Package: epistack 1.19.0
epistack: Heatmaps of Stack Profiles from Epigenetic Signals
The epistack package main objective is the visualizations of stacks of genomic tracks (such as, but not restricted to, ChIP-seq, ATAC-seq, DNA methyation or genomic conservation data) centered at genomic regions of interest. epistack needs three different inputs: 1) a genomic score objects, such as ChIP-seq coverage or DNA methylation values, provided as a `GRanges` (easily obtained from `bigwig` or `bam` files). 2) a list of feature of interest, such as peaks or transcription start sites, provided as a `GRanges` (easily obtained from `gtf` or `bed` files). 3) a score to sort the features, such as peak height or gene expression value.
Authors:
epistack_1.19.0.tar.gz
epistack_1.19.0.zip(r-4.7)epistack_1.19.0.zip(r-4.6)epistack_1.19.0.zip(r-4.5)
epistack_1.19.0.tgz(r-4.6-any)epistack_1.19.0.tgz(r-4.5-any)
epistack_1.19.0.tar.gz(r-4.7-any)epistack_1.19.0.tar.gz(r-4.6-any)
epistack_1.19.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
epistack/json (API)
NEWS
| # Install 'epistack' in R: |
| install.packages('epistack', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/genepi-genphyse/epistack/issues
- stackepi - Epistack example and test dataset
- stackepi_gr - Epistack backward compatibility dataset
On BioConductor:epistack-1.19.0(bioc 3.24)epistack-1.18.0(bioc 3.23)
rnaseqpreprocessingchipseqgeneexpressioncoveragebioinformatics
Last updated from:133a91de55. Checks:8 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 195 | ||
| linux-devel-x86_64 | NOTE | 290 | ||
| source / vignettes | OK | 312 | ||
| linux-release-x86_64 | NOTE | 352 | ||
| macos-release-arm64 | NOTE | 172 | ||
| macos-oldrel-arm64 | NOTE | 159 | ||
| windows-devel | NOTE | 207 | ||
| windows-release | NOTE | 231 | ||
| windows-oldrel | NOTE | 249 | ||
| wasm-release | OK | 170 |
Exports:addBinsaddMetricAndArrangeGRangesaddMetricAndArrangeRSEGRanges2RSEmeanColorplotAverageProfileplotBinningplotBoxMetricplotEpistackplotMetricplotStackProfileplotStackProfileLegendredimMatrix
Dependencies:abindBiobaseBiocGenericsDelayedArraygenericsGenomicRangesIRangeslatticeMatrixMatrixGenericsmatrixStatsplotrixS4ArraysS4VectorsSeqinfoSparseArraySummarizedExperimentXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| addBins() | addBins |
| addMetricAndArrangeGRanges() | addMetricAndArrangeGRanges |
| addMetricAndArrangeRSE() | addMetricAndArrangeRSE |
| GRanges2RSE() | GRanges2RSE |
| meanColor | meanColor |
| plotAverageProfile() | plotAverageProfile |
| plotBinning() | plotBinning |
| plotBoxMetric() | plotBoxMetric |
| plotEpistack() | plotEpistack |
| plotMetric() | plotMetric |
| plotStackProfile() | plotStackProfile |
| plotStackProfileLegend() | plotStackProfileLegend |
| redimMatrix() | redimMatrix |
| epistack example and test dataset | stackepi |
| epistack backward compatibility dataset | stackepi_gr |
