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
  ☆862Updated last year
• CGATOxford / UMI-tools
  Tools for handling Unique Molecular Identifiers in NGS data sets
  ☆535Updated this week
• macs3-project / MACS
  MACS -- Model-based Analysis of ChIP-Seq
  ☆767Updated 2 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…
  ☆536Updated last week
• deweylab / RSEM
  RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
  ☆459Updated last year
• FelixKrueger / Bismark
  A tool to map bisulfite converted sequence reads and determine cytosine methylation states
  ☆440Updated 5 months ago
• nservant / HiC-Pro
  HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
  ☆429Updated last year
• maxplanck-ie / snakepipes
  Customizable workflows based on snakemake and python for the analysis of NGS data
  ☆396Updated last week
• aidenlab / juicer
  A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
  ☆474Updated 4 months ago
• hbctraining / In-depth-NGS-Data-Analysis-Course
  ☆443Updated 5 years ago
• s-andrews / FastQC
  A quality control analysis tool for high throughput sequencing data
  ☆572Updated 3 weeks ago
• snakemake-workflows / rna-seq-star-deseq2
  RNA-seq workflow using STAR and DESeq2
  ☆351Updated last month
• DaehwanKimLab / hisat2
  Graph-based alignment (Hierarchical Graph FM index)
  ☆522Updated 4 months ago
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆558Updated last year
• gpertea / stringtie
  Transcript assembly and quantification for RNA-Seq
  ☆480Updated last month
• pachterlab / kallisto
  Near-optimal RNA-Seq quantification
  ☆715Updated last week
• lindenb / jvarkit
  Java utilities for Bioinformatics
  ☆515Updated last month
• NBISweden / AGAT
  Another Gtf/Gff Analysis Toolkit https://nbisweden.github.io/AGAT/
  ☆554Updated 2 weeks ago
• broadinstitute / gtex-pipeline
  GTEx & TOPMed data production and analysis pipelines
  ☆393Updated 4 months ago
• crazyhottommy / bioinformatics-one-liners
  Bioinformatics one liners from Ming Tang
  ☆500Updated 5 years ago
• hbctraining / Intro-to-ChIPseq
  Intro to ChIPseq using HPC
  ☆321Updated 3 years ago
• hbctraining / DGE_workshop
  ☆405Updated 4 years ago
• mskcc / vcf2maf
  Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
  ☆409Updated 5 months ago
• ENCODE-DCC / atac-seq-pipeline
  ENCODE ATAC-seq pipeline
  ☆444Updated last year
• dellytools / delly
  DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
  ☆505Updated 2 months ago
• crazyhottommy / ChIP-seq-analysis
  ChIP-seq analysis notes from Ming Tang
  ☆839Updated last year
• gpertea / gffread
  GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more
  ☆451Updated last year
• rvalieris / parallel-fastq-dump
  parallel fastq-dump wrapper
  ☆302Updated 2 years ago
• tanghaibao / jcvi
  Python library to facilitate genome assembly, annotation, and comparative genomics
  ☆886Updated last month
• jorvis / biocode
  Bioinformatics code libraries and scripts
  ☆555Updated 6 months ago