Alternatives and similar repositories for hic-bench

Users that are interested in hic-bench are comparing it to the libraries listed below

• dekkerlab / crane-nature-2015
  code associated with crane-nature-2015, 10.1038/nature14450
  ☆36Updated 10 years ago
• yezhengSTAT / CUTTag_tutorial
  Tutorial Website
  ☆59Updated 4 years ago
• dekkerlab / cworld-dekker
  perl cworld module and collection of utility/analysis scripts for C data (3C, 4C, 5C, Hi-C)
  ☆67Updated 6 years ago
• databio / pepatac
  A modular, containerized pipeline for ATAC-seq data processing
  ☆58Updated 3 months ago
• ENCODE-DCC / dna-me-pipeline
  DCC/DAC methylation pipeline source
  ☆56Updated 5 years ago
• marvin-jens / find_circ
  tools to find circRNAs in RNA-seq data
  ☆44Updated 7 years ago
• ParkerLab / ataqv
  A toolkit for QC and visualization of ATAC-seq results.
  ☆71Updated 7 months ago
• LiuLabUB / HMMRATAC
  HMMRATAC peak caller for ATAC-seq data
  ☆99Updated 9 months ago
• AmpliconSuite / AmpliconSuite-pipeline
  A quickstart tool for AmpliconArchitect. Performs all preliminary steps (alignment, CNV calling, seed interval detection) required prior …
  ☆68Updated last month
• lh3 / hickit
  TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C
  ☆111Updated 4 years ago
• dozmorovlab / TADCompare
  Package for analysis and characterization of differential TADs
  ☆25Updated 3 years ago
• Henikoff / Cut-and-Run
  ☆30Updated 7 years ago
• FelixKrueger / SNPsplit
  Allele-specific alignment sorting
  ☆58Updated 2 years ago
• tariks / peakachu
  Genome-wide contact analysis using sklearn
  ☆68Updated last year
• FenyoLab / L1EM
  Estimate locus specific human LINE-1 expression.
  ☆37Updated 2 years ago
• GreenleafLab / NucleoATAC
  nucleosome calling using ATAC-seq
  ☆106Updated 4 years ago
• zhqingit / giremi
  GIREMI is a method that can identify RNA editing sites using one RNA-seq data set without requiring genome sequence data.
  ☆44Updated 8 years ago
• ucagenomix / sicelore
  Single Cell Long Read is a suite of tools dedicated to Cell barcode / UMI assignment and analysis of highly multiplexed single cell Nanop…
  ☆75Updated 2 years ago
• kundajelab / idr
  IDR
  ☆31Updated 2 years ago
• tanlongzhi / dip-c
  Tools to analyze Dip-C (or other 3C/Hi-C) data
  ☆70Updated 9 months ago
• olarerin / metaPlotR
  A Perl/R pipeline for plotting metagenes
  ☆37Updated 3 years ago
• aryeelab / hichipper
  A preprocessing and QC pipeline for HiChIP data
  ☆40Updated 3 years ago
• Xinglab / CLAM
  CLIP-seq Analysis of Multi-mapped reads
  ☆31Updated 4 years ago
• XiaoTaoWang / HiC_pipeline
  An easy-to-use Hi-C data processing software supporting distributed computation.
  ☆61Updated last year
• smithlabcode / methpipe
  A pipeline for analyzing DNA methylation data from bisulfite sequencing.
  ☆70Updated 2 years ago
• dphansti / mango
  chia pet analysis software
  ☆25Updated 6 years ago
• nerettilab / RepEnrich2
  RepEnrich2 is an updated method to estimate repetitive element enrichment using high-throughput sequencing data.
  ☆40Updated 3 years ago
• parklab / HiNT
  HiC for copy Number variation and Translocation detection
  ☆39Updated 4 years ago
• vaquerizaslab / tadtool
  TADtool is an interactive tool for the identification of meaningful parameters in TAD-calling algorithms for Hi-C data.
  ☆48Updated 2 years ago
• 3UTR / DaPars2
  Dynamics analysis of Alternative PolyAdenylation from RNA-seq
  ☆61Updated last year