesList
+\item \code{getAnnotations(GRangesList)}: get annotation matrix from GRangesList
 
-\item \code{MatrixOrmatrix}: get annotation matrix from Matrix or matrix
+\item \code{getAnnotations(MatrixOrmatrix)}: get annotation matrix from Matrix or matrix
 
-\item \code{data.frame}: get annotation matrix from data.frame
+\item \code{getAnnotations(data.frame)}: get annotation matrix from data.frame
 
-\item \code{list}: get annotation matrix from list
+\item \code{getAnnotations(list)}: get annotation matrix from list
 
-\item \code{character}: get annotations from bed files
-}}
+\item \code{getAnnotations(character)}: get annotations from bed files
 
+}}
 \examples{
 
 # First get example counts
diff --git a/man/getBackgroundPeaks.Rd b/man/getBackgroundPeaks.Rd
index 99ef258..51d5356 100644
--- a/man/getBackgroundPeaks.Rd
+++ b/man/getBackgroundPeaks.Rd
@@ -1,6 +1,5 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/background_peaks.R
-\docType{methods}
 \name{getBackgroundPeaks}
 \alias{getBackgroundPeaks}
 \alias{getBackgroundPeaks,SummarizedExperiment-method}
@@ -10,14 +9,23 @@
 \usage{
 getBackgroundPeaks(object, ...)
 
-\S4method{getBackgroundPeaks}{SummarizedExperiment}(object,
-  bias = rowData(object)$bias, niterations = 50, w = 0.1, bs = 50)
+\S4method{getBackgroundPeaks}{SummarizedExperiment}(
+  object,
+  bias = rowData(object)$bias,
+  niterations = 50,
+  w = 0.1,
+  bs = 50
+)
 
-\S4method{getBackgroundPeaks}{RangedSummarizedExperiment}(object,
-  bias = rowRanges(object)$bias, niterations = 50, w = 0.1, bs = 50)
+\S4method{getBackgroundPeaks}{RangedSummarizedExperiment}(
+  object,
+  bias = rowRanges(object)$bias,
+  niterations = 50,
+  w = 0.1,
+  bs = 50
+)
 
-\S4method{getBackgroundPeaks}{MatrixOrmatrix}(object, bias, niterations = 50,
-  w = 0.1, bs = 50)
+\S4method{getBackgroundPeaks}{MatrixOrmatrix}(object, bias, niterations = 50, w = 0.1, bs = 50)
 }
 \arguments{
 \item{object}{fragment counts as SummarizedExperiment, RangedSummarized, 
@@ -51,13 +59,13 @@ are chosen for both.
 }
 \section{Methods (by class)}{
 \itemize{
-\item \code{SummarizedExperiment}: method for SummarizedExperiment
+\item \code{getBackgroundPeaks(SummarizedExperiment)}: method for SummarizedExperiment
 
-\item \code{RangedSummarizedExperiment}: method for RangedSummarizedExperiment
+\item \code{getBackgroundPeaks(RangedSummarizedExperiment)}: method for RangedSummarizedExperiment
 
-\item \code{MatrixOrmatrix}: method for Matrix or matrix
-}}
+\item \code{getBackgroundPeaks(MatrixOrmatrix)}: method for Matrix or matrix
 
+}}
 \examples{
 
 # Load very small example counts (already filtered)
diff --git a/man/getCisGroups.Rd b/man/getCisGroups.Rd
index 4808630..aa414c0 100644
--- a/man/getCisGroups.Rd
+++ b/man/getCisGroups.Rd
@@ -1,6 +1,5 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/cis.R
-\docType{methods}
 \name{getCisGroups}
 \alias{getCisGroups}
 \alias{getCisGroups,RangedSummarizedExperiment-method}
@@ -9,8 +8,7 @@
 \usage{
 getCisGroups(object, ...)
 
-\S4method{getCisGroups}{RangedSummarizedExperiment}(object, grpsize = 25,
-  stepsize = 10)
+\S4method{getCisGroups}{RangedSummarizedExperiment}(object, grpsize = 25, stepsize = 10)
 
 \S4method{getCisGroups}{GenomicRanges}(object, grpsize = 25, stepsize = 10)
 }
@@ -32,11 +30,11 @@ Function for grouping peaks based on proximity along chromosomes
 }
 \section{Methods (by class)}{
 \itemize{
-\item \code{RangedSummarizedExperiment}: method for RangedSummarizedExperiment
+\item \code{getCisGroups(RangedSummarizedExperiment)}: method for RangedSummarizedExperiment
 
-\item \code{GenomicRanges}: method for GenomicRanges
-}}
+\item \code{getCisGroups(GenomicRanges)}: method for GenomicRanges
 
+}}
 \examples{
 
 # Load very small example counts (already filtered)
diff --git a/man/getCounts.Rd b/man/getCounts.Rd
index 0b183d1..d98ad5b 100644
--- a/man/getCounts.Rd
+++ b/man/getCounts.Rd
@@ -4,8 +4,14 @@
 \alias{getCounts}
 \title{getCounts}
 \usage{
-getCounts(alignment_files, peaks, paired, by_rg = FALSE, format = c("bam",
-  "bed"), colData = NULL)
+getCounts(
+  alignment_files,
+  peaks,
+  paired,
+  by_rg = FALSE,
+  format = c("bam", "bed"),
+  colData = NULL
+)
 }
 \arguments{
 \item{alignment_files}{filenames for bam or bed files with aligned reads}
diff --git a/man/getFragmentsPerPeak.Rd b/man/getFragmentsPerPeak.Rd
index 7e9066f..44dfe1c 100644
--- a/man/getFragmentsPerPeak.Rd
+++ b/man/getFragmentsPerPeak.Rd
@@ -1,6 +1,5 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/helper_functions.R
-\docType{methods}
 \name{getFragmentsPerPeak}
 \alias{getFragmentsPerPeak}
 \alias{getFragmentsPerPeak,SummarizedExperiment-method}
@@ -24,12 +23,12 @@ getFragmentsPerPeak
 }
 \section{Methods (by class)}{
 \itemize{
-\item \code{SummarizedExperiment}: method for SummarizedExperiment object 
+\item \code{getFragmentsPerPeak(SummarizedExperiment)}: method for SummarizedExperiment object 
 with counts assay
 
-\item \code{MatrixOrmatrix}: method for Matrix or matrix object
-}}
+\item \code{getFragmentsPerPeak(MatrixOrmatrix)}: method for Matrix or matrix object
 
+}}
 \examples{
 # Load very small example counts (already filtered)
 data(mini_counts, package = "chromVAR")
diff --git a/man/getFragmentsPerSample.Rd b/man/getFragmentsPerSample.Rd
index bef62d8..3895393 100644
--- a/man/getFragmentsPerSample.Rd
+++ b/man/getFragmentsPerSample.Rd
@@ -1,6 +1,5 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/helper_functions.R
-\docType{methods}
 \name{getFragmentsPerSample}
 \alias{getFragmentsPerSample}
 \alias{getFragmentsPerSample,SummarizedExperiment-method}
@@ -24,12 +23,12 @@ getFragmentsPerSample
 }
 \section{Methods (by class)}{
 \itemize{
-\item \code{SummarizedExperiment}: method for SummarizedExperiment object 
+\item \code{getFragmentsPerSample(SummarizedExperiment)}: method for SummarizedExperiment object 
 with counts assay
 
-\item \code{MatrixOrmatrix}: method for Matrix or matrix object
-}}
+\item \code{getFragmentsPerSample(MatrixOrmatrix)}: method for Matrix or matrix object
 
+}}
 \examples{
 # Load very small example counts (already filtered)
 data(mini_counts, package = "chromVAR")
diff --git a/man/getJasparMotifs.Rd b/man/getJasparMotifs.Rd
index 608ef7f..2a38f40 100644
--- a/man/getJasparMotifs.Rd
+++ b/man/getJasparMotifs.Rd
@@ -4,15 +4,18 @@
 \alias{getJasparMotifs}
 \title{getJasparMotifs}
 \usage{
-getJasparMotifs(species = "Homo sapiens", collection = "CORE", ...)
+getJasparMotifs(species = "Homo sapiens", collection = "CORE",
+                jaspar_db = JASPAR2016::JASPAR2016, ...)
 }
 \arguments{
-\item{species}{Which species?  use eithe jaspar code or latin name. 
+\item{species}{Which species?  use eithe jaspar code or latin name.
 default is 'Homo sapiens'}
 
 \item{collection}{Which collection to use?  default is 'CORE'}
 
-\item{...}{additional arguments to opts for 
+\item{jaspar_db}{Which JASPAR database? default is \code{JASPAR2016::JASPAR2016}}
+
+\item{...}{additional arguments to opts for
 \code{\link[TFBSTools]{getMatrixSet}}}
 }
 \value{
diff --git a/man/getSampleDepths.Rd b/man/getSampleDepths.Rd
index 910c005..eedbc77 100644
--- a/man/getSampleDepths.Rd
+++ b/man/getSampleDepths.Rd
@@ -4,8 +4,12 @@
 \alias{getSampleDepths}
 \title{getSampleDepths}
 \usage{
-getSampleDepths(alignment_files, paired = TRUE, by_rg = FALSE,
-  format = c("bam", "bed"))
+getSampleDepths(
+  alignment_files,
+  paired = TRUE,
+  by_rg = FALSE,
+  format = c("bam", "bed")
+)
 }
 \arguments{
 \item{alignment_files}{filenames for bam or bed file(s) with aligned reads}
diff --git a/man/getSampleDistance.Rd b/man/getSampleDistance.Rd
index 46ea2be..2397ee1 100644
--- a/man/getSampleDistance.Rd
+++ b/man/getSampleDistance.Rd
@@ -4,8 +4,12 @@
 \alias{getSampleDistance}
 \title{getSampleDistance}
 \usage{
-getSampleDistance(object, threshold = 1.5, initial_dims = 50,
-  distance_function = dist)
+getSampleDistance(
+  object,
+  threshold = 1.5,
+  initial_dims = 50,
+  distance_function = dist
+)
 }
 \arguments{
 \item{object}{deviations result}
diff --git a/man/getTotalFragments.Rd b/man/getTotalFragments.Rd
index aadd30b..bdfa8e4 100644
--- a/man/getTotalFragments.Rd
+++ b/man/getTotalFragments.Rd
@@ -1,6 +1,5 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/helper_functions.R
-\docType{methods}
 \name{getTotalFragments}
 \alias{getTotalFragments}
 \alias{getTotalFragments,SummarizedExperiment-method}
@@ -24,12 +23,12 @@ getTotalFragments
 }
 \section{Methods (by class)}{
 \itemize{
-\item \code{SummarizedExperiment}: method for SummarizedExperiment object 
+\item \code{getTotalFragments(SummarizedExperiment)}: method for SummarizedExperiment object 
 with counts assay
 
-\item \code{MatrixOrmatrix}: method for Matrix or matrix object
-}}
+\item \code{getTotalFragments(MatrixOrmatrix)}: method for Matrix or matrix object
 
+}}
 \examples{
 # Load very small example counts (already filtered)
 data(mini_counts, package = "chromVAR")
diff --git a/man/makeBiasBins.Rd b/man/makeBiasBins.Rd
index 18640e7..2925f0c 100644
--- a/man/makeBiasBins.Rd
+++ b/man/makeBiasBins.Rd
@@ -1,6 +1,5 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/test_sets.R
-\docType{methods}
 \name{makeBiasBins}
 \alias{makeBiasBins}
 \alias{makeBiasBins,SummarizedExperiment-method}
@@ -10,14 +9,11 @@
 \usage{
 makeBiasBins(object, ...)
 
-\S4method{makeBiasBins}{SummarizedExperiment}(object,
-  bias = rowData(object)$bias, nbins = 25, frac = 0.3)
+\S4method{makeBiasBins}{SummarizedExperiment}(object, bias = rowData(object)$bias, nbins = 25, frac = 0.3)
 
-\S4method{makeBiasBins}{RangedSummarizedExperiment}(object,
-  bias = rowRanges(object)$bias, nbins = 25, frac = 0.3)
+\S4method{makeBiasBins}{RangedSummarizedExperiment}(object, bias = rowRanges(object)$bias, nbins = 25, frac = 0.3)
 
-\S4method{makeBiasBins}{MatrixOrmatrix}(object, bias, nbins = 25,
-  frac = 0.3)
+\S4method{makeBiasBins}{MatrixOrmatrix}(object, bias, nbins = 25, frac = 0.3)
 }
 \arguments{
 \item{object}{fragment counts stored as RangedSummarizedExperiment, 
@@ -44,13 +40,13 @@ a certain fragment count, fragment count, or fragment count & bias.
 }
 \section{Methods (by class)}{
 \itemize{
-\item \code{SummarizedExperiment}: method for SummarizedExperiment
+\item \code{makeBiasBins(SummarizedExperiment)}: method for SummarizedExperiment
 
-\item \code{RangedSummarizedExperiment}: method for RangedSummarizedExperiment
+\item \code{makeBiasBins(RangedSummarizedExperiment)}: method for RangedSummarizedExperiment
 
-\item \code{MatrixOrmatrix}: method for Matrix or matrix
-}}
+\item \code{makeBiasBins(MatrixOrmatrix)}: method for Matrix or matrix
 
+}}
 \examples{
 # Load very small example counts (already filtered)
 data(mini_counts, package = "chromVAR")
diff --git a/man/makePermutedSets.Rd b/man/makePermutedSets.Rd
index 248de1b..edd9529 100644
--- a/man/makePermutedSets.Rd
+++ b/man/makePermutedSets.Rd
@@ -1,6 +1,5 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/test_sets.R
-\docType{methods}
 \name{makePermutedSets}
 \alias{makePermutedSets}
 \alias{makePermutedSets,SummarizedExperiment,SummarizedExperiment-method}
@@ -16,33 +15,38 @@
 \usage{
 makePermutedSets(object, annotations, ...)
 
-\S4method{makePermutedSets}{SummarizedExperiment,SummarizedExperiment}(object,
-  annotations, bias = rowData(object)$bias, window = 10)
+\S4method{makePermutedSets}{SummarizedExperiment,SummarizedExperiment}(object, annotations, bias = rowData(object)$bias, window = 10)
 
+\S4method{makePermutedSets}{RangedSummarizedExperiment,SummarizedExperiment}(
+  object,
+  annotations,
+  bias = rowRanges(object)$bias,
+  window = 10
+)
 
-  \S4method{makePermutedSets}{RangedSummarizedExperiment,SummarizedExperiment}(object,
-  annotations, bias = rowRanges(object)$bias, window = 10)
+\S4method{makePermutedSets}{MatrixOrmatrix,SummarizedExperiment}(object, annotations, bias, window = 10)
 
-\S4method{makePermutedSets}{MatrixOrmatrix,SummarizedExperiment}(object,
-  annotations, bias, window = 10)
+\S4method{makePermutedSets}{SummarizedExperiment,MatrixOrmatrix}(object, annotations, bias = rowData(object)$bias, window = 10)
 
-\S4method{makePermutedSets}{SummarizedExperiment,MatrixOrmatrix}(object,
-  annotations, bias = rowData(object)$bias, window = 10)
+\S4method{makePermutedSets}{RangedSummarizedExperiment,MatrixOrmatrix}(
+  object,
+  annotations,
+  bias = rowRanges(object)$bias,
+  window = 10
+)
 
-\S4method{makePermutedSets}{RangedSummarizedExperiment,MatrixOrmatrix}(object,
-  annotations, bias = rowRanges(object)$bias, window = 10)
+\S4method{makePermutedSets}{MatrixOrmatrix,MatrixOrmatrix}(object, annotations, bias, window = 10)
 
-\S4method{makePermutedSets}{MatrixOrmatrix,MatrixOrmatrix}(object, annotations,
-  bias, window = 10)
+\S4method{makePermutedSets}{SummarizedExperiment,list}(object, annotations, bias = rowData(object)$bias, window = 10)
 
-\S4method{makePermutedSets}{SummarizedExperiment,list}(object, annotations,
-  bias = rowData(object)$bias, window = 10)
+\S4method{makePermutedSets}{RangedSummarizedExperiment,list}(
+  object,
+  annotations,
+  bias = rowRanges(object)$bias,
+  window = 10
+)
 
-\S4method{makePermutedSets}{RangedSummarizedExperiment,list}(object,
-  annotations, bias = rowRanges(object)$bias, window = 10)
-
-\S4method{makePermutedSets}{MatrixOrmatrix,list}(object, annotations, bias,
-  window = 10)
+\S4method{makePermutedSets}{MatrixOrmatrix,list}(object, annotations, bias, window = 10)
 }
 \arguments{
 \item{object}{fragment counts stored as RangedSummarizedExperiment, 
@@ -69,30 +73,39 @@ a certain fragment count, fragment count, or fragment count & bias.
 }
 \section{Methods (by class)}{
 \itemize{
-\item \code{object = SummarizedExperiment,annotations = SummarizedExperiment}: method for SummarizedExperiment and 
+\item \code{makePermutedSets(
+  object = SummarizedExperiment,
+  annotations = SummarizedExperiment
+)}: method for SummarizedExperiment and 
 SummarizedExperiment
 
-\item \code{object = RangedSummarizedExperiment,annotations = SummarizedExperiment}: method for RangedSummarizedExperiment and 
+\item \code{makePermutedSets(
+  object = RangedSummarizedExperiment,
+  annotations = SummarizedExperiment
+)}: method for RangedSummarizedExperiment and 
 SummarizedExperiment
 
-\item \code{object = MatrixOrmatrix,annotations = SummarizedExperiment}: method for Matrix or matrix and 
+\item \code{makePermutedSets(object = MatrixOrmatrix, annotations = SummarizedExperiment)}: method for Matrix or matrix and 
 SummarizedExperiment
 
-\item \code{object = SummarizedExperiment,annotations = MatrixOrmatrix}: method for SummarizedExperiment and 
+\item \code{makePermutedSets(object = SummarizedExperiment, annotations = MatrixOrmatrix)}: method for SummarizedExperiment and 
 MatrixOrmatrix
 
-\item \code{object = RangedSummarizedExperiment,annotations = MatrixOrmatrix}: method for RangedSummarizedExperiment and 
+\item \code{makePermutedSets(
+  object = RangedSummarizedExperiment,
+  annotations = MatrixOrmatrix
+)}: method for RangedSummarizedExperiment and 
 MatrixOrmatrix
 
-\item \code{object = MatrixOrmatrix,annotations = MatrixOrmatrix}: method for Matrix/matrix and Matrix/matrix
+\item \code{makePermutedSets(object = MatrixOrmatrix, annotations = MatrixOrmatrix)}: method for Matrix/matrix and Matrix/matrix
 
-\item \code{object = SummarizedExperiment,annotations = list}: method for SummarizedExperiment and list
+\item \code{makePermutedSets(object = SummarizedExperiment, annotations = list)}: method for SummarizedExperiment and list
 
-\item \code{object = RangedSummarizedExperiment,annotations = list}: method for RangedSummarizedExperiment and list
+\item \code{makePermutedSets(object = RangedSummarizedExperiment, annotations = list)}: method for RangedSummarizedExperiment and list
 
-\item \code{object = MatrixOrmatrix,annotations = list}: method for Matrix or matrix and list
-}}
+\item \code{makePermutedSets(object = MatrixOrmatrix, annotations = list)}: method for Matrix or matrix and list
 
+}}
 \examples{
 # Load very small example counts (already filtered)
 data(mini_counts, package = "chromVAR")
diff --git a/man/matchKmers.Rd b/man/matchKmers.Rd
index 1357a3d..f54e1ff 100644
--- a/man/matchKmers.Rd
+++ b/man/matchKmers.Rd
@@ -1,6 +1,5 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/match_kmers.R
-\docType{methods}
 \name{matchKmers}
 \alias{matchKmers}
 \alias{matchKmers,character,DNAStringSet-method}
@@ -15,17 +14,18 @@
 \usage{
 matchKmers(k, subject, ...)
 
-\S4method{matchKmers}{character,DNAStringSet}(k, subject, out = c("matches",
-  "positions"), ranges = NULL)
+\S4method{matchKmers}{character,DNAStringSet}(k, subject, out = c("matches", "positions"), ranges = NULL)
 
-\S4method{matchKmers}{character,character}(k, subject, out = c("matches",
-  "positions"), ranges = NULL)
+\S4method{matchKmers}{character,character}(k, subject, out = c("matches", "positions"), ranges = NULL)
 
-\S4method{matchKmers}{character,DNAString}(k, subject, out = c("matches",
-  "positions"), ranges = NULL)
+\S4method{matchKmers}{character,DNAString}(k, subject, out = c("matches", "positions"), ranges = NULL)
 
-\S4method{matchKmers}{character,GenomicRanges}(k, subject,
-  genome = GenomeInfoDb::genome(subject), out = c("matches", "positions"))
+\S4method{matchKmers}{character,GenomicRanges}(
+  k,
+  subject,
+  genome = Seqinfo::genome(subject),
+  out = c("matches", "positions")
+)
 
 \S4method{matchKmers}{character,RangedSummarizedExperiment}(k, subject, ...)
 
@@ -66,25 +66,25 @@ GenomicRanges  object with all the positions of matches
 }
 \section{Methods (by class)}{
 \itemize{
-\item \code{k = character,subject = DNAStringSet}: For DNAStringSet Objects
+\item \code{matchKmers(k = character, subject = DNAStringSet)}: For DNAStringSet Objects
 
-\item \code{k = character,subject = character}: For character strings
+\item \code{matchKmers(k = character, subject = character)}: For character strings
 
-\item \code{k = character,subject = DNAString}: For DNA String objects
+\item \code{matchKmers(k = character, subject = DNAString)}: For DNA String objects
 
-\item \code{k = character,subject = GenomicRanges}: For GenomicRanges
+\item \code{matchKmers(k = character, subject = GenomicRanges)}: For GenomicRanges
 
-\item \code{k = character,subject = RangedSummarizedExperiment}: For RangedSummarizedExperiment (containing GRanges in
+\item \code{matchKmers(k = character, subject = RangedSummarizedExperiment)}: For RangedSummarizedExperiment (containing GRanges in
 rowRanges)
 
-\item \code{k = numeric,subject = ANY}: Catch-all for other un-documented types
+\item \code{matchKmers(k = numeric, subject = ANY)}: Catch-all for other un-documented types
 
-\item \code{k = DNAStringSet,subject = ANY}: Catch-all for other un-documented types with 
+\item \code{matchKmers(k = DNAStringSet, subject = ANY)}: Catch-all for other un-documented types with 
 DNAStringSet
 
-\item \code{k = DNAString,subject = ANY}: Catch-all for other un-documented types with DNAString
-}}
+\item \code{matchKmers(k = DNAString, subject = ANY)}: Catch-all for other un-documented types with DNAString
 
+}}
 \examples{
 
 # Load very small example counts (already filtered)
diff --git a/man/plotDeviationsTsne.Rd b/man/plotDeviationsTsne.Rd
index c94a94c..d465838 100644
--- a/man/plotDeviationsTsne.Rd
+++ b/man/plotDeviationsTsne.Rd
@@ -4,8 +4,14 @@
 \alias{plotDeviationsTsne}
 \title{plotDeviationsTsne}
 \usage{
-plotDeviationsTsne(object, tsne, var_df = NULL, sample_column = NULL,
-  annotation_name = NULL, shiny = interactive())
+plotDeviationsTsne(
+  object,
+  tsne,
+  var_df = NULL,
+  sample_column = NULL,
+  annotation_name = NULL,
+  shiny = interactive()
+)
 }
 \arguments{
 \item{object}{deviations result object}
diff --git a/man/plotVariability.Rd b/man/plotVariability.Rd
index 11b4161..d7aec29 100644
--- a/man/plotVariability.Rd
+++ b/man/plotVariability.Rd
@@ -4,8 +4,13 @@
 \alias{plotVariability}
 \title{plotVariability}
 \usage{
-plotVariability(variability, xlab = "Sorted TFs", n = 3,
-  labels = variability$name, use_plotly = interactive())
+plotVariability(
+  variability,
+  xlab = "Sorted TFs",
+  n = 3,
+  labels = variability$name,
+  use_plotly = interactive()
+)
 }
 \arguments{
 \item{variability}{output from \code{\link{computeVariability}}}
diff --git a/man/rbind-chromVARDeviations-method.Rd b/man/rbind-chromVARDeviations-method.Rd
index 4197632..7d3c961 100644
--- a/man/rbind-chromVARDeviations-method.Rd
+++ b/man/rbind-chromVARDeviations-method.Rd
@@ -1,6 +1,5 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/compute_deviations.R
-\docType{methods}
 \name{rbind,chromVARDeviations-method}
 \alias{rbind,chromVARDeviations-method}
 \title{rbind method chromVARDeviations}
diff --git a/src/Makevars b/src/Makevars
index 22ebc63..9defeb6 100644
--- a/src/Makevars
+++ b/src/Makevars
@@ -1 +1,2 @@
+CXX_STD = CXX14
 PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
diff --git a/src/RcppExports.cpp b/src/RcppExports.cpp
index f2d73ec..a18a3de 100644
--- a/src/RcppExports.cpp
+++ b/src/RcppExports.cpp
@@ -6,6 +6,11 @@
 
 using namespace Rcpp;
 
+#ifdef RCPP_USE_GLOBAL_ROSTREAM
+Rcpp::Rostream<true>&  Rcpp::Rcout = Rcpp::Rcpp_cout_get();
+Rcpp::Rostream<false>& Rcpp::Rcerr = Rcpp::Rcpp_cerr_get();
+#endif
+
 // pwm_euclidean
 double pwm_euclidean(arma::mat mat1, arma::mat mat2);
 RcppExport SEXP _chromVAR_pwm_euclidean(SEXP mat1SEXP, SEXP mat2SEXP) {