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
  ☆294Updated 3 months ago
• mhammell-laboratory / TEtranscripts
  A package for including transposable elements in differential enrichment analysis of sequencing datasets.
  ☆276Updated 3 months ago
• suhrig / arriba
  Fast and accurate gene fusion detection from RNA-Seq data
  ☆259Updated 4 months ago
• jsh58 / Genrich
  Detecting sites of genomic enrichment
  ☆198Updated 2 years ago
• bli25 / RSEM_tutorial
  A short tutorial on how to use RSEM
  ☆138Updated 5 years ago
• rajewsky-lab / mirdeep2
  Discovering known and novel miRNAs from small RNA sequencing data
  ☆158Updated 2 months ago
• ewels / sra-explorer
  Web application to explore the Sequence Read Archive.
  ☆218Updated 6 months ago
• rvalieris / parallel-fastq-dump
  parallel fastq-dump wrapper
  ☆303Updated 2 years ago
• ConesaLab / SQANTI3
  Tool for the Quality Control of Long-Read Defined Transcriptomes
  ☆250Updated this week
• im3sanger / dndscv
  dN/dS methods to quantify selection in cancer and somatic evolution
  ☆231Updated 8 months ago
• nf-core / atacseq
  ATAC-seq peak-calling and QC analysis pipeline
  ☆222Updated 2 months ago
• snakemake-workflows / rna-seq-star-deseq2
  RNA-seq workflow using STAR and DESeq2
  ☆351Updated last month
• Boyle-Lab / Blacklist
  Application for making ENCODE Blacklists
  ☆332Updated 4 years ago
• nloyfer / wgbs_tools
  tools for working with Bisulfite Sequencing data while preserving reads intrinsic dependencies
  ☆178Updated last month
• deeptools / HiCExplorer
  HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
  ☆266Updated 6 months ago
• shenlab-sinai / ngsplot
  Quick mining and visualization of NGS data by integrating genomic databases
  ☆268Updated 2 years ago
• Xinglab / rmats-turbo
  ☆290Updated 3 months ago
• al2na / methylKit
  R package for DNA methylation analysis
  ☆247Updated 3 weeks ago
• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆262Updated 2 years ago
• CompEpigen / figeno
  Tool for plotting sequencing data along genomic coordinates.
  ☆335Updated 2 months ago
• GoekeLab / bambu
  Reference-guided transcript discovery and quantification for long read RNA-Seq data
  ☆224Updated last week
• sdparekh / zUMIs
  zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs
  ☆290Updated last year
• nf-core / chipseq
  ChIP-seq peak-calling, QC and differential analysis pipeline.
  ☆230Updated 2 months ago
• ENCODE-DCC / rna-seq-pipeline
  ☆156Updated 3 years ago
• nf-core / methylseq
  Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark/bwa-meth + MethylDackel or bwa-mem + rastair
  ☆187Updated 2 weeks ago
• saketkc / pysradb
  Package for fetching metadata and downloading data from SRA/ENA/GEO
  ☆348Updated 2 months ago
• Magdoll / cDNA_Cupcake
  Miscellaneous collection of Python and R scripts for processing Iso-Seq data
  ☆278Updated 2 years ago
• yupenghe / methylpy
  WGBS/NOMe-seq Data Processing & Differential Methylation Analysis
  ☆147Updated 2 years ago
• rpetit3 / fastq-dl
  Download FASTQ files from SRA or ENA repositories.
  ☆364Updated last week
• hbctraining / Intro-to-rnaseq-hpc-O2
  This repository has teaching materials for a 2 and 3-day Introduction to RNA-sequencing data analysis workshop using the O2 Cluster
  ☆173Updated 4 years ago