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This repository is for analyzing the Hi-C data.
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Use this script pre_environment.sh to prepare the analysis environment.
➡️ diffHic
- Detects differential interactions across biological conditions in a Hi-C experiment. Methods are provided for read alignment and data pre-processing into interaction counts. Statistical analysis is based on edgeR and supports normalization and filtering. Several visualization options are also available.
- Citation (from within R, enter citation("diffHic")):
Lun ATL, Smyth GK (2015). “diffHic: a Bioconductor package to detect differential genomic interactions in Hi-C data.” BMC Bioinformatics, 16, 258.
- Installation To install this package, start R (version "4.3") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("diffHic")
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Citation (from within R, enter citation("multiHiCcompare")):
Stansfield JC, Cresswell KG, Dozmorov MG (2019). “multiHiCcompare: joint normalization and comparative analysis of complex Hi-C experiments.” Bioinformatics, 35(17). doi:10.1093/bioinformatics/btz048, https://github.com/dozmorovlab/multiHiCcompare.
- Installation To install this package, start R (version "4.3") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("multiHiCcompare")