Search Results - RepositoryStats

scanpy scverse

622

2.1k

bsd-3-clause

48

Single-cell analysis in Python. Scales to >100M cells.

python scanpy anndata scverse data-science bioinformatics visualize-data transcriptomics machine-learning

Created 2017-01-29

3,563 commits to main branch, last one 3 days ago

gget pachterlab

76

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

2,905 commits to main branch, last one 7 days ago

cellxgene chanzuckerberg

132

667

mit

33

An interactive explorer for single-cell transcriptomics data

dataviz scrna-seq scientific visualization transcriptomics

Created 2017-10-03

1,577 commits to main branch, last one 7 months ago

PyDESeq2 owkin

74

640

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

349 commits to main branch, last one 6 days ago

anndata scverse

162

614

bsd-3-clause

12

Annotated data.

scanpy anndata scverse data-science bioinformatics transcriptomics machine-learning

Created 2017-08-11

1,505 commits to main branch, last one 2 days ago

pySCENIC aertslab

188

494

gpl-3.0

18

pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regula...

single-cell transcriptomics transcription-factors gene-regulatory-network

Created 2018-03-07

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

PathomicFusion mahmoodlab

85

301

gpl-3.0

13

Fusing Histology and Genomics via Deep Learning - IEEE TMI

fusion genomics pathomic pathology mahmoodlab multimodal histopathology transcriptomics multimodal-network computational-pathogenomics

Created 2019-12-14

46 commits to master branch, last one 2 years ago

scgen theislab

58

289

gpl-3.0

8

Single cell perturbation prediction

scrna-seq single-cell deep-learning bioinformatics transcriptomics generative-model single-cell-genomics

Created 2018-11-28

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

cobratoolbox opencobra

323

261

other

32

The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:

cobra tutorial gap-filling metabolomics cobra-toolbox reconstruction transcriptomics human-metabolism metabolic-models strain-engineering microbiome-analysis metabolic-engineering omics-data-integration metabolic-reconstruction constraint-based-modeling

Created 2012-11-02

9,538 commits to master branch, last one 13 days ago

starfish spacetx

68

232

mit

18

starfish: unified pipelines for image-based transcriptomics

python imaging transcriptomics human-cell-atlas

Created 2017-05-26

1,458 commits to master branch, last one 18 days ago

pagoda2 kharchenkolab

47

227

unknown

15

R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets

scrna-seq single-cell transcriptomics single-cell-rna-seq

Created 2017-04-25

1,483 commits to main branch, last one about a year 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

iSEE iSEE

43

225

other

16

R/shiny interface for interactive visualization of data in SummarizedExperiment objects

gui shiny clustering single-cell hacktoberfest visualization gene-expression transcriptomics human-cell-atlas feature-extraction dimension-reduction

Created 2017-12-06

3,253 commits to devel branch, last one 7 hours ago

bambu GoekeLab

24

206

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 2 months ago

diffxpy theislab

23

197

bsd-3-clause

6

Differential expression analysis for single-cell RNA-seq data.

tensorflow bioinformatics transcriptomics gene-set-enrichment single-cell-rna-seq differential-expression

Created 2018-07-02

478 commits to master branch, last one about a month ago

decoupler-py saezlab

28

189

gpl-3.0

5

Python package to perform enrichment analysis from omics data.

numba python enrichment single-cell data-science bioinformatics transcriptomics enrichment-analysis spatial-transcriptomics

Created 2021-11-16

643 commits to main branch, last one 2 months ago

awesome-biological-visualizations keller-mark

16

188

cc0-1.0

4

A list of web-based interactive biological data visualizations.

cancer awesome biology genomics medicine awesome-list visualization transcriptomics data-visualization

Created 2018-05-27

77 commits to main branch, last one 4 years ago

alevin-fry COMBINE-lab

16

181

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 about a month ago

scde hms-dbmi

66

174

other

23

R package for analyzing single-cell RNA-seq data

r ngs analysis single-cell heterogenity bioinformatics transcriptomics

Created 2015-05-06

157 commits to main branch, last one about a year ago

tidybulk stemangiola

24

171

unknown

5

Brings bulk and pseudobulk transcriptomics to the tidyverse

Created 2019-08-28

1,508 commits to master branch, last one 7 days ago

cell-ontology obophenotype

53

168

cc-by-4.0

23

An ontology of cell types

owl anatomy metazoa genomics ontology cell-types obofoundry semantic-web cell-ontology transcriptomics anatomy-ontology monarchinitiative

Created 2015-06-04

4,164 commits to master branch, last one 3 days ago

IsoQuant ablab

15

162

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 3 months ago

xpore GoekeLab

23

147

mit

8

Identification of differential RNA modifications from nanopore direct RNA sequencing

rna python rna-seq genomics nanopore modification transcriptomics machine-learning rna-modifications nanopore-sequencing

Created 2020-01-06

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

DNAnalyzer VerisimilitudeX

62

144

other

8

Democratizing on-device AI-powered DNA analysis for everyone, everywhere

dna genomics bioinformatics dna-sequencing transcriptomics machine-learning regulatory-elements computational-biology artificial-intelligence

Created 2022-07-31

1,547 commits to main branch, last one 6 hours ago

pandora genular

21

136

other

9

PANDORA :computer:

tsne umap pandora biomarkers clustering microbiome data-mining data-science clinical-data bioinformatics drug-discovery systems-biology transcriptomics data-integration machine-learning data-visualization predictive-analytics genomic-data-analysis unsupervised-machine-learning

Created 2018-07-03

1,637 commits to master branch, last one 10 days ago

RNAlysis GuyTeichman

13

132

mit

4

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

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

Created 2019-06-20

3,425 commits to master branch, last one 2 months ago

sg-nex-data GoekeLab

25

127

unknown

6

Nanopore RNA-Seq data from the Singapore Nanopore-Expression Project

rna-seq nanopore long-reads transcriptomics direct-rna-sequencing

Created 2019-02-28

303 commits to master branch, last one 2 months ago

Pando quadbio

22

120

mit

5

Multiome GRN inference.

epigenomics single-cell transcriptomics

Created 2021-06-08

354 commits to main branch, last one 12 months ago

scrattch.hicat AllenInstitute

31

110

other

14

Hierarchical, iterative clustering for analysis of transcriptomics data in R

r wgcna jaccard clustering transcriptomics

Created 2018-01-15

406 commits to master branch, last one 10 months ago

scDeepSort ZJUFanLab

19

103

gpl-3.0

5

Cell-type Annotation for Single-cell Transcriptomics using Deep Learning with a Weighted Graph Neural Network

gnn scrna-seq annotation single-cell deep-learning reference-free transcriptomics graph-neural-network cell-type-classification

Created 2020-04-18

102 commits to master branch, last one 2 years ago