Alternatives and similar repositories for HiC_pipeline:

Users that are interested in HiC_pipeline are comparing it to the libraries listed below

• XiaoTaoWang / HiCLift
  A fast and efficient tool for converting chromatin interaction data between genome assemblies
  ☆69Updated last year
• XiaoTaoWang / NeoLoopFinder
  A computation framework for genome-wide detection of enhancer-hijacking events from chromatin interaction data in re-arranged genomes
  ☆60Updated last year
• tariks / peakachu
  Genome-wide contact analysis using sklearn
  ☆60Updated 10 months ago
• hms-dbmi / 3d-genome-processing-tutorial
  A 3D genome data processing tutorial for ISMB/ECCB 2017
  ☆50Updated 7 years ago
• ay-lab / ATACProc
  ATAC-seq processing pipeline
  ☆32Updated 2 years ago
• tanlongzhi / dip-c
  Tools to analyze Dip-C (or other 3C/Hi-C) data
  ☆63Updated 3 months ago
• yezhengSTAT / CUTTag_tutorial
  Tutorial Website
  ☆56Updated 4 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
• kundajelab / 3DChromatin_ReplicateQC
  Software to compute reproducibility and quality scores for Hi-C data
  ☆46Updated 5 years ago
• olarerin / metaPlotR
  A Perl/R pipeline for plotting metagenes
  ☆37Updated 3 years ago
• LabTranslationalArchitectomics / riboWaltz
  optimization of ribosome P-site positioning in ribosome profiling data
  ☆46Updated last year
• ENCODE-DCC / hic-pipeline
  HiC uniform processing pipeline
  ☆58Updated last year
• XiaoTaoWang / TADLib
  A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains
  ☆40Updated 2 years ago
• NYU-BFX / hic-bench
  A set of pipelines for Hi-C and ChIP-Seq analysis.
  ☆46Updated 10 months ago
• ren-lab / hic-pipeline
  ☆24Updated 3 years ago
• XiaoTaoWang / EagleC
  A deep-learning framework for predicting a full range of structural variations from bulk and single-cell contact maps
  ☆57Updated last year
• FelixKrueger / SNPsplit
  Allele-specific alignment sorting
  ☆54Updated 2 years ago
• xryanglab / RiboCode
  release version
  ☆51Updated 2 years ago
• BioinfoUNIBA / REDItools2
  ☆54Updated 3 years ago
• xuzhougeng / R-ChIP-data-analysis
  ☆51Updated 6 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
• GuttmanLab / sprite-pipeline
  A self-contained repository of all code needed for SPRITE analysis
  ☆20Updated 3 years ago
• YaqiangCao / cLoops2
  Enhanced and elegant flexible peak/loop/domain -calling and analysis tool for 1D/3D genomic data.
  ☆45Updated 2 months ago
• 4dn-dcic / hic2cool
  Lightweight converter between hic and cool contact matrices.
  ☆68Updated 7 months ago
• dekkerlab / crane-nature-2015
  code associated with crane-nature-2015, 10.1038/nature14450
  ☆34Updated 9 years ago
• iprada / Circle-Map
  A method for circular DNA detection based on probabilistic mapping of ultrashort reads
  ☆61Updated 6 months ago
• brwnj / fastq-multx
  Demultiplexes a fastq.
  ☆44Updated 4 years ago
• Zhong-Lab-UCSD / HiCtool
  Python library for processing and visualizing Hi-C data
  ☆20Updated 4 years ago
• open2c / distiller-nf
  A modular Hi-C mapping pipeline
  ☆89Updated 2 months ago
• WGLab / LIQA
  Long-read Isoform Quantification and Analysis
  ☆39Updated last month