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
  ☆348Updated last week
• saketkc / pysradb
  Package for fetching metadata and downloading data from SRA/ENA/GEO
  ☆347Updated 3 weeks ago
• maxplanck-ie / snakepipes
  Customizable workflows based on snakemake and python for the analysis of NGS data
  ☆397Updated last week
• Teichlab / scg_lib_structs
  Collections of library structure and sequence of popular single cell genomic methods
  ☆486Updated 6 months ago
• hbctraining / DGE_workshop
  ☆403Updated 3 years ago
• crazyhottommy / bioinformatics-one-liners
  Bioinformatics one liners from Ming Tang
  ☆499Updated 5 years ago
• 10XGenomics / cellranger
  10x Genomics Single Cell Analysis
  ☆437Updated 10 months ago
• deeptools / pyGenomeTracks
  python module to plot beautiful and highly customizable genome browser tracks
  ☆851Updated last year
• rvalieris / parallel-fastq-dump
  parallel fastq-dump wrapper
  ☆301Updated 2 years ago
• CGATOxford / UMI-tools
  Tools for handling Unique Molecular Identifiers in NGS data sets
  ☆533Updated 5 months ago
• pyranges / pyranges
  Performant Pythonic GenomicRanges
  ☆491Updated last month
• rpetit3 / fastq-dl
  Download FASTQ files from SRA or ENA repositories.
  ☆350Updated this week
• thelovelab / DESeq2
  Differential expression of RNA-seq data using the Negative Binomial
  ☆426Updated last week
• Boyle-Lab / Blacklist
  Application for making ENCODE Blacklists
  ☆329Updated 4 years ago
• gpertea / gffread
  GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more
  ☆445Updated 11 months ago
• FelixKrueger / Bismark
  A tool to map bisulfite converted sequence reads and determine cytosine methylation states
  ☆438Updated 4 months ago
• hbctraining / Intro-to-ChIPseq
  Intro to ChIPseq using HPC
  ☆317Updated 2 years ago
• hbctraining / Intro-to-DGE
  ☆211Updated 3 months ago
• vanheeringen-lab / genomepy
  genes and genomes at your fingertips
  ☆404Updated 2 months ago
• broadinstitute / gtex-pipeline
  GTEx & TOPMed data production and analysis pipelines
  ☆390Updated 2 months ago
• j-andrews7 / awesome-bioinformatics-benchmarks
  A curated and summarized list of bioinformatics bench-marking papers and resources.
  ☆349Updated last month
• deweylab / RSEM
  RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
  ☆456Updated last year
• deeptools / deepTools
  Tools to process and analyze deep sequencing data.
  ☆747Updated 4 months ago
• CompEpigen / figeno
  Tool for plotting sequencing data along genomic coordinates.
  ☆322Updated 5 months ago
• ENCODE-DCC / atac-seq-pipeline
  ENCODE ATAC-seq pipeline
  ☆437Updated last year
• mdozmorov / HiC_tools
  A collection of tools for Hi-C data analysis
  ☆626Updated last month
• FelixKrueger / TrimGalore
  A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS…
  ☆533Updated 3 months ago
• nf-core / sarek
  Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
  ☆505Updated last week
• milaboratory / mixcr
  MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling.
  ☆378Updated 2 weeks ago
• Xinglab / rmats-turbo
  ☆282Updated last month