Alternatives and similar repositories for CoolBox:

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

• deeptools / HiCExplorer
  HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
  ☆237Updated 2 months ago
• ablab / IsoQuant
  Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)
  ☆155Updated last week
• open2c / cooltools
  The tools for your .cool's
  ☆144Updated 3 months ago
• htseq / htseq
  HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.
  ☆99Updated 3 months ago
• deeptools / pyBigWig
  A python extension for quick access to bigWig and bigBed files
  ☆224Updated 3 weeks ago
• comprna / SUPPA
  SUPPA: Fast quantification of splicing and differential splicing
  ☆268Updated 7 months ago
• igordot / genomics
  A collection of scripts and notes related to genomics and bioinformatics
  ☆204Updated this week
• ConesaLab / SQANTI3
  Tool for the Quality Control of Long-Read Defined Transcriptomes
  ☆206Updated this week
• haowenz / chromap
  Fast alignment and preprocessing of chromatin profiles
  ☆196Updated 2 months ago
• hms-dbmi / hic-data-analysis-bootcamp
  Workshop on measuring, analyzing, and visualizing the 3D genome with Hi-C data.
  ☆194Updated 6 years ago
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆538Updated 7 months ago
• nf-core / methylseq
  Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
  ☆157Updated last week
• saketkc / pysradb
  Package for fetching metadata and downloading data from SRA/ENA/GEO
  ☆320Updated 3 months ago
• Boyle-Lab / Blacklist
  Application for making ENCODE Blacklists
  ☆288Updated 3 years ago
• simon-anders / htseq
  HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.
  ☆123Updated 4 years ago
• sequana / sequana
  Sequana: a set of Snakemake NGS pipelines
  ☆145Updated this week
• g2nb / igv-jupyter
  Extension for Jupyter which integrates igv.js
  ☆153Updated 2 years ago
• nservant / HiC-Pro
  HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
  ☆394Updated 10 months ago
• mhammell-laboratory / TEtranscripts
  A package for including transposable elements in differential enrichment analysis of sequencing datasets.
  ☆240Updated last week
• akdemirlab / HiCPlotter
  “When everything is connected to everything else, for better or worse, everything matters.” Bruce Mau
  ☆183Updated 4 years ago
• davidaknowles / leafcutter
  Annotation-free quantification of RNA splicing. Yang I. Li, David A. Knowles, Jack Humphrey, Alvaro N. Barbeira, Scott P. Dickinson, Hae …
  ☆212Updated 8 months ago
• mdozmorov / HiC_data
  A (continuously updated) collection of references to Hi-C data. Predominantly human/mouse Hi-C data, with replicates.
  ☆181Updated 3 weeks ago
• gpertea / gffcompare
  classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF
  ☆211Updated 7 months ago
• pyranges / pyranges
  Performant Pythonic GenomicRanges
  ☆453Updated 8 months ago
• nextflow-io / training
  Nextflow training material
  ☆140Updated this week
• gosling-lang / gos
  A declarative interactive genomics visualization library for Python.
  ☆222Updated 3 weeks ago
• GoekeLab / sg-nex-data
  Nanopore RNA-Seq data from the Singapore Nanopore-Expression Project
  ☆115Updated last month
• nf-core / hic
  Analysis of Chromosome Conformation Capture data (Hi-C)
  ☆95Updated 2 weeks ago
• PacificBiosciences / IsoSeq
  Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads
  ☆202Updated 3 months ago
• open2c / bioframe
  Genomic interval operations on Pandas DataFrames
  ☆177Updated this week