NYU-BFX / hic-bench
A set of pipelines for Hi-C and ChIP-Seq analysis.
☆46Updated 9 months ago
Alternatives and similar repositories for hic-bench:
Users that are interested in hic-bench are comparing it to the libraries listed below
- code associated with crane-nature-2015, 10.1038/nature14450☆34Updated 9 years ago
- ATAC-seq processing pipeline☆31Updated 2 years ago
- Tutorial Website☆55Updated 3 years ago
- RepEnrich2 is an updated method to estimate repetitive element enrichment using high-throughput sequencing data.☆37Updated 2 years ago
- perl cworld module and collection of utility/analysis scripts for C data (3C, 4C, 5C, Hi-C)☆66Updated 5 years ago
- Software to compute reproducibility and quality scores for Hi-C data☆46Updated 5 years ago
- ☆30Updated 6 years ago
- HMMRATAC peak caller for ATAC-seq data☆100Updated 2 months ago
- A computation framework for genome-wide detection of enhancer-hijacking events from chromatin interaction data in re-arranged genomes☆60Updated last year
- TADtool is an interactive tool for the identification of meaningful parameters in TAD-calling algorithms for Hi-C data.☆44Updated 2 years ago
- Dynamics analysis of Alternative PolyAdenylation from RNA-seq☆54Updated last year
- A toolkit for QC and visualization of ATAC-seq results.☆67Updated 3 weeks ago
- TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C☆108Updated 3 years ago
- Estimate locus specific human LINE-1 expression.☆32Updated 2 years ago
- DCC/DAC methylation pipeline source☆55Updated 4 years ago
- tools to find circRNAs in RNA-seq data☆40Updated 7 years ago
- A modular, containerized pipeline for ATAC-seq data processing☆54Updated 2 weeks ago
- fork of RSeQC python RNAseq metrics suit of tools☆48Updated 6 years ago
- Allele-specific alignment sorting☆54Updated 2 years ago
- GIREMI is a method that can identify RNA editing sites using one RNA-seq data set without requiring genome sequence data.☆42Updated 7 years ago
- ROSE: RANK ORDERING OF SUPER-ENHANCERS☆43Updated 5 months ago
- A self-contained repository of all code needed for SPRITE analysis☆20Updated 3 years ago
- A Perl/R pipeline for plotting metagenes☆36Updated 3 years ago
- Single Cell Long Read is a suite of tools dedicated to Cell barcode / UMI assignment and analysis of highly multiplexed single cell Nanop…☆72Updated last year
- Package for analysis and characterization of differential TADs☆23Updated 2 years ago
- HiC uniform processing pipeline☆58Updated last year
- Pipelines to create and analyze ENCODE candidate cis-Regulatory Elements☆19Updated 3 weeks ago
- A fast and efficient tool for converting chromatin interaction data between genome assemblies☆69Updated last year
- A 3D genome data processing tutorial for ISMB/ECCB 2017☆50Updated 7 years ago
- Tools to analyze Dip-C (or other 3C/Hi-C) data☆63Updated 2 months ago