Table 1 Functions implemented in the ATACseqQC package
From: ATACseqQC: a Bioconductor package for post-alignment quality assessment of ATAC-seq data
Function Name | Usage Description |
|---|---|
readBamFile | Read in bam files to R leveraging Rsamtools and create a GAlignments object |
bamQC | Perform quality assessment on alignments and Filter BAM files to remove duplicates, mitochondrial reads and low-quality or discordant alignments |
fragSizeDist | Plot size distribution of sequenced fragments in ATAC-seq libraries |
IGVSnapshot | Streamline the visualization of read distribution along genomic regions of interest, such as those containing housekeeping genes |
shiftGAlignmentsList | Shift 5′ end of aligned reads in GAlignments object |
shiftReads | |
splitGAlignmentsByCut | Split the shifted bam files based on ranges of fragment sizes in nucleosome-free, mono-, di-, tri-nucleosome bins and so on |
splitBam | Shift 5′ end of aligned reads and split the updated bam files in one step |
writeListOfGAlignments | Export lists of GAlignment objects back into bam files |
enrichedFragments | Get enrichment signals for nucleosome-free and nucleosome-bound signals |
pwmscore | Calculate the maximal similarity score for each given sequence against a PWM of a TF binding motif |
factorFootprints | Discover and visualize footprints of a given transcription factor |
plotFootprints | |
readsDupFreq | Estimate library complexity, available for version 1.3.12 or later |
estimateLibComplexity | |
saturationPlot | Plot saturation curves based on the total number or width of significant peaks detected for a serial of subsamples, available for version 1.3.12 or later |