Alternatives and similar repositories for genomics:

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

• mhammell-laboratory / TEtranscripts
  A package for including transposable elements in differential enrichment analysis of sequencing datasets.
  ☆246Updated 2 months ago
• comprna / SUPPA
  SUPPA: Fast quantification of splicing and differential splicing
  ☆274Updated 9 months ago
• ConesaLab / SQANTI3
  Tool for the Quality Control of Long-Read Defined Transcriptomes
  ☆217Updated 2 weeks ago
• im3sanger / dndscv
  dN/dS methods to quantify selection in cancer and somatic evolution
  ☆220Updated 2 weeks ago
• Boyle-Lab / Blacklist
  Application for making ENCODE Blacklists
  ☆296Updated 3 years ago
• ewels / sra-explorer
  Web application to explore the Sequence Read Archive.
  ☆216Updated 2 weeks ago
• snakemake-workflows / rna-seq-star-deseq2
  RNA-seq workflow using STAR and DESeq2
  ☆338Updated 8 months ago
• FredHutch / SEACR
  SEACR: Sparse Enrichment Analysis for CUT&RUN
  ☆109Updated 2 years ago
• bli25 / RSEM_tutorial
  A short tutorial on how to use RSEM
  ☆136Updated 4 years ago
• jsh58 / Genrich
  Detecting sites of genomic enrichment
  ☆189Updated last year
• rvalieris / parallel-fastq-dump
  parallel fastq-dump wrapper
  ☆290Updated last year
• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆251Updated last year
• shenlab-sinai / ngsplot
  Quick mining and visualization of NGS data by integrating genomic databases
  ☆264Updated last year
• Magdoll / cDNA_Cupcake
  Miscellaneous collection of Python and R scripts for processing Iso-Seq data
  ☆265Updated last year
• rpetit3 / fastq-dl
  Download FASTQ files from SRA or ENA repositories.
  ☆319Updated 3 weeks ago
• rajewsky-lab / mirdeep2
  Discovering known and novel miRNAs from small RNA sequencing data
  ☆147Updated 7 months ago
• PacificBiosciences / IsoSeq
  Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads
  ☆210Updated this week
• zhxiaokang / RASflow
  RNA-Seq analysis workflow
  ☆104Updated 3 years ago
• suhrig / arriba
  Fast and accurate gene fusion detection from RNA-Seq data
  ☆235Updated 3 weeks ago
• ENCODE-DCC / rna-seq-pipeline
  ☆148Updated 2 years ago
• nf-core / atacseq
  ATAC-seq peak-calling and QC analysis pipeline
  ☆200Updated last month
• GoekeLab / bambu
  Reference-guided transcript discovery and quantification for long read RNA-Seq data
  ☆206Updated last week
• nf-core / methylseq
  Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
  ☆165Updated this week
• gpertea / gffcompare
  classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF
  ☆215Updated 9 months ago
• vanheeringen-lab / seq2science
  Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workf…
  ☆156Updated last year
• davidaknowles / leafcutter
  Annotation-free quantification of RNA splicing. Yang I. Li, David A. Knowles, Jack Humphrey, Alvaro N. Barbeira, Scott P. Dickinson, Hae …
  ☆213Updated 10 months ago
• ENCODE-DCC / chip-seq-pipeline
  ENCODE Uniform processing pipeline for ChIP-seq
  ☆123Updated 5 years ago
• signalbash / how_are_we_stranded_here
  Check strandedness of RNA-Seq fastq files
  ☆122Updated 2 years ago
• yupenghe / methylpy
  WGBS/NOMe-seq Data Processing & Differential Methylation Analysis
  ☆140Updated last year
• VanLoo-lab / ascat
  ASCAT R package
  ☆179Updated 3 weeks ago