Man pages for wzthu/esATAC
An Easy-to-use Systematic pipeline for ATACseq data analysis

AddMissingCellsAddMissingCells
ApplyMatrixByGroupApply function to integration sites per base per group
AssignFragCellnamesAssignFragCellnames
atacPipe2Pipeline for single replicate case-control paired-end...
ATACProc-classBase class of this package
atacRepsPipePipeline for multi-replicates case paired-end sequencing data
atacRepsPipe2Pipeline for multi-replicates case-control paired-end...
BamToBedConvert bam format to bed format.
BedToBigWiggenerate BigWig file from BED file
BedUtilsprocess bed file with limit memory
BinarizeCountsBinarize counts
Bowtie2MappingUse bowtie2 aligner to map reads to reference genome
Cells-setSet and get cell barcode information for a Fragment object
Cells-set-.FragmentCells
ChunkGRangesChunkGRanges
CollapseToLongestTranscriptCollapseToLongestTranscript
CountFragmentsCount fragments
CreateFragmentObjectCreate a Fragment object
CutSiteCountRCount cut site number in given motif region and plot...
CutSitePreExtract ATAC-seq cutting site from bed file.
dot-f_dowle2replace NA to 0
dot-write10xCountsWrite count data in the 10x format
esATAC-packageAn Easy-to-use Systematic pipeline for ATACseq data analysis
ExtendExtend
ExtractCellExtractCell
ExtractFragmentsExtractFragments
FastQCQuality control for ATAC-seq data.
FeatureMatrixConstruct a feature x cell matrix from a genomic fragments...
FilterCellsFilter cells from fragment file
FindAdapterUse AdapterRemoval to identify adapters
fragCreateCreate Fragment object
FragInRegionsFragInRegions
FragLenDistrQuality control for fragment length distribution
Fragment-classThe Fragment class
FragmentsGet the Fragment objects
Fragments-setFragments
FRiPQCQuality control for fraction of reads in peaks (FRiP)
GetCellsInRegionGetCellsInRegion
GetFragmentDataGet Fragment object data
GetGRangesFromEnsDbGetGRangesFromEnsDb
getMotifInfoGenerate PFMatrix or PFMatrixList from file.
GetReadsInRegionExtract reads for each cell within a given genomic region or...
GetTSSPositionsFind transcriptional start sites
GRangesToStringGRangesToString
isRemoteisRemote
LibComplexQCQuality control for library complexity
LinksGet or set links information
Links-setLinks
mergeDFMerge two dataframe by rowname
MultiRegionCutMatrixMultiRegionCutMatrix
PartialMatrixPartialMatrix
PeakCallingFseqUse F-seq to call peak
PeakCallingMACS2Use MACS2 to call peak
PeakQCQuality control for peak overlap
RegionMatrixRegion enrichment analysis
RegionStatsCompute base composition information for genomic ranges
RemoveAdapterUse AdapterRemoval to remove adapters
RenamerRename reads name in fastq
ReturnsReturn the first rows of a fragment file
RGoGene Ontology Analysis
RMotifScanSearch Motif Position in Given Regions
RMotifScanPairSearch Motif Position in Given Regions
RPeakAnnoAnnotate ATAC-seq Peak
RPeakCompFind the overlap or differential peaks between two samples.
RSNPsFind whether snps are in the given regions.
RsortbamSort bam file and rebuild bai index.
SamToBamConvert sam format to bam format.
SamToBedConvert SAM file to BED file
SCBowtie2MappingUse bowtie2 aligner to map reads to reference genome
SCCellFilterFiltering valid single cells
SCFindAdapterUse AdapterRemoval to identify adapters
scNucleosomeQCQuality Control for Nucleosome Signal per Cell
scPlotNucleosomeQCPlot Nucleosome signal enrichment
scPlotTssQCPlot signal enrichment around TSSs
SCQCGet Single Cell Pre-processing Information
SCRemoveAdapterUse AdapterRemoval to remove adapters
SCRenamerRename reads name in fastq
SCSamToBamConvert sam format to bam format.
scTssQCCompute TSS enrichment score per cell
SCUnzipAndMergeUnzip and merge fastq files
SetIfNullSet a default value if an object is null
SingleFeatureMatrixSingleFeatureMatrix
SingleFileCutMatrixGenerate matrix of integration sites
SingleRepReportFinal report for single group of regions
SplitFragmentsSplit fragment file by cell identities
StringToGRangesStringToGRanges
TabixOutputToDataFrameTabixOutputToDataFrame
ThisSet and get cell barcode information for a 'Fragment' object
TSSQCQuality control for transcription start site(TSS) reads...
UnzipAndMergeUnzip and merge fastq files
UpdatePathUpdate the file path for a Fragment object
ValidateCellsValidate cells present in fragment file
ValidateFragmentsValidate Fragment object
ValidateHashValidate hashes for Fragment object
wzthu/esATAC documentation built on Aug. 12, 2022, 7:41 a.m.