Hi-C in R
The HiCExperiment ecosystem: from raw reads to tidy, analysis-ready contact maps, within Bioconductor.
- Process HiCool
- Import HiCExperiment
- Analyze HiContactsplyinteractions
HiCool
RProcess paired-end Hi-C reads into normalized .mcool contact maps, with shareable QC reports.
Docs• GitHub• Bioconductor• Paper
BiocManager::install("HiCool")
HiCExperiment
RImport .cool, .mcool, .hic, HiC-Pro and pairs files into R, with memory-efficient random access.
Docs• GitHub• Bioconductor• Paper
BiocManager::install("HiCExperiment")
HiContacts
RAnalyze and visualize Hi-C maps: distance laws, virtual 4C, compartments, insulation and more.
Docs• GitHub• Bioconductor• Paper
BiocManager::install("HiContacts")
plyinteractions
Rdplyr-like verbs to filter, mutate, join and summarize genomic interactions, as part of tidyomics.
Docs• GitHub• Bioconductor• Paper
BiocManager::install("plyinteractions")
OHCA
R · bookOpen online book on Hi-C analysis with Bioconductor, from raw reads to biological insights.
HiContactsData
R · dataExample Hi-C files (fastq, pairs, .cool, .mcool) used throughout the ecosystem's documentation.
BiocManager::install("HiContactsData")
fourDNData
R · dataProgrammatic access to Hi-C contact maps uniformly processed by the 4D Nucleome consortium.
BiocManager::install("fourDNData")
DNAZooData
R · dataProgrammatic access to DNA Zoo Hi-C contact maps and chromosome-length genome assemblies.
BiocManager::install("DNAZooData")
Hi-C toolkits & viewers
Command-line tools, file formats and a viewer to build, mine and explore contact maps, from single genomes to entire metagenomes.
hicstuff
PythonHi-C processing pipeline and library: alignment, read filtering, binning, normalization and plotting.
pip install hicstuff
chromosight
PythonComputer-vision detection of loops, borders, hairpins and other patterns in contact maps.
pip install chromosight
instaGRAAL
PythonChromosome-level genome scaffolding from Hi-C contacts, with GPU-accelerated MCMC.
pip install instagraal
metaTOR
PythonBin metagenomic contigs into genomes using metaHiC / meta3C contact networks.
pip install metator
metacooler
PythonExtends the cooler format to metagenomes: genome-aware contact maps that remain readable by cooler.
ChromLens
TypeScript · web appIn-browser viewer for contact maps, genome tracks and 3D chromatin models. No server, no upload, no preprocessing.
Coverage & sequence features
Extract, store and aggregate genome-wide signal; profile fragment sizes and DNA sequence periodicity.
tidyCoverage
RExtract, aggregate and visualize genomic coverage over thousands of loci, the tidy way.
Docs• GitHub• Bioconductor• Paper
BiocManager::install("tidyCoverage")
momics
PythonStore and query genomic coverage tracks and sequences in TileDB arrays, e.g. to train deep-learning models.
pip install momics
VplotR
RV-plots and footprint profiles from paired-end fragment densities, e.g. ATAC-seq or MNase-seq.
Docs• GitHub• Bioconductor• Paper
BiocManager::install("VplotR")
periodicDNA
RIdentify k-mers occurring periodically in DNA sequences, such as the ~10-bp periodicity of WW dinucleotides.
Docs• GitHub• Bioconductor• Paper
BiocManager::install("periodicDNA")
Pipelines & infrastructure
Read mapping for common genomic assays, and building blocks for the Bioconductor community.
tinyMapper
PythonMinimalist mapping workflow for ChIP-seq, RNA-seq, ATAC-seq, MNase-seq, Hi-C and shotgun reads.
pip install tinymapper
BiocBook
RWrite, containerize, publish and version Quarto books with Bioconductor.
BiocManager::install("BiocBook")
GenomicCoordinates
RParse genomic coordinates written in many formats into GRanges, GPos or GInteractions objects.
BiocManager::install("GenomicCoordinates")