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bioc
ChIPseeker:ChIPseeker for ChIP peak Annotation, Comparison, and Visualization
This package implements functions to retrieve the nearest genes around the peak, annotate genomic region of the peak, statstical methods for estimate the significance of overlap among ChIP peak data sets, and incorporate GEO database for user to compare the own dataset with those deposited in database. The comparison can be used to infer cooperative regulation and thus can be used to generate hypotheses. Several visualization functions are implemented to summarize the coverage of the peak experiment, average profile and heatmap of peaks binding to TSS regions, genomic annotation, distance to TSS, and overlap of peaks or genes.
Maintained by Guangchuang Yu. Last updated 5 months ago.
annotationchipseqsoftwarevisualizationmultiplecomparisonatac-seqchip-seqcomparisonepigeneticsepigenomics
233 stars 13.05 score 1.6k scripts 5 dependentsbioc
esATAC:An Easy-to-use Systematic pipeline for ATACseq data analysis
This package provides a framework and complete preset pipeline for quantification and analysis of ATAC-seq Reads. It covers raw sequencing reads preprocessing (FASTQ files), reads alignment (Rbowtie2), aligned reads file operations (SAM, BAM, and BED files), peak calling (F-seq), genome annotations (Motif, GO, SNP analysis) and quality control report. The package is managed by dataflow graph. It is easy for user to pass variables seamlessly between processes and understand the workflow. Users can process FASTQ files through end-to-end preset pipeline which produces a pretty HTML report for quality control and preliminary statistical results, or customize workflow starting from any intermediate stages with esATAC functions easily and flexibly.
Maintained by Zheng Wei. Last updated 5 months ago.
immunooncologysequencingdnaseqqualitycontrolalignmentpreprocessingcoverageatacseqdnaseseqatac-seqbioconductorpipelinecppopenjdk
23 stars 6.11 score 3 scripts
eonurk
cinaR:A Computational Pipeline for Bulk 'ATAC-Seq' Profiles
Differential analyses and Enrichment pipeline for bulk 'ATAC-seq' data analyses. This package combines different packages to have an ultimate package for both data analyses and visualization of 'ATAC-seq' data. Methods are described in 'Karakaslar et al.' (2021) <doi:10.1101/2021.03.05.434143>.
Maintained by Onur Karakaslar. Last updated 10 months ago.
atac-seqdifferential-analysisenrichment-analysisgene-sets
13 stars 5.52 score 51 scripts