Alternatives and similar repositories for RCMC_analysis_code

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

• XiaoTaoWang / HiCPeaks
  A Python implementation for BH-FDR and HiCCUPS
  ☆53Updated 8 months 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…
  ☆26Updated 8 months ago
• XiaoTaoWang / HiCLift
  A fast and efficient tool for converting chromatin interaction data between genome assemblies
  ☆76Updated 5 months ago
• magnitov / pentad
  A simple tool to perform the calculation and visualization of the average chromatin A/B compartment.
  ☆14Updated 2 years ago
• XiaoTaoWang / NeoLoopFinder
  A computation framework for genome-wide detection of enhancer-hijacking events from chromatin interaction data in re-arranged genomes
  ☆75Updated 2 years ago
• deLaatLab / pipe4C
  4C-seq processing pipeline
  ☆26Updated 9 months 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
• XiaoTaoWang / domaincaller
  A Python implementation of the original DI domain caller
  ☆12Updated 5 years ago
• wyang17 / SQuIRE
  Software for Quantifying Interspersed Repeat Expression
  ☆63Updated 3 years ago
• zhongmicai / Hic_tools_collection
  ☆12Updated 6 years ago
• XiaoTaoWang / EagleC
  A deep-learning framework for predicting a full range of structural variations from bulk and single-cell contact maps
  ☆61Updated 4 months ago
• XiaoTaoWang / TADLib
  A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains
  ☆45Updated 3 years ago
• shawnzhangyx / cvdc_scripts
  scripts for analyzing the CVDC data.
  ☆20Updated 6 years ago
• CSOgroup / CALDER
  ☆22Updated 2 years ago
• YaqiangCao / cLoops2
  Enhanced and elegant flexible peak/loop/domain -calling and analysis tool for 1D/3D genomic data.
  ☆52Updated 6 months ago
• open2c / coolpuppy
  A versatile tool to perform pile-up analysis on Hi-C data in .cool format.
  ☆80Updated last year
• Tian-Dechao / diffDomain
  DiffDomain is a statistically sound method for detecting differential TADs between conditions
  ☆17Updated 6 months ago
• dozmorovlab / TADCompare
  Package for analysis and characterization of differential TADs
  ☆26Updated 3 years ago
• FelixKrueger / SNPsplit
  Allele-specific alignment sorting
  ☆61Updated 2 years ago
• dixonlab / hic_breakfinder
  ☆37Updated 6 years ago
• ChenFengling / HiCpipe
  an efficient Hi-C data processing pipeline
  ☆17Updated last year
• lh3 / hickit
  TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C
  ☆113Updated 4 years ago
• josiegleeson / BamSlam
  Summarise and plot data from long-read ONT (direct RNA/cDNA) BAM files
  ☆15Updated last year
• tariks / peakachu
  Genome-wide contact analysis using sklearn
  ☆71Updated last year
• ay-lab / dcHiC
  dcHiC: Differential compartment analysis for Hi-C datasets
  ☆73Updated last year
• ENCODE-DCC / long-read-rna-pipeline
  ENCODE long read RNA-seq pipeline
  ☆52Updated 2 years ago
• anlin00007 / OnTAD
  An Optimized Nested TAD caller for Hi-C data
  ☆25Updated 4 years ago
• 4dn-dcic / docker-4dn-hic
  Docker for 4DN Hi-C processing pipeline
  ☆60Updated last year
• kundajelab / 3DChromatin_ReplicateQC
  Software to compute reproducibility and quality scores for Hi-C data
  ☆50Updated 6 years ago
• Xinglab / espresso
  ☆64Updated 3 months ago