Alternatives and similar repositories for cooltools

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

• open2c / distiller-nf
  A modular Hi-C mapping pipeline
  ☆100Updated 11 months ago
• vaquerizaslab / fanc
  FAN-C: Framework for the ANalysis of C-like data
  ☆120Updated last year
• open2c / pairtools
  Extract 3D contacts (.pairs) from sequencing alignments
  ☆117Updated last week
• deeptools / HiCExplorer
  HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
  ☆256Updated 3 months ago
• 4dn-dcic / hic2cool
  Lightweight converter between hic and cool contact matrices.
  ☆74Updated last year
• haowenz / chromap
  Fast alignment and preprocessing of chromatin profiles
  ☆206Updated last month
• ay-lab / fithic
  Fit-Hi-C is a tool for assigning statistical confidence estimates to chromosomal contact maps produced by genome-wide genome architecture…
  ☆91Updated 3 years ago
• open2c / coolpuppy
  A versatile tool to perform pile-up analysis on Hi-C data in .cool format.
  ☆80Updated last year
• ablab / IsoQuant
  Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)
  ☆192Updated last week
• GoekeLab / m6anet
  Detection of m6A from direct RNA-Seq data
  ☆129Updated 5 months ago
• ENCODE-DCC / hic-pipeline
  HiC uniform processing pipeline
  ☆61Updated 2 years ago
• XiaoTaoWang / HiCLift
  A fast and efficient tool for converting chromatin interaction data between genome assemblies
  ☆75Updated 3 months ago
• open2c / cooler
  A cool place to store your Hi-C
  ☆228Updated this week
• mlbendall / telescope
  Quantification of transposable element expression using RNA-seq
  ☆76Updated last year
• yupenghe / methylpy
  WGBS/NOMe-seq Data Processing & Differential Methylation Analysis
  ☆146Updated 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
• nloyfer / wgbs_tools
  tools for working with Bisulfite Sequencing data while preserving reads intrinsic dependencies
  ☆172Updated last week
• GoekeLab / sg-nex-data
  Nanopore RNA-Seq data from the Singapore Nanopore-Expression Project
  ☆143Updated 2 months ago
• mortazavilab / TALON
  Technology agnostic long read analysis pipeline for transcriptomes
  ☆152Updated last year
• hms-dbmi / hic-data-analysis-bootcamp
  Workshop on measuring, analyzing, and visualizing the 3D genome with Hi-C data.
  ☆205Updated 7 years ago
• tariks / peakachu
  Genome-wide contact analysis using sklearn
  ☆70Updated 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
• ConesaLab / SQANTI3
  Tool for the Quality Control of Long-Read Defined Transcriptomes
  ☆244Updated this week
• signalbash / how_are_we_stranded_here
  Check strandedness of RNA-Seq fastq files
  ☆127Updated 3 years ago
• ENCODE-DCC / rna-seq-pipeline
  ☆157Updated 3 years ago
• Xinglab / rmats2sashimiplot
  ☆153Updated 5 months ago
• nf-core / hic
  Analysis of Chromosome Conformation Capture data (Hi-C)
  ☆102Updated last month
• mdozmorov / HiC_data
  A (continuously updated) collection of references to Hi-C data. Predominantly human/mouse Hi-C data, with replicates.
  ☆200Updated 4 months ago
• dpryan79 / MethylDackel
  A (mostly) universal methylation extractor for BS-seq experiments.
  ☆173Updated last year
• skrakau / PureCLIP
  Capturing protein-RNA interaction footprints from single-nucleotide CLIP-seq data
  ☆31Updated 4 years ago