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bioc
DiffBind:Differential Binding Analysis of ChIP-Seq Peak Data
Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions.
Maintained by Rory Stark. Last updated 2 months ago.
sequencingchipseqatacseqdnaseseqmethylseqripseqdifferentialpeakcallingdifferentialmethylationgeneregulationhistonemodificationpeakdetectionbiomedicalinformaticscellbiologymultiplecomparisonnormalizationreportwritingepigeneticsfunctionalgenomicscurlbzip2xz-utilszlibcpp
7.13 score 512 scripts 2 dependentsbioc
ChIPQC:Quality metrics for ChIPseq data
Quality metrics for ChIPseq data.
Maintained by Tom Carroll. Last updated 5 months ago.
sequencingchipseqqualitycontrolreportwriting
5.45 score 140 scriptsbioc
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.
Maintained by Pedro Baldoni. Last updated 5 months ago.
chipseqatacseqdnaseseqhiddenmarkovmodelepigeneticszlibopenblascppopenmp
4.94 score 88 scriptsbioc
vulcan:VirtUaL ChIP-Seq data Analysis using Networks
Vulcan (VirtUaL ChIP-Seq Analysis through Networks) is a package that interrogates gene regulatory networks to infer cofactors significantly enriched in a differential binding signature coming from ChIP-Seq data. In order to do so, our package combines strategies from different BioConductor packages: DESeq for data normalization, ChIPpeakAnno and DiffBind for annotation and definition of ChIP-Seq genomic peaks, csaw to define optimal peak width and viper for applying a regulatory network over a differential binding signature.
Maintained by Federico M. Giorgi. Last updated 5 months ago.
systemsbiologynetworkenrichmentgeneexpressionchipseq
3.38 score 12 scripts