Alternatives and similar repositories for CALDER2:

Users that are interested in CALDER2 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 5 years ago
• deLaatLab / pipe4C
  4C-seq processing pipeline
  ☆23Updated last month
• Tian-Dechao / diffDomain
  DiffDomain is a statistically sound method for detecting differential TADs between conditions
  ☆18Updated 6 months ago
• ay-lab / dcHiC
  dcHiC: Differential compartment analysis for Hi-C datasets
  ☆68Updated last year
• nerettilab / RepEnrich2
  RepEnrich2 is an updated method to estimate repetitive element enrichment using high-throughput sequencing data.
  ☆39Updated 3 years ago
• CSOgroup / CALDER
  ☆22Updated last year
• kundajelab / 3DChromatin_ReplicateQC
  Software to compute reproducibility and quality scores for Hi-C data
  ☆46Updated 6 years ago
• XiaoTaoWang / NeoLoopFinder
  A computation framework for genome-wide detection of enhancer-hijacking events from chromatin interaction data in re-arranged genomes
  ☆64Updated last year
• dixonlab / hic_breakfinder
  ☆37Updated 5 years ago
• magnitov / pentad
  A simple tool to perform the calculation and visualization of the average chromatin A/B compartment.
  ☆14Updated 2 years ago
• hsinyenwu / RiboPlotR
  RiboPlotR package for Ribo-plot
  ☆15Updated last year
• ahansenlab / RCMC_analysis_code
  Code associated with with the 2023 Nature Genetics Paper "Region Capture Micro-C reveals coalescence of enhancers and promoters into nest…
  ☆11Updated last year
• 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 / TADLib
  A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains
  ☆42Updated 2 years ago
• shawnzhangyx / cvdc_scripts
  scripts for analyzing the CVDC data.
  ☆18Updated 5 years ago
• XiaoTaoWang / HiCLift
  A fast and efficient tool for converting chromatin interaction data between genome assemblies
  ☆71Updated last year
• anlin00007 / OnTAD
  An Optimized Nested TAD caller for Hi-C data
  ☆20Updated 3 years ago
• dekkerlab / crane-nature-2015
  code associated with crane-nature-2015, 10.1038/nature14450
  ☆34Updated 9 years ago
• tariks / peakachu
  Genome-wide contact analysis using sklearn
  ☆64Updated last year
• open2c / quaich
  snakemake pipeline for Hi-C post-processing
  ☆22Updated 9 months ago
• dovetail-genomics / Micro-C
  Micro-C QC and data analysis
  ☆16Updated last year
• ay-lab / FitHiChIP
  Statistically Significant loops from HiChIP data
  ☆42Updated last year
• parklab / HiNT
  HiC for copy Number variation and Translocation detection
  ☆38Updated 3 years ago
• ren-lab / hic-pipeline
  ☆24Updated 3 years ago
• yezhengSTAT / CUTTag_tutorial
  Tutorial Website
  ☆59Updated 4 years ago
• FenyoLab / L1EM
  Estimate locus specific human LINE-1 expression.
  ☆34Updated 2 years ago
• olarerin / metaPlotR
  A Perl/R pipeline for plotting metagenes
  ☆37Updated 3 years ago
• dejunlin / hicrep
  Python implementation of HiCRep stratum-adjusted correlation coefficient of Hi-C data with Cooler sparse contact matrix support
  ☆38Updated last year
• twlab / TEProf2Paper
  TEProf2 Pipeline used to find promoters and predict protein sequences from RNA-sequencing data
  ☆23Updated last year
• GuttmanLab / sprite-pipeline
  A self-contained repository of all code needed for SPRITE analysis
  ☆20Updated 3 years ago