rna-seq

There are 36 repositories under rna-seq topic.

crazyhottommy / RNA-seq-analysis
RNAseq analysis notes from Ming Tang
rna-seq snakemake
Language:Python 840
nf-core / rnaseq
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
nf-core nextflow workflow rna-seq rna pipeline
Language:Nextflow 785
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++ 734
deeptools / deepTools
Tools to process and analyze deep sequencing data.
python bioinformatics genomics ngs rna-seq chip-seq
Language:Python 651
theislab / single-cell-best-practices
https://www.sc-best-practices.org
book rna-seq single-cell tutorial
Language:Jupyter Notebook 647
pachterlab / kallisto
Near-optimal RNA-Seq quantification
kallisto rna-seq pseudoalignment
Language:C 623
owkin / PyDESeq2
A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.
bioinformatics differential-expression python rna-seq transcriptomics
Language:Python 518
saeyslab / nichenetr
NicheNet: predict active ligand-target links between interacting cells
single-cell-omics intercellular-communication ligand-receptor ligand-target data-integration single-cell-rna-seq rna-seq gene-expression network-inference cell-cell-communication
Language:R 437
agitter / single-cell-pseudotime
An overview of algorithms for estimating pseudotime in single-cell RNA-seq data
bioinformatics pseudotime-algorithms rna-seq single-cell
384
twbattaglia / RNAseq-workflow
A repository for setting up a RNAseq workflow
bioinformatics genes pipeline rna-seq science sequencing workflow
Language:R 382
maxplanck-ie / snakepipes
Customizable workflows based on snakemake and python for the analysis of NGS data
ngs rna-seq chip-seq workflow atac-seq hi-c bisulfite-sequencing snakemake
Language:Python 371
milaboratory / mixcr
MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling.
bioinformatics immunology antibody t-cell-receptor t-cell rep-seq 10x rna-seq sequencing single-cell
Language:Kotlin 310
pachterlab / sleuth
Differential analysis of RNA-Seq
rna-seq
Language:R 300
scRNA-tools / scRNA-tools
Table of software for the analysis of single-cell RNA-seq data.
database rna-seq scrna-seq single-cell single-cell-rna-seq software tools
Language:R 295
sdparekh / zUMIs
zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs
barcodes dge expression fastq pipeline rna-seq rnaseq single-cell umi
Language:R 265
GoekeLab / bioinformatics-workflows
minimal example implementations for bioinformatics workflow managers
bioinformatics workflow-management bioinformatics-workflows pipeline rna-seq workflow
Language:Python 245
kpatel427 / YouTubeTutorials
bioinformatics bioinformatics-analysis rna-seq single-cell tutorials youtube
Language:R 222
suhrig / arriba
Fast and accurate gene fusion detection from RNA-Seq data
gene-fusions rna-seq cancer gene-fusion fusion-gene fusion-genes variant-calling structural-variation star virus-integration
Language:C++ 209
ZJUFanLab / scCATCH
Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
marker-genes cell-markers cluster-annotation seurat single-cell rna-seq transcriptomics sequencing transcriptome
Language:R 203
nf-core / scrnaseq
A single-cell RNAseq pipeline for 10X genomics data
nf-core nextflow workflow pipeline 10x-genomics 10xgenomics alevin bustools cellranger kallisto rna-seq single-cell star-solo
Language:Nextflow 169
dtm2451 / dittoSeq
Color blindness friendly visualization of single-cell and bulk RNA-sequencing data
rna-seq single-cell single-cell-rna-seq visualization color-blindness color-blind
Language:R 167
bambu
GoekeLab / bambu
Reference-guided transcript discovery and quantification for long read RNA-Seq data
bambu transcript-reconstruction transcript-quantification long-reads nanopore-sequencing transcriptomics rna-seq-analysis bioconductor r nanopore rna-seq
Language:R 163
csoneson / ARMOR
Light-weight Snakemake workflow for preprocessing and statistical analysis of RNA-seq data
rna-seq workflow
Language:R 156
COMBINE-lab / alevin-fry
🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.
10x quantification rna-seq rust single-cell single-cell-rna-seq transcriptomics
Language:Rust 153
velocyto-team / velocyto.py
RNA velocity estimation in Python
rna-velocity-estimation rna-seq single-cell
Language:Python 153
zhangyuqing / ComBat-seq
Batch effect adjustment based on negative binomial regression for RNA sequencing count data
batch-effects negative-binomial-regression rna-seq
Language:R 147
seq2science
vanheeringen-lab / seq2science
Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workflows. Works equally easy with public as local data.
snakemake bioinformatics bioinformatics-pipeline atac-seq rna-seq chip-seq reproducible-research ngs pipeline sra workflows fastq
Language:Python 145
sequana / sequana
Sequana: a set of Snakemake NGS pipelines
ngs variant-calling taxonomy de-novo pacbio sequanix snakemake coverage rna-seq
Language:Jupyter Notebook 141
rnaseqc
getzlab / rnaseqc
Fast, efficient RNA-Seq metrics for quality control and process optimization
bioinformatics rna-seq rnaseq
Language:C++ 140
ndaniel / fusioncatcher
Finder of Somatic Fusion Genes in RNA-seq data
fusion-genes rna-seq somatic-fusion-genes
Language:Python 136
kanaverse / kana
Single cell analysis in the browser
bioinformatics cite-seq exploratory-data-analysis interactive-analysis interactive-visualizations rna-seq single-cell webassembly
Language:JavaScript 133
broadinstitute / wot
A software package for analyzing snapshots of developmental processes
single-cell rna-seq time-series trajectory optimal-transport
Language:Jupyter Notebook 132
guma44 / GEOparse
Python library to access Gene Expression Omnibus Database (GEO)
geo-database high-throughput-sequencing htseq microarray bioinformatics rna-sequencing rna-seq
Language:Jupyter Notebook 130
CRG-CNAG / CalliNGS-NF
GATK RNA-Seq Variant Calling in Nextflow
nextflow ngs variant-calling rna-seq gatk bioinformatics genomics
Language:Nextflow 129
nf-core / rnafusion
RNA-seq analysis pipeline for detection of gene-fusions
fusion fusion-genes gene-fusion nextflow nf-core pipeline rna rna-seq workflow
Language:Nextflow 129
xpore
GoekeLab / xpore
Identification of differential RNA modifications from nanopore direct RNA sequencing
rna modification transcriptomics machine-learning genomics nanopore-sequencing rna-seq rna-modifications nanopore python
Language:Python 127

rna-seq

crazyhottommy / RNA-seq-analysis

nf-core / rnaseq

COMBINE-lab / salmon

deeptools / deepTools

theislab / single-cell-best-practices

pachterlab / kallisto

owkin / PyDESeq2

saeyslab / nichenetr

agitter / single-cell-pseudotime

twbattaglia / RNAseq-workflow

maxplanck-ie / snakepipes

milaboratory / mixcr

pachterlab / sleuth

scRNA-tools / scRNA-tools

sdparekh / zUMIs

GoekeLab / bioinformatics-workflows

kpatel427 / YouTubeTutorials

suhrig / arriba

ZJUFanLab / scCATCH

nf-core / scrnaseq

dtm2451 / dittoSeq

GoekeLab / bambu

csoneson / ARMOR

COMBINE-lab / alevin-fry

velocyto-team / velocyto.py

zhangyuqing / ComBat-seq

vanheeringen-lab / seq2science

sequana / sequana

getzlab / rnaseqc

ndaniel / fusioncatcher

kanaverse / kana

broadinstitute / wot

guma44 / GEOparse

CRG-CNAG / CalliNGS-NF

nf-core / rnafusion

GoekeLab / xpore