Search Results - RepositoryStats

75

1.0k

bsd-2-clause

8

🧬 gget enables efficient querying of genomic reference databases

gget ncbi blast archs4 enrichr ensembl rna-seq uniprot genomics alphafold databases reference alphafold2 proteomics transcriptomics enrichment-analysis

Created 2022-05-04

2,890 commits to main branch, last one a day ago

rnaseq nf-core

746

1.0k

mit

177

RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

rna nf-core rna-seq nextflow pipeline workflow

Created 2018-03-29

5,806 commits to master branch, last one 3 months ago

RNA-seq-analysis crazyhottommy

309

992

mit

78

RNAseq analysis notes from Ming Tang

rna-seq snakemake

Created 2015-08-26

322 commits to master branch, last one 3 years ago

single-cell-best-practices theislab

207

870

other

17

https://www.sc-best-practices.org

book rna-seq tutorial single-cell

Created 2021-08-13

676 commits to main branch, last one 8 hours ago

salmon COMBINE-lab

166

799

gpl-3.0

37

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

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

Created 2015-03-19

1,907 commits to master branch, last one about a year ago

deepTools deeptools

217

709

other

41

Tools to process and analyze deep sequencing data.

ngs python rna-seq chip-seq genomics bioinformatics

Created 2013-07-08

3,515 commits to master branch, last one 2 months ago

kallisto pachterlab

173

673

bsd-2-clause

47

Near-optimal RNA-Seq quantification

rna-seq kallisto pseudoalignment

Created 2014-11-13

1,401 commits to master branch, last one 6 months ago

PyDESeq2 owkin

71

633

mit

11

A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.

python rna-seq bioinformatics transcriptomics differential-expression

Created 2022-11-22

347 commits to main branch, last one 7 days ago

nichenetr saeyslab

121

526

unknown

13

NicheNet: predict active ligand-target links between interacting cells

rna-seq ligand-target gene-expression ligand-receptor data-integration network-inference single-cell-omics single-cell-rna-seq cell-cell-communication intercellular-communication

Created 2018-02-05

495 commits to master branch, last one 6 months ago

single-cell-pseudotime agitter

62

421

cc-by-4.0

32

An overview of algorithms for estimating pseudotime in single-cell RNA-seq data

rna-seq single-cell bioinformatics pseudotime-algorithms

Created 2016-06-25

278 commits to master branch, last one 13 days ago

snakepipes maxplanck-ie

87

395

unknown

20

Customizable workflows based on snakemake and python for the analysis of NGS data

ngs hi-c rna-seq atac-seq chip-seq workflow snakemake bisulfite-sequencing

Created 2016-03-23

4,059 commits to master branch, last one 5 months ago

mixcr milaboratory

80

346

other

29

MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling.

10x t-cell rep-seq rna-seq antibody immunology sequencing single-cell bioinformatics t-cell-receptor

Created 2015-03-30

4,002 commits to develop branch, last one 18 hours ago

scRNA-tools scRNA-tools

76

317

mit

20

Table of software for the analysis of single-cell RNA-seq data.

tools rna-seq database software scrna-seq single-cell single-cell-rna-seq

Created 2016-09-09

3,669 commits to main branch, last one 24 days ago

YouTubeTutorials kpatel427

139

312

mit

10

This repository has no description...

rna-seq youtube tutorials single-cell bioinformatics bioinformatics-analysis

Created 2021-11-29

119 commits to main branch, last one 6 months ago

sleuth pachterlab

95

304

gpl-3.0

38

Differential analysis of RNA-Seq

rna-seq

Created 2015-02-13

661 commits to master branch, last one 2 years ago

zUMIs sdparekh

69

278

gpl-3.0

12

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

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

Created 2017-06-20

291 commits to main branch, last one 2 years ago

bioinformatics-workflows GoekeLab

47

271

mit

10

minimal example implementations for bioinformatics workflow managers

rna-seq pipeline workflow bioinformatics workflow-management bioinformatics-workflows

Created 2020-09-14

142 commits to master branch, last one 3 years ago

scrnaseq nf-core

187

261

mit

156

Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-droplet detection

alevin nf-core rna-seq bustools kallisto nextflow pipeline workflow star-solo cellranger 10xgenomics single-cell 10x-genomics

Created 2019-04-08

1,761 commits to master branch, last one 21 days ago

arriba suhrig

52

235

other

12

Fast and accurate gene fusion detection from RNA-Seq data

star cancer rna-seq fusion-gene gene-fusion fusion-genes gene-fusions variant-calling virus-integration structural-variation

Created 2017-10-23

724 commits to master branch, last one 6 days ago

scCATCH ZJUFanLab

37

226

gpl-3.0

5

Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data

seurat rna-seq sequencing single-cell cell-markers marker-genes transcriptome transcriptomics cluster-annotation

Created 2019-08-06

118 commits to master branch, last one about a year ago

bambu GoekeLab

24

204

gpl-3.0

6

Reference-guided transcript discovery and quantification for long read RNA-Seq data

r bambu rna-seq nanopore long-reads bioconductor transcriptomics rna-seq-analysis nanopore-sequencing transcript-quantification transcript-reconstruction

Created 2020-02-07

2,175 commits to devel branch, last one about a month ago

dittoSeq dtm2451

18

197

mit

4

Color blindness friendly visualization of single-cell and bulk RNA-sequencing data

rna-seq color-blind single-cell visualization color-blindness single-cell-rna-seq

Created 2019-02-18

828 commits to devel branch, last one 11 months ago

alevin-fry COMBINE-lab

16

178

bsd-3-clause

9

🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.

10x rust rna-seq single-cell quantification transcriptomics single-cell-rna-seq

Created 2020-07-15

842 commits to master branch, last one 29 days ago

velocyto.py velocyto-team

86

165

bsd-2-clause

12

RNA velocity estimation in Python

rna-seq single-cell rna-velocity-estimation

Created 2017-10-17

303 commits to master branch, last one 6 years ago

ARMOR csoneson

33

162

mit

14

Light-weight Snakemake workflow for preprocessing and statistical analysis of RNA-seq data

rna-seq workflow

Created 2017-09-15

653 commits to master branch, last one 3 months ago

IsoQuant ablab

15

161

other

12

Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)

ngs pacbio rna-seq nanopore bioinformatics transcriptomics

Created 2020-04-15

1,401 commits to master branch, last one 2 months ago

rnaseqc getzlab

19

160

other

10

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

rnaseq rna-seq bioinformatics

Created 2017-08-10

410 commits to master branch, last one 5 months ago

seq2science vanheeringen-lab

28

156

mit

4

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.

ngs sra fastq rna-seq atac-seq chip-seq pipeline snakemake workflows bioinformatics reproducible-research bioinformatics-pipeline

Created 2019-07-11

1,483 commits to master branch, last one about a year ago

rnafusion nf-core

108

151

mit

168

RNA-seq analysis pipeline for detection of gene-fusions

rna fusion nf-core rna-seq nextflow pipeline workflow gene-fusion fusion-genes

Created 2018-10-05

1,913 commits to master branch, last one 2 months ago

GEOparse guma44

50

151

bsd-3-clause

7

Python library to access Gene Expression Omnibus Database (GEO)

htseq rna-seq microarray geo-database bioinformatics rna-sequencing high-throughput-sequencing

Created 2015-08-16

238 commits to master branch, last one 11 months ago