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.
  ☆258Updated 4 months ago
• deeptools / pyBigWig
  A python extension for quick access to bigWig and bigBed files
  ☆237Updated 10 months ago
• igordot / genomics
  A collection of scripts and notes related to genomics and bioinformatics
  ☆217Updated last month
• open2c / cooltools
  The tools for your .cool's
  ☆157Updated 5 months ago
• wckdouglas / diffexpr
  Porting DESeq2 into python via rpy2
  ☆68Updated 2 years ago
• vanheeringen-lab / seq2science
  Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workf…
  ☆167Updated 2 weeks ago
• hms-dbmi / hic-data-analysis-bootcamp
  Workshop on measuring, analyzing, and visualizing the 3D genome with Hi-C data.
  ☆207Updated 7 years ago
• g2nb / igv-jupyter
  Extension for Jupyter which integrates igv.js
  ☆154Updated 2 years ago
• htseq / htseq
  HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.
  ☆107Updated 6 months ago
• saketkc / pysradb
  Package for fetching metadata and downloading data from SRA/ENA/GEO
  ☆346Updated 2 weeks ago
• mdozmorov / HiC_data
  A (continuously updated) collection of references to Hi-C data. Predominantly human/mouse Hi-C data, with replicates.
  ☆200Updated 5 months ago
• maxplanck-ie / snakepipes
  Customizable workflows based on snakemake and python for the analysis of NGS data
  ☆397Updated last week
• jrderuiter / pybiomart
  A simple pythonic interface to biomart.
  ☆57Updated 5 years ago
• vanheeringen-lab / genomepy
  genes and genomes at your fingertips
  ☆404Updated 2 months ago
• simon-anders / htseq
  HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.
  ☆128Updated 5 years ago
• nf-core / methylseq
  Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
  ☆182Updated this week
• GuyTeichman / RNAlysis
  Analyze your RNA sequencing data without writing a single line of code
  ☆139Updated 6 months ago
• bioinform / somaticseq
  An ensemble approach to accurately detect somatic mutations using SomaticSeq
  ☆201Updated 4 months ago
• daler / pybedtools
  Python wrapper -- and more -- for BEDTools (bioinformatics tools for "genome arithmetic")
  ☆328Updated 8 months ago
• vanheeringen-lab / gimmemotifs
  Suite of motif tools, including a motif prediction pipeline for ChIP-seq experiments. See full GimmeMotifs documentation for detailed in…
  ☆122Updated 2 months ago
• comprna / SUPPA
  SUPPA: Fast quantification of splicing and differential splicing
  ☆287Updated last month
• pachterlab / kallistobustools
  kallisto | bustools workflow for pre-processing single-cell RNA-seq data
  ☆118Updated 3 years ago
• CompEpigen / figeno
  Tool for plotting sequencing data along genomic coordinates.
  ☆322Updated 5 months ago
• ConesaLab / SQANTI3
  Tool for the Quality Control of Long-Read Defined Transcriptomes
  ☆246Updated this week
• ENCODE-DCC / rna-seq-pipeline
  ☆156Updated 3 years ago
• open2c / cooler
  A cool place to store your Hi-C
  ☆230Updated this week
• saketkc / gencode_regions
  Extract 3'UTR, 5'UTR, CDS, Promoter, Genes, Introns, Exons from GTF files
  ☆116Updated 4 years ago
• ablab / IsoQuant
  Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)
  ☆195Updated last week
• haowenz / chromap
  Fast alignment and preprocessing of chromatin profiles
  ☆207Updated 2 months ago
• vaquerizaslab / fanc
  FAN-C: Framework for the ANalysis of C-like data
  ☆120Updated last year