Function reference

All functions

alignmentBowtie2()

Alignment with Bowtie 2

bamToBigWig()

Conversion from BAM to visualization formats

callPeak()

Peak calling with MACS2

.getBDGforSEACR()

Obtain bedgraph files for SEACR input

fastqc()

Quality Control with FastQC

filtOutBAM()

Filter out reads from BAM file

getNameFromPath()

Get name from path

getStats()

Get alignment and processing stats from BAM files

mergeBAMs()

Merge BAM files

offsetATAC()

Offset correction for ATAC-seq data

offsetATACSE()

Offset correction for SE ATAC-seq data

paramdata

Data parameters for different experiments

peakCallingSEACR()

CUT&TAG peak calling with SEACR

pipelineNGS

Pipeline for Next-Generation Sequencing Experiments

plotAlignment()

Plot alignment statistics

processCUTTAG()

Automated processing of CUT&TAG samples

process_epigenome()

Automated processing of ChIP-seq and ATAC-seq samples

tableFromIdxstats()

Table form idxstats