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:
epistack_1.13.0.tar.gz
epistack_1.13.0.zip(r-4.5)epistack_1.13.0.zip(r-4.4)epistack_1.13.0.zip(r-4.3)
epistack_1.13.0.tgz(r-4.4-any)epistack_1.13.0.tgz(r-4.3-any)
epistack_1.13.0.tar.gz(r-4.5-noble)epistack_1.13.0.tar.gz(r-4.4-noble)
epistack_1.13.0.tgz(r-4.4-emscripten)epistack_1.13.0.tgz(r-4.3-emscripten)
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')) |
Bug tracker:https://github.com/genepi-genphyse/epistack/issues
- stackepi - Epistack example and test dataset
- stackepi_gr - Epistack backward compatibility dataset
On BioConductor:epistack-1.13.0(bioc 3.21)epistack-1.12.0(bioc 3.20)
rnaseqpreprocessingchipseqgeneexpressioncoveragebioinformatics
Last updated 2 months agofrom:dab3b9d4b5. Checks:OK: 3 NOTE: 4. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 18 2024 |
| R-4.5-win | NOTE | Dec 18 2024 |
| R-4.5-linux | NOTE | Dec 18 2024 |
| R-4.4-win | NOTE | Dec 18 2024 |
| R-4.4-mac | NOTE | Dec 18 2024 |
| R-4.3-win | OK | Dec 18 2024 |
| R-4.3-mac | OK | Dec 18 2024 |
Exports:addBinsaddMetricAndArrangeGRangesaddMetricAndArrangeRSEGRanges2RSEmeanColorplotAverageProfileplotBinningplotBoxMetricplotEpistackplotMetricplotStackProfileplotStackProfileLegendredimMatrix
Dependencies:abindaskpassBiobaseBiocGenericscrayoncurlDelayedArraygenericsGenomeInfoDbGenomeInfoDbDataGenomicRangeshttrIRangesjsonlitelatticeMatrixMatrixGenericsmatrixStatsmimeopensslplotrixR6S4ArraysS4VectorsSparseArraySummarizedExperimentsysUCSC.utilsXVectorzlibbioc
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 |
