Alternatives and similar repositories for ChIA-PIPE

Users that are interested in ChIA-PIPE are comparing it to the libraries listed below

• dekkerlab / cworld-dekker
  perl cworld module and collection of utility/analysis scripts for C data (3C, 4C, 5C, Hi-C)
  ☆65Updated 6 years ago
• 4dn-dcic / docker-4dn-hic
  Docker for 4DN Hi-C processing pipeline
  ☆61Updated 7 months ago
• dozmorovlab / TADCompare
  Package for analysis and characterization of differential TADs
  ☆25Updated 3 years ago
• yezhengSTAT / CUTTag_tutorial
  Tutorial Website
  ☆59Updated 4 years ago
• tariks / peakachu
  Genome-wide contact analysis using sklearn
  ☆68Updated last year
• dekkerlab / crane-nature-2015
  code associated with crane-nature-2015, 10.1038/nature14450
  ☆36Updated 9 years ago
• CSOgroup / CALDER2
  CALDER is a Hi-C analysis tool that allows: (1) compute chromatin domains from whole chromosome contacts; (2) derive their non-linear hie…
  ☆23Updated 3 months ago
• XiaoTaoWang / HiCLift
  A fast and efficient tool for converting chromatin interaction data between genome assemblies
  ☆73Updated 2 years ago
• GuipengLi / ChIA-PET2
  a versatile and flexible pipeline for analysing different variants of ChIA-PET data
  ☆34Updated 7 months 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…
  ☆74Updated 2 years ago
• Tian-Dechao / diffDomain
  DiffDomain is a statistically sound method for detecting differential TADs between conditions
  ☆18Updated 3 weeks ago
• AmpliconSuite / AmpliconSuite-pipeline
  A quickstart tool for AmpliconArchitect. Performs all preliminary steps (alignment, CNV calling, seed interval detection) required prior …
  ☆67Updated 2 weeks ago
• tanlongzhi / dip-c
  Tools to analyze Dip-C (or other 3C/Hi-C) data
  ☆69Updated 8 months ago
• iprada / Circle-Map
  A method for circular DNA detection based on probabilistic mapping of ultrashort reads
  ☆64Updated last year
• nerettilab / RepEnrich2
  RepEnrich2 is an updated method to estimate repetitive element enrichment using high-throughput sequencing data.
  ☆39Updated 3 years ago
• shawnzhangyx / cvdc_scripts
  scripts for analyzing the CVDC data.
  ☆19Updated 5 years ago
• databio / awesome-atac-analysis
  Links to ATAC-seq analysis tools
  ☆68Updated 3 years ago
• hms-dbmi / 3d-genome-processing-tutorial
  A 3D genome data processing tutorial for ISMB/ECCB 2017
  ☆50Updated 7 years ago
• anlin00007 / OnTAD
  An Optimized Nested TAD caller for Hi-C data
  ☆22Updated 4 years ago
• NYU-BFX / hic-bench
  A set of pipelines for Hi-C and ChIP-Seq analysis.
  ☆46Updated last year
• ren-lab / hic-pipeline
  ☆24Updated 4 years ago
• olarerin / metaPlotR
  A Perl/R pipeline for plotting metagenes
  ☆37Updated 3 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
• XiaoTaoWang / NeoLoopFinder
  A computation framework for genome-wide detection of enhancer-hijacking events from chromatin interaction data in re-arranged genomes
  ☆67Updated last year
• xuzhougeng / R-ChIP-data-analysis
  ☆50Updated 6 years ago
• 3UTR / DaPars2
  Dynamics analysis of Alternative PolyAdenylation from RNA-seq
  ☆61Updated last year
• ay-lab / dcHiC
  dcHiC: Differential compartment analysis for Hi-C datasets
  ☆69Updated last year
• kundajelab / 3DChromatin_ReplicateQC
  Software to compute reproducibility and quality scores for Hi-C data
  ☆50Updated 6 years ago
• XiaoTaoWang / HiC_pipeline
  An easy-to-use Hi-C data processing software supporting distributed computation.
  ☆61Updated 11 months ago
• dejunlin / hicrep
  Python implementation of HiCRep stratum-adjusted correlation coefficient of Hi-C data with Cooler sparse contact matrix support
  ☆38Updated last year