Alternatives and similar repositories for rnaseq

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

• nerettilab / RepEnrich2
  RepEnrich2 is an updated method to estimate repetitive element enrichment using high-throughput sequencing data.
  ☆41Updated 3 years ago
• nf-core / circdna
  Pipeline for the identification of extrachromosomal circular DNA (ecDNA) from Circle-seq, WGS, and ATAC-seq data that were generated from…
  ☆31Updated 8 months ago
• a2iEditing / RNAEditingIndexer
  A tool for the calculation of RNA-editing index for RNA seq data
  ☆45Updated last month
• gatk-workflows / gatk4-rnaseq-germline-snps-indels
  Workflows for processing RNA data for germline short variant discovery with GATK v4 and related tools
  ☆84Updated 4 years ago
• jsh58 / DMRfinder
  Identifying differentially methylated regions from MethylC-seq (bisulfite-sequencing) data
  ☆28Updated 2 years ago
• parklab / ShatterSeek
  ☆75Updated 2 years ago
• crazyhottommy / pyflow-RNAseq
  RNAseq pipeline based on snakemake
  ☆26Updated 2 years ago
• shimlab / BLAZE
  SingleCell Nanopore sequencing data analysis
  ☆63Updated 8 months ago
• Xinglab / espresso
  ☆64Updated 4 months ago
• BioinfoUNIBA / REDItools
  REDItools are python scripts to investigate RNA editing at genomic scale.
  ☆69Updated 6 months ago
• LosicLab / starchip
  Detection of Circular RNA and Fusions from RNA-Seq
  ☆32Updated 7 years ago
• mdozmorov / RNA-seq_notes
  A continually expanding collection of RNA-seq tools
  ☆53Updated this week
• hartwigmedical / pipeline5
  ☆23Updated 2 months ago
• harbourlab / SparK
  Publication quality NGS track plotting
  ☆117Updated 4 months ago
• mlbendall / telescope
  Quantification of transposable element expression using RNA-seq
  ☆82Updated 2 years ago
• dariober / bioinformatics-cafe
  Unsorted scripts for bioinformatics
  ☆61Updated 4 years ago
• williamritchie / IRFinder
  Detecting intron retention from RNA-Seq experiments
  ☆55Updated last year
• nunofonseca / fastq_utils
  Validation and manipulation of FASTQ files, scRNA-seq barcode pre-processing and UMI quantification.
  ☆37Updated 7 months ago
• YeoLab / outrigger
  Create a *de novo* alternative splicing database, validate splicing events, and quantify percent spliced-in (Psi) from RNA seq data
  ☆67Updated 5 years ago
• TRON-Bioinformatics / EasyFuse
  EasyFuse is a pipeline for accurate fusion gene detection from RNA-seq data.
  ☆64Updated 3 weeks ago
• kundajelab / phantompeakqualtools
  This package computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to…
  ☆62Updated 5 years ago
• kundajelab / 3DChromatin_ReplicateQC
  Software to compute reproducibility and quality scores for Hi-C data
  ☆50Updated 6 years ago
• jlab-code / MethylStar
  A fast and robust pre-processing pipeline for bulk or single-cell whole-genome bisulfite sequencing (WGBS) data.
  ☆37Updated 4 years ago
• hyunhwan-bcm / SalmonTE
  SalmonTE is an ultra-Fast and Scalable Quantification Pipeline of Transpose Element (TE) Abundances
  ☆92Updated 3 years ago
• ygidtu / trackplot
  trackplot is a tool for visualizing various next-generation sequencing (NGS) data, including DNA-seq, RNA-seq, single-cell RNA-seq and fu…
  ☆99Updated 2 months ago
• GooglingTheCancerGenome / sv-callers
  Snakemake-based workflow for detecting structural variants in genomic data
  ☆82Updated 11 months ago
• ucagenomix / sicelore
  Single Cell Long Read is a suite of tools dedicated to Cell barcode / UMI assignment and analysis of highly multiplexed single cell Nanop…
  ☆78Updated 2 years ago
• khuang28jhu / bs3
  BS-Seeker3: An Ultra-fast, Versatile Pipeline for Mapping Bisulfite-treated Reads.
  ☆29Updated 6 years ago
• hamidghaedi / Enrichment-Analysis
  From RNA-seq raw reads to enriched pathways by DEGs
  ☆33Updated last year
• mhammell-laboratory / TElocal
  A package for quantifying transposable elements at a locus level for RNAseq datasets.
  ☆30Updated last week