Alternatives and similar repositories for snakepipes

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

• snakemake-workflows / rna-seq-star-deseq2
  RNA-seq workflow using STAR and DESeq2
  ☆342Updated 11 months ago
• saketkc / pysradb
  Package for fetching metadata and downloading data from SRA/ENA/GEO
  ☆335Updated 3 weeks ago
• Boyle-Lab / Blacklist
  Application for making ENCODE Blacklists
  ☆313Updated 4 years ago
• rvalieris / parallel-fastq-dump
  parallel fastq-dump wrapper
  ☆298Updated 2 years ago
• hbctraining / Intro-to-ChIPseq
  Intro to ChIPseq using HPC
  ☆309Updated 2 years ago
• broadinstitute / gtex-pipeline
  GTEx & TOPMed data production and analysis pipelines
  ☆374Updated last month
• nservant / HiC-Pro
  HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
  ☆412Updated last year
• CGATOxford / UMI-tools
  Tools for handling Unique Molecular Identifiers in NGS data sets
  ☆515Updated this week
• comprna / SUPPA
  SUPPA: Fast quantification of splicing and differential splicing
  ☆276Updated last year
• FelixKrueger / Bismark
  A tool to map bisulfite converted sequence reads and determine cytosine methylation states
  ☆425Updated 2 months ago
• pachterlab / ffq
  A tool to find sequencing data and metadata from public databases.
  ☆580Updated 11 months ago
• sdparekh / zUMIs
  zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs
  ☆281Updated last year
• nf-core / chipseq
  ChIP-seq peak-calling, QC and differential analysis pipeline.
  ☆216Updated this week
• gpertea / gffread
  GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more
  ☆422Updated 6 months ago
• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆254Updated 2 years ago
• ENCODE-DCC / chip-seq-pipeline2
  ENCODE ChIP-seq pipeline
  ☆270Updated last year
• igordot / genomics
  A collection of scripts and notes related to genomics and bioinformatics
  ☆214Updated 3 months ago
• nf-core / atacseq
  ATAC-seq peak-calling and QC analysis pipeline
  ☆206Updated this week
• deweylab / RSEM
  RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
  ☆444Updated last year
• suhrig / arriba
  Fast and accurate gene fusion detection from RNA-Seq data
  ☆244Updated 3 months ago
• Magdoll / cDNA_Cupcake
  Miscellaneous collection of Python and R scripts for processing Iso-Seq data
  ☆271Updated last year
• shenlab-sinai / ngsplot
  Quick mining and visualization of NGS data by integrating genomic databases
  ☆267Updated 2 years ago
• vanheeringen-lab / genomepy
  genes and genomes at your fingertips
  ☆393Updated 2 months ago
• Teichlab / scg_lib_structs
  Collections of library structure and sequence of popular single cell genomic methods
  ☆471Updated last month
• igvteam / igv-reports
  Python application to generate self-contained pages embedding IGV visualizations, with no dependency on original input files.
  ☆369Updated 3 weeks ago
• pyranges / pyranges
  Performant Pythonic GenomicRanges
  ☆477Updated 4 months ago
• hbctraining / Intro-to-DGE
  ☆202Updated 3 months ago
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆544Updated last year
• mhammell-laboratory / TEtranscripts
  A package for including transposable elements in differential enrichment analysis of sequencing datasets.
  ☆254Updated 5 months ago
• ENCODE-DCC / atac-seq-pipeline
  ENCODE ATAC-seq pipeline
  ☆424Updated 11 months ago