Package: epigraHMM 1.21.2

Pedro Baldoni

epigraHMM: Epigenomic R-based analysis with hidden Markov models

epigraHMM provides a set of tools for the analysis of epigenomic data based on hidden Markov Models. It contains two separate peak callers, one for consensus peaks from biological or technical replicates, and one for differential peaks from multi-replicate multi-condition experiments. In differential peak calling, epigraHMM provides window-specific posterior probabilities associated with every possible combinatorial pattern of read enrichment across conditions.

Authors:Pedro Baldoni [aut, cre]

epigraHMM_1.21.2.tar.gz
epigraHMM_1.21.2.zip(r-4.7)epigraHMM_1.21.2.zip(r-4.6)epigraHMM_1.21.2.zip(r-4.5)
epigraHMM_1.21.2.tgz(r-4.6-x86_64)epigraHMM_1.21.2.tgz(r-4.6-arm64)epigraHMM_1.21.2.tgz(r-4.5-x86_64)epigraHMM_1.21.2.tgz(r-4.5-arm64)
epigraHMM_1.21.2.tar.gz(r-4.7-arm64)epigraHMM_1.21.2.tar.gz(r-4.7-x86_64)epigraHMM_1.21.2.tar.gz(r-4.6-arm64)epigraHMM_1.21.2.tar.gz(r-4.6-x86_64)
manual.pdf |manual.html✨
card.svg |card.png
epigraHMM/json (API)
NEWS

# Install 'epigraHMM' in R:
install.packages('epigraHMM', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))
Uses libs:
  • curl– Easy-to-use client-side URL transfer library
  • openssl– Secure Sockets Layer toolkit
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
  • openmp– GCC OpenMP (GOMP) support library
Datasets:
  • helas3 - ENCODE ChIP-seq broad data from Helas3 cell line

On BioConductor:epigraHMM-1.21.1(bioc 3.24)epigraHMM-1.20.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

chipseqatacseqdnaseseqhiddenmarkovmodelepigeneticscurlopensslopenblascppopenmp

4.56 score 91 scripts 306 downloads 18 exports 136 dependencies

Last updated from:17ec9bb8e2. Checks:12 WARNING, 1 ERROR, 1 FAIL. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING336
linux-devel-arm64WARNING559
linux-devel-x86_64WARNING592
source / vignettesERROR520
linux-release-arm64WARNING552
linux-release-x86_64WARNING666
macos-release-arm64WARNING379
macos-release-x86_64WARNING939
macos-oldrel-arm64WARNING429
macos-oldrel-x86_64WARNING694
windows-develWARNING608
windows-releaseWARNING644
windows-oldrelWARNING534
wasm-releaseFAIL288

Exports:addOffsetscallPatternscallPeakscleanCountscontrolEMepigraHMMepigraHMMDataSetFromBamepigraHMMDataSetFromMatrixestimateTransitionProbexpStepinfoinitializermaxStepProbnormalizeCountsplotCountsplotPatternssegmentGenomesimulateMarkovChain

Dependencies:abindaskpassbackportsBHBiobaseBiocBaseUtilsBiocGenericsBiocIObiocmakeBiocParallelBiostringsbitopsbootbroomBSgenomecarcarDatacigarilloclicodetoolscolorspacecorrplotcowplotcpp11crayoncsawcurldata.tableDelayedArrayDerivdir.expirydoBydplyredgeRfarverfilelockforecastformatRFormulafracdifffutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangesggplot2ggpubrggrepelggsciggsignifglueGreyListChIPgridExtragtablehttrIRangesisobandjsonlitelabelinglambda.rlatticelifecyclelimmalme4lmtestlocfitmagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmetapodmgcvmicrobenchmarkmimeminqamodelrnlmenloptrnnetnumDerivopensslpbkrtestpheatmappillarpkgconfigpolynompurrrquantregR6rbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRCurlRdpackreformulasrestfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangRsamtoolsrstatixrtracklayerS4ArraysS4VectorsS7scalesSeqinfosnowSparseArraySparseMstatmodstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttimeDateurcautf8vctrsviridisLitewithrXMLXVectoryamlzoo