Man pages for RamsinghLab/ATACseeker
Utilities for ATACseq QC, differential accessibility, and integration
| addMtGeneLabel | Set gene names for bp ranges. Original code by Stephen Turner... |
| atacPairedEnd | pull in (filter and assemble as an object) some or all of the... |
| ATACseeker-package | A short title line describing what the package does |
| callMT | call mitochondrial variants from the results of... |
| collectStats | collect various cross-correlation and window size stats for... |
| fragmentLengths | get fragment sizes for a GAlignmentPairs object (can be slow) |
| fragPlot | Plot fragment size density for a set of samples. |
| get5primeCuts | get the 5' cut sites from a GAlignmentPairs (usually of an... |
| getComplexity | complexity estimates from a GAlignmentPairs object, formatted... |
| getEnds | convert a galp into a gr of 5' cuts |
| getEsts | Complexity estimation for ATACseq libraries. |
| getFeatureCounts | utility fn for getComplexity and preseqR |
| getMT | grab the mitochondrial reads from a BAM and estimate their... |
| getQC | obtain QC information used by csaw from paired-end BAM files |
| plotComplexity | plot results from preseq (complexity estimation around... |
| plotCoverage | utility fn from Patrick Abouyoun's 2010 seminar |
| plotMT | plot mitochondrial variant calls in the context of... |
| plotStranded | convenience function |
| processUcscCytoband | utility function to pull in UCSC cytoband / arm files this is... |
| shrinkPairs | This seems to work better than anything else for "shifting"... |
| tssQcPlot | what you would expect. not terribly novel; maybe use... |
