Name Mode Size
R 040000
data-raw 040000
data 040000
inst 040000
man 040000
src 040000
tests 040000
vignettes 040000
.Rbuildignore 100644 0 kb
.gitignore 100644 0 kb
.travis.yml 100644 2 kb
DESCRIPTION 100644 1 kb
LICENSE 100644 0 kb
NAMESPACE 100644 4 kb
NEWS 100644 1 kb 100644 5 kb
_pkgdown.yml 100644 1 kb
--- [![Build Status](]( # chromVAR chromVAR is an R package for the analysis of sparse chromatin accessibility data from single cell or bulk ATAC or DNAse-seq data. The package aims to identify motifs or other genomic annotations associated with variability in chromatin accessibility between individual cells or samples. For a more detail overview of the method, please see the [publication]( ([pdf](, [supplement]( ## Installation The recommended installation method for `chromVAR` is using BiocManager. You will first have to have installed the [BiocManager package ]( ```r if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("chromVAR") ``` A number of needed packages are installed in this process. One of the dependencies has a system requirement for the gsl library, so if this is not installed already it may need to be installed separately. Several people have reported issues with the GO.db package (a dependency of one of the dependencies) not being installed automatically -- if you see an error relating to that package, try installing it separately first (`BiocManager::install("GO.db")`). For Windows users, some have reported that the S4Vector dependency does not currently function on windows R 3.3.3, but that installation was successful on R 3.3.2. For Mac users, some have encountered installation difficulties relating to compiling the C++ code. If you encounter problems, please see the threads and advice in Issues [11]( and [20]( Two additional packages that are recommended and used in the vignettes: * motifmatchr - available on [GitHub]( or [development version of Bioconductor]( * JASPAR2016 - available from Bioconductor Additionally, the package chromVARmotifs can be useful for loading additional motif collections: * chromVARmotifs - available on [GitHub]( ## Parallelization Before running chromVAR functions, it is advisable to use the `register` function from BiocParallel to specify your preferred method of parallelization. For unix systems, ```r library(BiocParallel) register(MulticoreParam(8)) # Use 8 cores ``` For Windows, `MulticoreParam` will not work, but you can use SnowParam: ```r register(SnowParam(SnowParam(workers=1, type = "SOCK"))) ``` Even if you don't want to use more than one core, it is recommended to explicitly register that choice using SerialParam: ```r register(SerialParam()) ``` Please see the documentation for [BiocParallel]( for more information about the `register` function and the various options for multi-processing. ## Quickstart ``` r library(chromVAR) library(motifmatchr) library(BSgenome.Hsapiens.UCSC.hg19) ### Example of how to read in counts ------------------------------------------- # Caution: FAKE FILENAMES -- Replace with real as appropriate! If you want to # run on example data in package, start at next section with example_counts data peakfile <- "mypeaks.bed" peaks <- getPeaks(peakfile) bamfiles <- c("mybam1.bam","mybam2.bam") fragment_counts <- getCounts(bamfiles, peaks, paired = TRUE, by_rg = TRUE, format = "bam", colData = DataFrame(celltype = c("GM","K562"))) ### ---------------------------------------------------------------------------- ### Using example counts from package ------------------------------------------ data(example_counts, package = "chromVAR") example_counts <- addGCBias(example_counts, genome = BSgenome.Hsapiens.UCSC.hg19) counts_filtered <- filterSamples(example_counts, min_depth = 1500, min_in_peaks = 0.15) counts_filtered <- filterPeaks(counts_filtered) motifs <- getJasparMotifs() motif_ix <- matchMotifs(motifs, counts_filtered, genome = BSgenome.Hsapiens.UCSC.hg19) # computing deviations dev <- computeDeviations(object = counts_filtered, annotations = motif_ix) ``` See [documentation website]( for more information!