Alternatives and similar repositories for deepTools:

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

• deeptools / pyGenomeTracks
  python module to plot beautiful and highly customizable genome browser tracks
  ☆805Updated 9 months ago
• FelixKrueger / Bismark
  A tool to map bisulfite converted sequence reads and determine cytosine methylation states
  ☆417Updated 2 weeks ago
• deweylab / RSEM
  RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
  ☆438Updated last year
• snakemake-workflows / rna-seq-star-deseq2
  RNA-seq workflow using STAR and DESeq2
  ☆339Updated 9 months ago
• hbctraining / Intro-to-ChIPseq
  Intro to ChIPseq using HPC
  ☆303Updated 2 years ago
• maxplanck-ie / snakepipes
  Customizable workflows based on snakemake and python for the analysis of NGS data
  ☆396Updated last week
• mskcc / vcf2maf
  Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
  ☆386Updated 4 months ago
• aidenlab / juicer
  A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
  ☆439Updated 5 months ago
• FelixKrueger / TrimGalore
  A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS…
  ☆501Updated last month
• crazyhottommy / bioinformatics-one-liners
  Bioinformatics one liners from Ming Tang
  ☆483Updated 4 years ago
• macs3-project / MACS
  MACS -- Model-based Analysis of ChIP-Seq
  ☆735Updated 3 weeks ago
• nservant / HiC-Pro
  HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
  ☆402Updated last year
• CGATOxford / UMI-tools
  Tools for handling Unique Molecular Identifiers in NGS data sets
  ☆508Updated 2 months ago
• ENCODE-DCC / atac-seq-pipeline
  ENCODE ATAC-seq pipeline
  ☆413Updated 9 months ago
• hbctraining / In-depth-NGS-Data-Analysis-Course
  ☆442Updated 4 years ago
• gpertea / stringtie
  Transcript assembly and quantification for RNA-Seq
  ☆433Updated last week
• nf-core / sarek
  Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
  ☆440Updated this week
• Teichlab / scg_lib_structs
  Collections of library structure and sequence of popular single cell genomic methods
  ☆461Updated 4 months ago
• shenlab-sinai / ngsplot
  Quick mining and visualization of NGS data by integrating genomic databases
  ☆264Updated 2 years ago
• igvteam / igv-reports
  Python application to generate self-contained pages embedding IGV visualizations, with no dependency on original input files.
  ☆363Updated 4 months ago
• broadinstitute / gtex-pipeline
  GTEx & TOPMed data production and analysis pipelines
  ☆363Updated 3 months ago
• dpryan79 / ChromosomeMappings
  This repository contains chromosome/contig name mappings between UCSC <-> Ensembl <-> Gencode for a variety of genomes.
  ☆241Updated 2 years ago
• hbctraining / DGE_workshop
  ☆390Updated 3 years ago
• eggnogdb / eggnog-mapper
  Fast genome-wide functional annotation through orthology assignment
  ☆614Updated 11 months ago
• ENCODE-DCC / chip-seq-pipeline2
  ENCODE ChIP-seq pipeline
  ☆265Updated last year
• DaehwanKimLab / hisat2
  Graph-based alignment (Hierarchical Graph FM index)
  ☆499Updated 5 months ago
• dellytools / delly
  DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
  ☆463Updated last week
• rvalieris / parallel-fastq-dump
  parallel fastq-dump wrapper
  ☆292Updated 2 years ago
• Boyle-Lab / Blacklist
  Application for making ENCODE Blacklists
  ☆303Updated 4 years ago
• WGLab / doc-ANNOVAR
  Documentation for the ANNOVAR software
  ☆244Updated last month