Alternatives and similar repositories for genomics

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

• comprna / SUPPA
  SUPPA: Fast quantification of splicing and differential splicing
  ☆279Updated last year
• mhammell-laboratory / TEtranscripts
  A package for including transposable elements in differential enrichment analysis of sequencing datasets.
  ☆259Updated 6 months ago
• Boyle-Lab / Blacklist
  Application for making ENCODE Blacklists
  ☆317Updated 4 years ago
• jsh58 / Genrich
  Detecting sites of genomic enrichment
  ☆193Updated 2 years ago
• ConesaLab / SQANTI3
  Tool for the Quality Control of Long-Read Defined Transcriptomes
  ☆236Updated this week
• nf-core / atacseq
  ATAC-seq peak-calling and QC analysis pipeline
  ☆208Updated last month
• suhrig / arriba
  Fast and accurate gene fusion detection from RNA-Seq data
  ☆245Updated last week
• Xinglab / rmats-turbo
  ☆272Updated 9 months ago
• Magdoll / cDNA_Cupcake
  Miscellaneous collection of Python and R scripts for processing Iso-Seq data
  ☆273Updated last year
• nf-core / methylseq
  Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
  ☆172Updated 2 weeks ago
• rvalieris / parallel-fastq-dump
  parallel fastq-dump wrapper
  ☆298Updated 2 years ago
• bli25 / RSEM_tutorial
  A short tutorial on how to use RSEM
  ☆138Updated 5 years ago
• snakemake-workflows / rna-seq-star-deseq2
  RNA-seq workflow using STAR and DESeq2
  ☆344Updated last year
• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆257Updated 2 years ago
• im3sanger / dndscv
  dN/dS methods to quantify selection in cancer and somatic evolution
  ☆223Updated 3 months ago
• rajewsky-lab / mirdeep2
  Discovering known and novel miRNAs from small RNA sequencing data
  ☆153Updated last year
• rpetit3 / fastq-dl
  Download FASTQ files from SRA or ENA repositories.
  ☆341Updated 2 months ago
• ewels / sra-explorer
  Web application to explore the Sequence Read Archive.
  ☆219Updated last month
• deeptools / HiCExplorer
  HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
  ☆256Updated last month
• shenlab-sinai / ngsplot
  Quick mining and visualization of NGS data by integrating genomic databases
  ☆266Updated 2 years ago
• ENCODE-DCC / rna-seq-pipeline
  ☆154Updated 2 years ago
• nf-core / chipseq
  ChIP-seq peak-calling, QC and differential analysis pipeline.
  ☆218Updated last month
• davidaknowles / leafcutter
  Annotation-free quantification of RNA splicing. Yang I. Li, David A. Knowles, Jack Humphrey, Alvaro N. Barbeira, Scott P. Dickinson, Hae …
  ☆224Updated last year
• GoekeLab / bambu
  Reference-guided transcript discovery and quantification for long read RNA-Seq data
  ☆216Updated last week
• VanLoo-lab / ascat
  ASCAT R package
  ☆186Updated 5 months ago
• al2na / methylKit
  R package for DNA methylation analysis
  ☆234Updated 6 months ago
• PacificBiosciences / IsoSeq
  Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads
  ☆219Updated last month
• getzlab / rnaseqc
  Fast, efficient RNA-Seq metrics for quality control and process optimization
  ☆171Updated 9 months ago
• sdparekh / zUMIs
  zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs
  ☆283Updated last year
• dpryan79 / ChromosomeMappings
  This repository contains chromosome/contig name mappings between UCSC <-> Ensembl <-> Gencode for a variety of genomes.
  ☆243Updated 2 years ago