Package: epistack 1.13.0

DEVAILLY Guillaume

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:SACI Safia [aut], DEVAILLY Guillaume [cre, aut]

epistack_1.13.0.tar.gz
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epistack.pdf |epistack.html
epistack/json (API)
NEWS

# Install 'epistack' in R:
install.packages('epistack', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/genepi-genphyse/epistack/issues

Datasets:
  • stackepi - Epistack example and test dataset
  • stackepi_gr - Epistack backward compatibility dataset

On BioConductor:epistack-1.13.0(bioc 3.21)epistack-1.12.0(bioc 3.20)

rnaseqpreprocessingchipseqgeneexpressioncoveragebioinformatics

5.26 score 6 stars 5 scripts 132 downloads 13 exports 30 dependencies

Last updated 25 days agofrom:dab3b9d4b5. Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 18 2024
R-4.5-winWARNINGNov 18 2024
R-4.5-linuxWARNINGNov 18 2024
R-4.4-winWARNINGNov 18 2024
R-4.4-macWARNINGNov 18 2024
R-4.3-winWARNINGNov 18 2024
R-4.3-macWARNINGNov 18 2024

Exports:addBinsaddMetricAndArrangeGRangesaddMetricAndArrangeRSEGRanges2RSEmeanColorplotAverageProfileplotBinningplotBoxMetricplotEpistackplotMetricplotStackProfileplotStackProfileLegendredimMatrix

Dependencies:abindaskpassBiobaseBiocGenericscrayoncurlDelayedArraygenericsGenomeInfoDbGenomeInfoDbDataGenomicRangeshttrIRangesjsonlitelatticeMatrixMatrixGenericsmatrixStatsmimeopensslplotrixR6S4ArraysS4VectorsSparseArraySummarizedExperimentsysUCSC.utilsXVectorzlibbioc

An overview of the epistack package

Rendered fromusing_epistack.Rmdusingknitr::rmarkdownon Nov 18 2024.

Last update: 2023-07-24
Started: 2021-05-28

Readme and manuals

Help Manual

Help pageTopics
addBins()addBins
addMetricAndArrangeGRanges()addMetricAndArrangeGRanges
addMetricAndArrangeRSE()addMetricAndArrangeRSE
GRanges2RSE()GRanges2RSE
meanColormeanColor
plotAverageProfile()plotAverageProfile
plotBinning()plotBinning
plotBoxMetric()plotBoxMetric
plotEpistack()plotEpistack
plotMetric()plotMetric
plotStackProfile()plotStackProfile
plotStackProfileLegend()plotStackProfileLegend
redimMatrix()redimMatrix
epistack example and test datasetstackepi
epistack backward compatibility datasetstackepi_gr