Alternatives and similar repositories for ffq

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

• snakemake-workflows / rna-seq-star-deseq2
  RNA-seq workflow using STAR and DESeq2
  ☆341Updated 10 months ago
• maxplanck-ie / snakepipes
  Customizable workflows based on snakemake and python for the analysis of NGS data
  ☆397Updated 3 weeks ago
• hbctraining / Intro-to-ChIPseq
  Intro to ChIPseq using HPC
  ☆307Updated 2 years ago
• Boyle-Lab / Blacklist
  Application for making ENCODE Blacklists
  ☆313Updated 4 years ago
• rpetit3 / fastq-dl
  Download FASTQ files from SRA or ENA repositories.
  ☆336Updated this week
• saketkc / pysradb
  Package for fetching metadata and downloading data from SRA/ENA/GEO
  ☆332Updated 4 months ago
• FelixKrueger / Bismark
  A tool to map bisulfite converted sequence reads and determine cytosine methylation states
  ☆424Updated 2 months ago
• 10XGenomics / cellranger
  10x Genomics Single Cell Analysis
  ☆414Updated 4 months ago
• Teichlab / scg_lib_structs
  Collections of library structure and sequence of popular single cell genomic methods
  ☆468Updated last month
• deeptools / pyGenomeTracks
  python module to plot beautiful and highly customizable genome browser tracks
  ☆819Updated 11 months ago
• deweylab / RSEM
  RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
  ☆442Updated last year
• eggnogdb / eggnog-mapper
  Fast genome-wide functional annotation through orthology assignment
  ☆625Updated this week
• hbctraining / Intro-to-DGE
  ☆199Updated 3 months ago
• sdparekh / zUMIs
  zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs
  ☆281Updated 11 months ago
• rvalieris / parallel-fastq-dump
  parallel fastq-dump wrapper
  ☆297Updated 2 years ago
• gpertea / gffread
  GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more
  ☆419Updated 5 months ago
• crazyhottommy / bioinformatics-one-liners
  Bioinformatics one liners from Ming Tang
  ☆485Updated 4 years ago
• hbctraining / DGE_workshop
  ☆392Updated 3 years ago
• nf-core / atacseq
  ATAC-seq peak-calling and QC analysis pipeline
  ☆205Updated 3 weeks ago
• ENCODE-DCC / atac-seq-pipeline
  ENCODE ATAC-seq pipeline
  ☆422Updated 11 months ago
• suhrig / arriba
  Fast and accurate gene fusion detection from RNA-Seq data
  ☆242Updated 2 months ago
• comprna / SUPPA
  SUPPA: Fast quantification of splicing and differential splicing
  ☆275Updated last year
• vanheeringen-lab / genomepy
  genes and genomes at your fingertips
  ☆393Updated last month
• broadinstitute / gtex-pipeline
  GTEx & TOPMed data production and analysis pipelines
  ☆371Updated 3 weeks ago
• thelovelab / DESeq2
  Differential expression of RNA-seq data using the Negative Binomial
  ☆394Updated 2 weeks ago
• pyranges / pyranges
  Performant Pythonic GenomicRanges
  ☆474Updated 3 months ago
• nf-core / sarek
  Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
  ☆451Updated last week
• FelixKrueger / TrimGalore
  A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS…
  ☆510Updated 3 months ago
• nf-core / chipseq
  ChIP-seq peak-calling, QC and differential analysis pipeline.
  ☆215Updated 3 weeks ago
• igordot / genomics
  A collection of scripts and notes related to genomics and bioinformatics
  ☆213Updated 2 months ago