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
  ☆35Updated 9 years ago
• dekkerlab / cworld-dekker
  perl cworld module and collection of utility/analysis scripts for C data (3C, 4C, 5C, Hi-C)
  ☆66Updated 5 years ago
• yezhengSTAT / CUTTag_tutorial
  Tutorial Website
  ☆59Updated 4 years ago
• ay-lab / ATACProc
  ATAC-seq processing pipeline
  ☆33Updated 3 years ago
• FelixKrueger / SNPsplit
  Allele-specific alignment sorting
  ☆56Updated 2 years ago
• kundajelab / 3DChromatin_ReplicateQC
  Software to compute reproducibility and quality scores for Hi-C data
  ☆47Updated 6 years ago
• marvin-jens / find_circ
  tools to find circRNAs in RNA-seq data
  ☆43Updated 7 years ago
• nerettilab / RepEnrich2
  RepEnrich2 is an updated method to estimate repetitive element enrichment using high-throughput sequencing data.
  ☆39Updated 3 years ago
• lh3 / hickit
  TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C
  ☆109Updated 4 years ago
• ParkerLab / ataqv
  A toolkit for QC and visualization of ATAC-seq results.
  ☆70Updated 4 months ago
• XiaoTaoWang / NeoLoopFinder
  A computation framework for genome-wide detection of enhancer-hijacking events from chromatin interaction data in re-arranged genomes
  ☆65Updated last year
• Henikoff / Cut-and-Run
  ☆30Updated 6 years ago
• XiaoTaoWang / EagleC
  A deep-learning framework for predicting a full range of structural variations from bulk and single-cell contact maps
  ☆59Updated last year
• databio / pepatac
  A modular, containerized pipeline for ATAC-seq data processing
  ☆58Updated 2 weeks ago
• 3UTR / DaPars2
  Dynamics analysis of Alternative PolyAdenylation from RNA-seq
  ☆59Updated last year
• vaquerizaslab / tadtool
  TADtool is an interactive tool for the identification of meaningful parameters in TAD-calling algorithms for Hi-C data.
  ☆44Updated 2 years ago
• LiuLabUB / HMMRATAC
  HMMRATAC peak caller for ATAC-seq data
  ☆100Updated 6 months ago
• aryeelab / hichipper
  A preprocessing and QC pipeline for HiChIP data
  ☆38Updated 2 years ago
• ren-lab / hic-pipeline
  ☆24Updated 4 years ago
• ENCODE-DCC / dna-me-pipeline
  DCC/DAC methylation pipeline source
  ☆55Updated 4 years ago
• tariks / peakachu
  Genome-wide contact analysis using sklearn
  ☆65Updated last year
• databio / awesome-atac-analysis
  Links to ATAC-seq analysis tools
  ☆66Updated 3 years ago
• ratschlab / pancanatlas_code_public
  Public repository containing research code for the TCGA PanCanAtlas Splicing project
  ☆41Updated 4 years ago
• olarerin / metaPlotR
  A Perl/R pipeline for plotting metagenes
  ☆37Updated 3 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…
  ☆73Updated 2 years ago
• tobiasrausch / ATACseq
  Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)
  ☆75Updated last year
• FenyoLab / L1EM
  Estimate locus specific human LINE-1 expression.
  ☆35Updated 2 years ago
• MonashBioinformaticsPlatform / RSeQC
  fork of RSeQC python RNAseq metrics suit of tools
  ☆48Updated 6 years ago
• ZhengXia / dapars
  DaPars(Dynamic analysis of Alternative PolyAdenylation from RNA-seq)
  ☆48Updated 2 years ago
• shawnzhangyx / cvdc_scripts
  scripts for analyzing the CVDC data.
  ☆18Updated 5 years ago