The following software packages can be downloaded freely. If you have any question, please email me at hum@ccf.org or afhuming@gmail.com.
17. SnapHiC: single nucleus analysis pipeline for Hi-C data. Available from: https://github.com/HuMingLab/SnapHiC
16. TWO-SIGMA: TWO-component SInGle cell Model-based Association method. Available from: https://github.com/edvanburen/twosigma
15. FIREcaller: an R package for detecting frequently interacting regions from Hi-C data. Available from: https://github.com/yycunc/FIREcaller
14. MAPS: Model-based analysis of long-range chromatin interactions from PLAC-Seq and HiChIP experiments. Available from: https://github.com/ijuric/MAPS
13. BAMM-SC: a Bayesian mixture model for clustering droplet-based single cell transcriptomic data from multiple studies. Available from: https://github.com/lichen-lab/BAMMSC.
12. DIMM-SC: a Dirichlet mixture model for clustering droplet-based single cell transcrip tomic data. Available from: http://www.pitt.edu/~wec47/singlecell.html.
11. HUGIn (Hi-C Unifying Genomic INterrogator): a genome browser of the integrative analysis of Hi-C data, SNP data and epigenetic data from 7 human cell lines and 14 human tissues. Available at: https://yunliweb.its.unc.edu/HUGIn/.
10. FastHiC: a fast algorithm to detect long-range chromosomal interactions from Hi-C data. Available at https://yunliweb.its.unc.edu/fasthic/.
9. hichelix: inferring spatial organizations of chromosomes via helix models. Available at: http://www.stat.purdue.edu/~zhan1602/phm.
8. HiView: a genome browser for the integrative analysis of Hi-C data, SNP data and epigenetic data. Available at: https://yunliweb.its.unc.edu/HiView/.
7. HMRFBayesHiC: A hidden Markov random field based Bayesian method for the detection of long-range chromosomal interactions in Hi-C data. Available at: https://yunliweb.its.unc.edu/HMRFBayesHiC/.
6. Bayesian 3D constructor for Hi-C data (BACH): infer chromosome 3D structures and characterize chromatin structural variations. Available at: http://www.people.fas.harvard.edu/~junliu/BACH/
5. HiCNorm: removing biases in Hi-C data via Poisson regression: Available at: http://www.people.fas.harvard.edu/~junliu/HiCNorm/ and https://github.com/ren-lab/HiCNorm (HiCNorm has been included in the HiTC Bioconductor package)
4. GPUmotif: An ultra-fast and energy-efficient motif analysis program using graphics processing units. Available at: http://sourceforge.net/projects/gpumotif/
3. Poisson Mixed-Effects Regression for RNA-Seq Data (POME): quantifying exon-level gene expression in RNA-Seq. Available at: http://www.stat.purdue.edu/~yuzhu/pome.html.
2. Hybrid Motif Sampler (HMS): de novo motif discovery using ChIP-Seq data. Available at: https://sourceforge.net/projects/hybridmotifsampler/
1. Bayesian Expression Search Tool (BEST): query large scale microarray compendium datasets. Available at: https://sourceforge.net/projects/bayesianexpressionsearchtool/