rnaseq

There are 13 repositories under rnaseq topic.

COMBINE-lab / salmon
🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
quasi-mapping bioinformatics rna-seq rnaseq salmon quantification sailfish c-plus-plus gene-expression scrna-seq single-cell 10x selective-alignment rna-seq-quantification single-cell-rna-seq transcriptome
Language:C++ 727
training-material
galaxyproject / training-material
A collection of Galaxy-related training material
usegalaxy training materials ngs tutorial metagenomics proteomics rnaseq chip-seq hacktoberfest
Language:HTML 293
sdparekh / zUMIs
zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs
rnaseq rna-seq single-cell umi expression barcodes fastq dge pipeline
Language:R 263
mikelove / bioc-refcard
Bioconductor cheat sheet
bioconductor bioinformatics r rnaseq compbio guide howto cheatsheet microarray
Language:R 182
rnaseqc
getzlab / rnaseqc
Fast, efficient RNA-Seq metrics for quality control and process optimization
bioinformatics rna-seq rnaseq
Language:C++ 140
thelovelab / tximport
Transcript quantification import for modular pipelines
rnaseq bioconductor deseq2
Language:R 130
RNAlysis
GuyTeichman / RNAlysis
RNA sequencing analysis software
rna-seq rna-seq-analysis rna-seq-pipeline rnaseq bioinformatics bioinformatics-pipeline bioinformatics-tool bioinformatics-analysis transcriptomics smallrna smallrna-seq gui-application
Language:Python 119
nextflow-io / rnaseq-nf
A proof of concept of RNAseq pipeline
nextflow rnaseq genomics
Language:Nextflow 62
SciLifeLab / NGI-RNAseq
Nextflow RNA-Seq Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.
bioinformatics rna-seq rnaseq rna-sequencing pipeline nextflow
Language:Groovy 51
earmingol / cell2cell
User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
bioinformatics rnaseq rna-seq sc-rna-seq single-cell single-cell-rna-seq cell-cell-communication cell-cell-interaction bulk-rna-seq computational-biology machine-learning
Language:Python 49
Russel88 / DAtest
Compare different differential abundance and expression methods
microbiome rnaseq relative-abundances compare-methods differential-abundance-methods otu marker-gene-analysis 16s proteomics metabolomics metagenomics differential-expression auc false-positive-control
Language:R 48
patidarr / ngs_pipeline
Exome/Capture/RNASeq Pipeline Implementation using snakemake
annovar exome fastq gatk ngs ngs-pipeline panel pipeline rnaseq snakemake snpeff tophat
Language:Python 44
lcolladotor / derfinder
Annotation-agnostic differential expression analysis of RNA-seq data via expressed regions-level or single base-level approaches
rstats bioconductor derfinder rnaseq annotation-agnostic r
Language:R 42
leekgroup / recount
R package for the recount2 project. Documentation website: http://leekgroup.github.io/recount/
bioconductor rstats rnaseq derfinder deseq2 count gene exon junction annotation-agnostic illumina human r recount
Language:R 41
aristoteleo / Scribe-py
Regulatory networks with Direct Information in python
rnaseq singlecell network causality velocity slam-seq
Language:Python 38
greenelab / RNAseq_titration_results
Cross-platform normalization enables machine learning model training on microarray and RNA-seq data simultaneously
bioinformatics rnaseq microarray normalization machine-learning cancer supplement analysis gene-expression
Language:HTML 33
nextflow-io / rnatoy
A proof of concept RNA-Seq pipeline with Nextflow
nextflow docker rnaseq rna-seq
Language:Nextflow 32
qbic-pipelines / rnadeseq
Differential gene expression analysis and pathway analysis of RNAseq data
deseq2 nextflow rnaseq pipeline pathway-analysis
Language:Nextflow 32
yyoshiaki / VIRTUS
A bioinformatics pipeline for viral transcriptome detection and quantification considering splicing.
virus-detection rnaseq cwl
Language:Common Workflow Language 32
chanzuckerberg / ExpressionMatrix2
Software for exploration of gene expression data from single-cell RNA sequencing.
clustering locality-sensitive-hashing rnaseq single-cell
Language:C++ 29
LieberInstitute / recount3
Explore and download data from the recount3 project
bioconductor rstats rnaseq derfinder count gene exon junction annotation-agnostic illumina human mouse r recount recount3
Language:R 28
nf-core / rnavar
gatk4 RNA variant calling pipeline
gatk4 nextflow nf-core pipeline rna rnaseq variant-calling worflow workflow
Language:Nextflow 28
Novartis / pisces
PISCES is a pipeline for rapid transcript quantitation, genetic fingerprinting, and quality control assessment of RNAseq libraries using Salmon.
bioinformatics-pipeline rnaseq-pipeline transcriptomics salmon bioinformatics rnaseq
Language:Python 28
amarinderthind / RNA-seq-tutorial-for-gene-differential-expression-analysis
This tutorial is created for educational purpose
rnaseq-pipeline rnaseq rnaseq-workshop deseq2 edger enrichment-analysis bioconductor-packages reactome-pathway pca-analysis rna-seq-dge tutorial gene-expression analysis rna-seq r ngs ngs-analysis
Language:R 26
ICBI / viGEN
viGEN - A bioinformatics pipeline for the exploration of viral RNA in human NGS data
rnaseq virus bacteria bioinformatics r genomics metagenomics viroinformatics
Language:Shell 26
jmw86069 / splicejam
Sashimi plots for RNA-seq data using detected transcripts
rnaseq rstats sashimi sashimi-plot
Language:R 26
ncbi / pm4ngs
Project Manager for NGS data analysis
ngs-analysis ngs-pipeline cwl-workflow bioinformatics next-generation-sequencing rnaseq chipseq chipexo
Language:Python 25
mikelove / alpine
Modeling and correcting fragment sequence bias for RNA-seq
bioconductor rnaseq
Language:R 24
nf-core / scflow
Complete analysis workflow for single-cell/nuclei RNA-sequencing data.
nextflow nf-core pipeline rnaseq single-cell single-nuclei single-nuclei-rna-sequencing workflow
Language:Nextflow 24
thelovelab / fishpond
Differential expression and allelic analysis, nonparametric statistics
rnaseq bioconductor statistics genomics transcriptomics gene-expression salmon scrnaseq
Language:R 24
crazyhottommy / pyflow-RNAseq
RNAseq pipeline based on snakemake
rnaseq snakemake
Language:Python 22
mikelove / deseq2_or_edger
DESeq2 or edgeR
deseq2 rnaseq bioconductor
Language:R 22
BIMSBbioinfo / pigx
Pipelines in genomics
bisulfite-sequencing chipseq dropseq genomics guix rnaseq snakemake
Language:HTML 20
BIMSBbioinfo / pigx_rnaseq
Pipeline for RNAseq
rnaseq pipeline snakemake guix reproducibility
Language:Python 20
sunyumail93 / PipeRNAseq
A comprehensive pipeline for RNAseq data analysis
rnaseq-pipeline transcriptome-analysis bioinformatics rnaseq bioinformatics-analysis bioinformatics-pipeline gene-expression rna rna-seq-analysis rna-sequencing
Language:Shell 19
FNL-MoCha / nextgenseq_pipeline
Exome/Capture/RNASeq Pipeline Implementation using snakemake
wes wgs rnaseq pipeline
Language:Python 18