IRanges

ENCODE tools provide access to the Encyclopedia of DNA Elements data, including genomic functional elements, ChIP-seq, RNA-seq, and ATAC-seq data. Facilitates data retrieval, query, and analysis for e

2 shared topics • 2 shared operations

GenomicRanges — Bioconductor R package for representing, manipulating, and analyzing genomic intervals (GRanges, GRangesList). Provides operations for finding overlaps (findOverlaps, subsetByOverlaps)

2 shared topics • 2 shared operations

Use when working with pybedtools — pybedtools — Python interface to BEDTools

2 shared topics • 2 shared operations

Use when working with Borzoi — a sequence-to-function DNA foundation model — for predicting genome-wide regulatory activity from DNA sequences. Borzoi predicts RNA-seq, ATAC-seq, ChIP-seq, and histone

2 shared topics • 1 shared operation

Roadmap Epigenomics — NIH Roadmap Epigenomics Mapping Consortium reference epigenomes spanning 111 primary human tissues and cell types. Provides ChIP-seq histone mark tracks (H3K4me1, H3K4me3, H3K27m

2 shared topics • 1 shared operation