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
  ☆97Updated 7 months ago
• vaquerizaslab / fanc
  FAN-C: Framework for the ANalysis of C-like data
  ☆115Updated last year
• open2c / pairtools
  Extract 3D contacts (.pairs) from sequencing alignments
  ☆113Updated 2 weeks ago
• haowenz / chromap
  Fast alignment and preprocessing of chromatin profiles
  ☆203Updated 3 weeks ago
• deeptools / HiCExplorer
  HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
  ☆251Updated 3 weeks ago
• ablab / IsoQuant
  Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)
  ☆169Updated last week
• 4dn-dcic / hic2cool
  Lightweight converter between hic and cool contact matrices.
  ☆73Updated last year
• ay-lab / fithic
  Fit-Hi-C is a tool for assigning statistical confidence estimates to chromosomal contact maps produced by genome-wide genome architecture…
  ☆86Updated 2 years ago
• nf-core / hic
  Analysis of Chromosome Conformation Capture data (Hi-C)
  ☆99Updated last week
• open2c / coolpuppy
  A versatile tool to perform pile-up analysis on Hi-C data in .cool format.
  ☆80Updated 8 months ago
• GoekeLab / m6anet
  Detection of m6A from direct RNA-Seq data
  ☆124Updated last month
• XiaoTaoWang / HiCLift
  A fast and efficient tool for converting chromatin interaction data between genome assemblies
  ☆73Updated 2 years ago
• mortazavilab / TALON
  Technology agnostic long read analysis pipeline for transcriptomes
  ☆144Updated last year
• GoekeLab / sg-nex-data
  Nanopore RNA-Seq data from the Singapore Nanopore-Expression Project
  ☆129Updated 2 weeks ago
• GoekeLab / bambu
  Reference-guided transcript discovery and quantification for long read RNA-Seq data
  ☆212Updated 2 weeks ago
• ConesaLab / SQANTI3
  Tool for the Quality Control of Long-Read Defined Transcriptomes
  ☆231Updated last week
• dpryan79 / MethylDackel
  A (mostly) universal methylation extractor for BS-seq experiments.
  ☆173Updated last year
• 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
• mlbendall / telescope
  Quantification of transposable element expression using RNA-seq
  ☆71Updated last year
• yupenghe / methylpy
  WGBS/NOMe-seq Data Processing & Differential Methylation Analysis
  ☆143Updated 2 years ago
• nloyfer / wgbs_tools
  tools for working with Bisulfite Sequencing data while preserving reads intrinsic dependencies
  ☆163Updated last month
• ENCODE-DCC / hic-pipeline
  HiC uniform processing pipeline
  ☆60Updated last year
• epi2me-labs / wf-transcriptomes
  ☆98Updated 3 weeks ago
• saketkc / gencode_regions
  Extract 3'UTR, 5'UTR, CDS, Promoter, Genes, Introns, Exons from GTF files
  ☆110Updated 3 years ago
• signalbash / how_are_we_stranded_here
  Check strandedness of RNA-Seq fastq files
  ☆124Updated 2 years ago
• htseq / htseq
  HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.
  ☆102Updated last month
• hms-dbmi / hic-data-analysis-bootcamp
  Workshop on measuring, analyzing, and visualizing the 3D genome with Hi-C data.
  ☆201Updated 7 years ago
• novoalab / EpiNano
  Detection of RNA modifications from Oxford Nanopore direct RNA sequencing reads (Liu*, Begik* et al., Nature Comm 2019)
  ☆115Updated last week
• Xinglab / rmats2sashimiplot
  ☆147Updated last month
• vanheeringen-lab / gimmemotifs
  Suite of motif tools, including a motif prediction pipeline for ChIP-seq experiments. See full GimmeMotifs documentation for detailed in…
  ☆120Updated last year