We implement our methods as the R packages deployed on Bioconductor.

preciseTAD - Prediction of boundaries of topologically associating domains (TADs) and chromatin loops from epigenomic data at base-level precision. preciseTADhub - Pre-trained random forest models obtained using preciseTAD. preciseTAD predicted boundaries for 60 cell lines - BED files, hg38
[ Bioconductor, GitHub, Paper ]
excluderanges - Genomic ranges of deny (aka problematic, exclusion, blacklisted) regions that should be avoided when working with genomic data. For human, mouse, and selected other organisms.
[ Bioconductor, GitHub, Preprint ]
CTCF - Genomic coordinates of FIMO-predicted CTCF binding sites with motif MA0139.1 (Jaspar).
[ Bioconductor, GitHub, Paper ]
TADcompare - Differential and time course analysis of Topologically Associated Domains
[ Bioconductor, GitHub, Paper ]
SpectralTAD - Calling Topologically Associated Domains (TADs) using spectral clustering
[ Bioconductor, GitHub, Preprint, Paper ]
multiHiCcompare - Joint normalization of multiple Hi-C datasets and comparative analysis of complex Hi-C experiments
[ Bioconductor, GitHub, Paper ]
HiCcompare - Joint normalization and differential analysis of pairs of chromatin interaction matrices obtained from Hi-C sequencing
[ Bioconductor, GitHub, Preprint, Paper ]
HMP2data - An R package for data access from the integrative Human Microbiome data portal
[ Bioconductor, GitHub ]

Non Bioconductor

GenomeRunner - A web server and a standalone tool for enrichment analysis of genomic regions in epigenomic annotations
[ GitHub, SourceForge, Paper1, Paper2 ]
lrcde - An R package for cell type-specific deconvolution and differential gene expression analysis
[ GitHub, Paper ]

Contributor

nullranges - Generation of null ranges via bootstrapping or covariate matching.
[ website ]