Name Mode Size
..
AllGenerics.R 100644 2 kb
aaa.R 100644 0 kb
addDiffStatus.R 100644 4 kb
asTibble.R 100644 5 kb
bestOverlap.R 100644 3 kb
chopMC.R 100644 2 kb
colToRanges.R 100644 3 kb
collapseGenes.R 100644 1 kb
data.R 100644 2 kb
defineRegions.R 100644 6 kb
defineSeqinfo.R 100644 4 kb
distinctMC.R 100644 1 kb
dualFilter.R 100644 10 kb
extraChIPs.R 100644 3 kb
fitAssayDiff.R 100644 11 kb
getProfileData.R 100644 6 kb
grlToSE.R 100644 9 kb
importPeaks.R 100644 8 kb
makeConsensus.R 100644 4 kb
mapByFeature.R 100644 17 kb
mapGrlCols.R 100644 7 kb
mergeByCol.R 100644 7 kb
mergeByHMP.R 100644 11 kb
mergeBySig.R 100644 8 kb
partitionRanges.R 100644 4 kb
plotAssayDensities.R 100644 5 kb
plotAssayHeatmap.R 100644 6 kb
plotAssayPCA.R 100644 6 kb
plotAssayRle.R 100644 4 kb
plotGrlCol.R 100644 6 kb
plotHFGC.R 100644 46 kb
plotOverlaps.R 100644 9 kb
plotPairwise.R 100644 17 kb
plotPie.R 100644 18 kb
plotProfileHeatmap.R 100644 16 kb
plotSplitDonut.R 100644 21 kb
propOverlaps.R 100644 1 kb
reduceMC.R 100644 1 kb
setoptsMC.R 100644 6 kb
stitchRanges.R 100644 2 kb
voomWeightsFromCPM.R 100644 7 kb
README.md
# extraChIPs <img id="extrachips_logo" src="man/figures/extraChIPs.png" align="right" width = "125" /> <!-- badges: start --> [![Build Status](https://github.com/smped/extraChIPs/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/smped/extraChIPs/actions) [![Codecov test coverage](https://codecov.io/gh/smped/extraChIPs/branch/main/graph/badge.svg)](https://codecov.io/gh/smped/extraChIPs?branch=main) [![Repo Status](https://img.shields.io/badge/repo%20status-Active-green.svg)](https://shields.io/) <!-- badges: end --> `extraChIPs` is a package primarily designed to enable ChIP-Seq analysis. Whilst the package was primarily built for the [GRAVI: Gene Regulatory Analysis using Variable Inputs](https://github.com/smped/GRAVI) workflow, the functionality extends beyond this specific application. Functions focus primarily on - Retaining `mcols()` when manipulating `GRanges` objects - Common visualisation utilities for ChIP-Seq analysis - Enabling sliding window analysis for differential ChIP-target binding It is intended that these functions will integrate seamlessly with other packages such as those provided in `csaw`, `plyranges` and `limma`. In addition to enabling workflows, simple coercion to `tibble` objects from `DataFrame`, `GRanges` and `GInteractions` objects is implemented. ## Installation Instructions To install this package from Bioconductor, please use `BiocManager`. ```r install.packages("BiocManager") BiocManager::install("extraChIPs") ``` To install the development version from github ```r BiocManager::install("smped/extraChIPs") ```