Alternatives and similar repositories for Intro-to-rnaseq-hpc-salmon

Users that are interested in Intro-to-rnaseq-hpc-salmon are comparing it to the libraries listed below

• pachterlab / aggregationDE

  View on GitHub
  Scripts and software supplement for "Gene-level differential analysis at transcript-level resolution" by Yi, Pimentel, Bray and Pachter
  ☆19Feb 20, 2018Updated 7 years ago
• hbctraining / Accessing_public_genomic_data

  View on GitHub
  Tutorials on accessing public reference and genomic data
  ☆30Feb 18, 2025Updated 11 months ago
• hbctraining / bioinformatics_online

  View on GitHub
  Resource list and preparation instructions for online learning and teaching for Bioinformatics
  ☆19Nov 13, 2023Updated 2 years ago
• statOmics / stageR

  View on GitHub
  stageR package
  ☆13Feb 28, 2023Updated 2 years ago
• iobio / clin.iobio

  View on GitHub
  Clin.iobio - Workflow and reporting for iobio variant analysis pipeline
  ☆12Oct 7, 2025Updated 4 months ago
• YeoLab / outrigger

  View on GitHub
  Create a *de novo* alternative splicing database, validate splicing events, and quantify percent spliced-in (Psi) from RNA seq data
  ☆67Apr 10, 2020Updated 5 years ago
• Mangul-Lab-USC / benchmarking_SV

  View on GitHub
  Updated figures for "A benchmarking of WGS-based structural variant callers" paper
  ☆27Apr 3, 2022Updated 3 years ago
• statgen / fastQValidator

  View on GitHub
  Validate FastQ Files
  ☆36Oct 30, 2018Updated 7 years ago
• neurogenomics / EnformerCelltyping

  View on GitHub
  Enformer Celltyping is a tensorflow, multi-headed attention based model that incorporates distal effects of Deoxyribonucleic Acid (DNA) i…
  ☆15Jun 25, 2025Updated 7 months ago
• pachterlab / kallisto-sleuth-workshop-2016

  View on GitHub
  materials and website for the 2016 kallisto sleuth workshop
  ☆11Nov 7, 2016Updated 9 years ago
• xguse / cookiecutter-snakemake-analysis-pipeline

  View on GitHub
  A cookiecutter template that reflects my favored structure for setting up Snakemake-based analysis pipelines.
  ☆16Jul 25, 2016Updated 9 years ago
• UCA-MSI / NiPTUNE

  View on GitHub
  NiPTUNE. A Python library for NIPT analyses.
  ☆12Nov 22, 2021Updated 4 years ago
• raulossio / VCF-plotein

  View on GitHub
  Visualisation and prioritisation of genomic variants from human exome sequencing projects
  ☆13Apr 23, 2019Updated 6 years ago
• ihh / gfftools

  View on GitHub
  Perl scripts for working with the GFF format
  ☆16Aug 24, 2011Updated 14 years ago
• broadinstitute / CODECsuite

  View on GitHub
  analysis pipeline for CODEC data
  ☆13Oct 27, 2025Updated 3 months ago
• hbctraining / In-depth-NGS-Data-Analysis-Course

  View on GitHub
  ☆444Jun 15, 2020Updated 5 years ago
• COMBINE-lab / RapClust

  View on GitHub
  Accurate, Lightweight Clustering of de novo Transcriptomes using Fragment Equivalence Classes
  ☆31Jun 16, 2024Updated last year
• hbctraining / Training-modules

  View on GitHub
  Materials for short, half-day workshops
  ☆346Jan 20, 2026Updated 3 weeks ago
• brentp / seqcover

  View on GitHub
  seqcover allows users to view coverage for hundreds of genes and dozens of samples
  ☆52Apr 9, 2021Updated 4 years ago
• alpreyes / GENAVi

  View on GitHub
  ☆16Apr 29, 2020Updated 5 years ago
• Transipedia / dekupl

  View on GitHub
  Exhaustive capture of biological variation in RNA-seq data through k-mer decomposition.
  ☆15Oct 15, 2018Updated 7 years ago
• chgibb / PHAT

  View on GitHub
  Pathogen-Host Analysis Tool - A modern Next-Generation Sequencing (NGS) analysis platform
  ☆17Dec 12, 2022Updated 3 years ago
• Gaius-Augustus / clamsa

  View on GitHub
  ClaMSA (Classify Multiple Sequence Alignments).
  ☆13Nov 21, 2024Updated last year
• jsalignon / cactus

  View on GitHub
  Chromatin ACcessibility and Transcriptomics Unifying Software
  ☆17Oct 25, 2024Updated last year
• hellosunking / Ktrim

  View on GitHub
  Ktrim: an extra-fast and accurate adapter- and quality-trimmer for sequencing data
  ☆31Feb 7, 2026Updated last week
• NCBI-Hackathons / GoodDoc

  View on GitHub
  A Template for Clear and Simple Documentation of Bioinformatics Code
  ☆16Jan 24, 2018Updated 8 years ago
• NBISweden / nbis-meta

  View on GitHub
  A snakemake workflow for metagenomic projects
  ☆15Feb 16, 2023Updated 2 years ago
• Askarbek-orakov / ASAR

  View on GitHub
  Advanced metagenomic Sequence Analysis in R
  ☆15Aug 17, 2018Updated 7 years ago
• coolbutuseless / ggqr

  View on GitHub
  ggplot2 geom for QR codes
  ☆16Jul 27, 2021Updated 4 years ago
• Picani / fastax

  View on GitHub
  Make phylogenetic trees and lineages from the NCBI Taxonomy database
  ☆14Mar 19, 2023Updated 2 years ago
• amkozlov / cellphy

  View on GitHub
  CellPhy: accurate and fast probabilistic inference of single-cell phylogenies
  ☆20Jan 8, 2026Updated last month
• nuno-agostinho / psichomics

  View on GitHub
  Interactive R package to quantify, analyse and visualise alternative splicing
  ☆37Feb 9, 2026Updated last week
• attayeb / snaq

  View on GitHub
  Qiime2 snakemake pipeline
  ☆20Dec 21, 2023Updated 2 years ago
• gatk-workflows / seq-format-conversion

  View on GitHub
  Workflows for converting between sequence data formats
  ☆40Sep 5, 2021Updated 4 years ago
• rnajena / poseidon

  View on GitHub
  PoSeiDon: positive selection detection and recombination analysis pipeline
  ☆39Sep 22, 2025Updated 4 months ago
• guigolab / geneidx

  View on GitHub
  Nextflow pipeline for genome annotation of protein-coding genes
  ☆16Dec 21, 2023Updated 2 years ago
• philippdre / omniCLIP

  View on GitHub
  omniCLIP is a CLIP-Seq peak caller
  ☆16Nov 14, 2020Updated 5 years ago
• roryk / bcbio.rnaseq

  View on GitHub
  Mostly deprecated in favor of : https://github.com/hbc/bcbioRNASeq. Quality control, differential gene/transcript expression and pathway …
  ☆24Dec 11, 2017Updated 8 years ago
• flemingtonlab / SpliceTools

  View on GitHub
  ☆17Jul 19, 2024Updated last year