Alternatives and similar repositories for pycallingcards

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

• AmpliconSuite / AmpliconClassifier
  Classify output of AmpliconArchitect to detect types of focal amplifications present
  ☆21Updated 3 weeks ago
• ay-lab / dcHiC
  dcHiC: Differential compartment analysis for Hi-C datasets
  ☆73Updated 2 years ago
• shawnzhangyx / cvdc_scripts
  scripts for analyzing the CVDC data.
  ☆20Updated 6 years ago
• STOmics / ST_BarcodeMap
  ☆21Updated 2 years ago
• ysora / stripenn
  Architectural stripe detection from 3D genome conformation data
  ☆18Updated 3 months ago
• wyang17 / SQuIRE
  Software for Quantifying Interspersed Repeat Expression
  ☆63Updated 3 years ago
• XiaoTaoWang / HiCLift
  A fast and efficient tool for converting chromatin interaction data between genome assemblies
  ☆77Updated 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
• Tian-Dechao / diffDomain
  DiffDomain is a statistically sound method for detecting differential TADs between conditions
  ☆17Updated 6 months ago
• YaqiangCao / cLoops2
  Enhanced and elegant flexible peak/loop/domain -calling and analysis tool for 1D/3D genomic data.
  ☆52Updated 6 months 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
• 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
• crickbabs / DRB_TT-seq
  Scripts for the analysis of TT-seq and DRB/TT-seq data.
  ☆11Updated 5 years ago
• raphael-group / hatchet
  HATCHet (Holistic Allele-specific Tumor Copy-number Heterogeneity) is an algorithm that infers allele and clone-specific CNAs and WGDs jo…
  ☆70Updated 10 months ago
• XiaoTaoWang / HiCPeaks
  A Python implementation for BH-FDR and HiCCUPS
  ☆53Updated 2 weeks ago
• bvaldebenitom / SoloTE
  ☆33Updated last year
• WGLab / SCOTCH
  Single-Cell Omics for Transcriptome CHaracterization (SCOTCH): isoform-level characterization of gene expression through long-read single…
  ☆17Updated this week
• XiaoTaoWang / TADLib
  A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains
  ☆45Updated 3 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
• josiegleeson / BamSlam
  Summarise and plot data from long-read ONT (direct RNA/cDNA) BAM files
  ☆15Updated last year
• dejunlin / hicrep
  Python implementation of HiCRep stratum-adjusted correlation coefficient of Hi-C data with Cooler sparse contact matrix support
  ☆41Updated last year
• lrylaarsdam / amethyst
  A comprehensive toolkit for single-cell methylation sequencing data analysis
  ☆30Updated this week
• open2c / coolpuppy
  A versatile tool to perform pile-up analysis on Hi-C data in .cool format.
  ☆80Updated 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…
  ☆12Updated 2 years ago
• dixonlab / hic_breakfinder
  ☆37Updated 6 years ago
• dovetail-genomics / Micro-C
  Micro-C QC and data analysis
  ☆16Updated 2 years ago
• vaquerizaslab / fanc
  FAN-C: Framework for the ANalysis of C-like data
  ☆121Updated last year
• LUMC / fastqsplitter
  Splits fastq files evenly
  ☆23Updated 5 years ago
• zhongmicai / Hic_tools_collection
  ☆12Updated 6 years ago
• mlbendall / telescope
  Quantification of transposable element expression using RNA-seq
  ☆78Updated last year