rnaseq

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COMBINE-lab /salmon

Star795

🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment

c-plus-plus bioinformatics rna-seq gene-expression rnaseq scrna-seq quantification transcriptome single-cell quasi-mapping salmon sailfish 10x single-cell-rna-seq selective-alignment rna-seq-quantification

UpdatedMay 29, 2024
C++

galaxyproject /training-material

Star328

A collection of Galaxy-related training material

training tutorial materials ngs metagenomics rnaseq proteomics chip-seq usegalaxy hacktoberfest

UpdatedMar 20, 2025
HTML

sdparekh /zUMIs

Star278

zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs

rna-seq pipeline expression rnaseq umi single-cell fastq barcodes dge

UpdatedJul 12, 2024
R

mikelove /bioc-refcard

Star187

Bioconductor cheat sheet

bioinformatics r howto guide cheatsheet bioconductor rnaseq compbio microarray

UpdatedAug 26, 2024
HTML

getzlab /rnaseqc

Star159

Fast, efficient RNA-Seq metrics for quality control and process optimization

bioinformatics rna-seq rnaseq

UpdatedNov 2, 2024
C++

thelovelab /tximport

Star137

Transcript quantification import for modular pipelines

bioconductor rnaseq deseq2

UpdatedMar 23, 2024
R

GuyTeichman /RNAlysis

Sponsor

Star131

Analyze your RNA sequencing data without writing a single line of code

bioinformatics rna-seq gui-application bioinformatics-pipeline rnaseq transcriptomics rna-seq-analysis bioinformatics-analysis smallrna rna-seq-pipeline bioinformatics-tool smallrna-seq

UpdatedJan 30, 2025
Python

helicalAI /helical

Star102

This repository contains the python package for Helical

data bioinformatics rna-seq deep-learning biology gene-expression vcf artificial-intelligence transformer neural-networks rnaseq dna-sequences uce pre-training pre-trained-model foundation-models evo-2 scgpt geneformer

UpdatedMar 7, 2025
Python

nextflow-io /rnaseq-nf

Star76

A proof of concept of RNAseq pipeline

genomics nextflow rnaseq

UpdatedNov 8, 2024
Nextflow

genome /bfx-workshop

Star66

A course on genomics and bioinformatics from WU

bioinformatics dataviz genomics analysis biology sequencing dna alignment rnaseq rna single-cell atacseq scrna chipseq

UpdatedMar 18, 2025
HTML

earmingol /cell2cell

Star59

User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins

machine-learning bioinformatics rna-seq computational-biology rnaseq single-cell single-cell-rna-seq bulk-rna-seq sc-rna-seq cell-cell-interaction cell-cell-communication

UpdatedJun 14, 2024
Python

cantinilab /scPRINT

Star56

single cell foundation model for Gene network inference and more

open-source embeddings rnaseq zero-shot-learning denoising single-cell-rna-seq cell-biology batch-correction gene-regulatory-network celltype-annotation large-language-models llms large-cell-models zero-imputation

UpdatedMar 20, 2025
Jupyter Notebook

SciLifeLab /NGI-RNAseq

Star51

Nextflow RNA-Seq Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.

bioinformatics rna-seq pipeline nextflow rnaseq rna-sequencing

UpdatedAug 20, 2018
Groovy

Russel88 /DAtest

Star51

Compare different differential abundance and expression methods

metagenomics rnaseq auc proteomics metabolomics microbiome false-positive-control differential-expression 16s otu marker-gene-analysis relative-abundances compare-methods differential-abundance-methods

UpdatedMar 8, 2022
R

patidarr /ngs_pipeline

Star45

Exome/Capture/RNASeq Pipeline Implementation using snakemake

snakemake pipeline panel ngs tophat gatk rnaseq fastq exome ngs-pipeline annovar snpeff

UpdatedMar 26, 2018
Python

nf-core /rnavar

Star44

gatk4 RNA variant calling pipeline

workflow pipeline nextflow rnaseq rna variant-calling nf-core gatk4 worflow

UpdatedMar 17, 2025
Nextflow

lcolladotor /derfinder

Sponsor

Star43

Annotation-agnostic differential expression analysis of RNA-seq data via expressed regions-level or single base-level approaches

r rstats bioconductor rnaseq derfinder annotation-agnostic

UpdatedDec 13, 2024
R

leekgroup /recount

Star41

R package for the recount2 project. Documentation website:http://leekgroup.github.io/recount/

count gene r human rstats bioconductor rnaseq deseq2 illumina exon junction derfinder annotation-agnostic recount

UpdatedDec 12, 2024
R

aristoteleo /Scribe-py

Star40

Regulatory networks with Direct Information in python

network velocity rnaseq causality singlecell slam-seq

UpdatedMar 9, 2023
Python

greenelab /RNAseq_titration_results

Star35

Cross-platform normalization enables machine learning model training on microarray and RNA-seq data simultaneously

machine-learning bioinformatics analysis cancer gene-expression rnaseq microarray normalization supplement

UpdatedMar 20, 2023
HTML

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