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EpiCompare

Bioc current

Comparison, Benchmarking & QC of Epigenomic Datasets

v1.16.0 · software · GPL-3
View on Bioconductor ↗ Source ↗

Release Lineage

Entered 3.15 · Apr 27, 2022

Current · Requires R 4.6

1.0 In 9 of 49 releases 3.23

Description

EpiCompare is used to compare and analyse epigenetic datasets for quality control and benchmarking purposes. The package outputs an HTML report consisting of three sections: (1. General metrics) Metrics on peaks (percentage of blacklisted and non-standard peaks, and peak widths) and fragments (duplication rate) of samples, (2. Peak overlap) Percentage and statistical significance of overlapping and non-overlapping peaks. Also includes upset plot and (3. Functional annotation) functional annotation (ChromHMM, ChIPseeker and enrichment analysis) of peaks. Also includes peak enrichment around TSS.

Code

Code metrics have not been computed for this package yet.

Topics

Software › ResearchField › Epigenetics
Software › ResearchField › Genetics
Software › WorkflowStep › QualityControl
Software › Technology › Sequencing › ChIPSeq
Software › WorkflowStep › MultipleComparison
Software › ResearchField › FunctionalGenomics
Software › Technology › Sequencing › ATACSeq
Software › Technology › Sequencing › DNaseSeq

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