Alternatives and similar repositories for pipe4C

Users that are interested in pipe4C 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
• vaquerizaslab / tadtool
  TADtool is an interactive tool for the identification of meaningful parameters in TAD-calling algorithms for Hi-C data.
  ☆46Updated 2 years ago
• FelixKrueger / SNPsplit
  Allele-specific alignment sorting
  ☆58Updated 2 years ago
• kundajelab / 3DChromatin_ReplicateQC
  Software to compute reproducibility and quality scores for Hi-C data
  ☆50Updated 6 years ago
• yezhengSTAT / CUTTag_tutorial
  Tutorial Website
  ☆59Updated 4 years ago
• khuang28jhu / bs3
  BS-Seeker3: An Ultra-fast, Versatile Pipeline for Mapping Bisulfite-treated Reads.
  ☆27Updated 6 years ago
• olarerin / metaPlotR
  A Perl/R pipeline for plotting metagenes
  ☆37Updated 3 years ago
• 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 / TADLib
  A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains
  ☆44Updated 2 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
• twlab / TEProf2Paper
  TEProf2 Pipeline used to find promoters and predict protein sequences from RNA-sequencing data
  ☆26Updated 2 years ago
• XiaoTaoWang / NeoLoopFinder
  A computation framework for genome-wide detection of enhancer-hijacking events from chromatin interaction data in re-arranged genomes
  ☆67Updated last year
• dixonlab / hic_breakfinder
  ☆37Updated 5 years ago
• ay-lab / dcHiC
  dcHiC: Differential compartment analysis for Hi-C datasets
  ☆69Updated last year
• ENCODE-DCC / long-read-rna-pipeline
  ENCODE long read RNA-seq pipeline
  ☆49Updated 2 years ago
• XiaoTaoWang / domaincaller
  A Python implementation of the original DI domain caller
  ☆12Updated 4 years ago
• parklab / HiNT
  HiC for copy Number variation and Translocation detection
  ☆39Updated 3 years ago
• guoweilong / cgmaptools
  toolbox for analysing BS-seq data, advance features in SNV, ASM and DMR
  ☆62Updated last year
• XiaoTaoWang / HiCLift
  A fast and efficient tool for converting chromatin interaction data between genome assemblies
  ☆73Updated 2 years ago
• a-slide / NanoCount
  EM based transcript abundance from nanopore reads mapped to a transcriptome with minimap2
  ☆61Updated 9 months ago
• NYU-BFX / hic-bench
  A set of pipelines for Hi-C and ChIP-Seq analysis.
  ☆46Updated last year
• shawnzhangyx / cvdc_scripts
  scripts for analyzing the CVDC data.
  ☆19Updated 5 years ago
• AndreasHeger / gat
  Genomic Association Tester
  ☆31Updated 2 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…
  ☆74Updated 2 years ago
• nloyfer / UXM_deconv
  ☆44Updated 2 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
• 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
• iprada / Circle-Map
  A method for circular DNA detection based on probabilistic mapping of ultrashort reads
  ☆64Updated 11 months ago