Search Results - RepositoryStats

scanpy scverse

599

1.9k

bsd-3-clause

51

Single-cell analysis in Python. Scales to >1M cells.

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

Created 2017-01-29

3,473 commits to main branch, last one a day ago

cellxgene chanzuckerberg

118

631

mit

32

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 about a month ago

PyDESeq2 owkin

62

585

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

314 commits to main branch, last one a day ago

anndata scverse

153

576

bsd-3-clause

14

Annotated data.

scanpy anndata scverse data-science bioinformatics transcriptomics machine-learning

Created 2017-08-11

1,399 commits to main branch, last one 20 hours ago

pySCENIC aertslab

181

435

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 7 months ago

PathomicFusion mahmoodlab

80

276

gpl-3.0

14

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

56

266

gpl-3.0

9

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

313

251

other

33

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

9,125 commits to master branch, last one about a month ago

starfish spacetx

68

226

mit

18

starfish: unified pipelines for image-based transcriptomics

python imaging transcriptomics human-cell-atlas

Created 2017-05-26

1,438 commits to master branch, last one 26 days ago

iSEE iSEE

42

224

other

18

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

3,242 commits to devel branch, last one about a month ago

scCATCH ZJUFanLab

38

217

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

pagoda2 kharchenkolab

47

210

unknown

16

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 8 months ago

diffxpy theislab

23

193

bsd-3-clause

7

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 year ago

bambu GoekeLab

23

188

gpl-3.0

7

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

2,159 commits to devel branch, last one 13 days ago

scde hms-dbmi

66

172

other

25

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

awesome-biological-visualizations keller-mark

17

169

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 3 years ago

alevin-fry COMBINE-lab

15

168

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

807 commits to master branch, last one 3 months ago

tidybulk stemangiola

25

165

unknown

6

Brings bulk and pseudobulk transcriptomics to the tidyverse

Created 2019-08-28

1,474 commits to master branch, last one 19 days ago

decoupler-py saezlab

24

161

gpl-3.0

7

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

612 commits to main branch, last one about a month ago

IsoQuant ablab

13

150

other

12

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

ngs pacbio rna-seq nanopore bioinformatics transcriptomics

Created 2020-04-15

1,394 commits to master branch, last one about a month ago

cell-ontology obophenotype

49

145

cc-by-4.0

24

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

4,014 commits to master branch, last one a day ago

xpore GoekeLab

23

137

mit

9

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 11 months ago

pandora genular

21

135

other

11

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

1,466 commits to master branch, last one a day ago

DNAnalyzer VerisimilitudeX

56

134

other

8

Revolutionizing DNA analysis and making it accessible to all through innovative ML-powered analysis and interpretive tools.

dna genomics sequencing metagenomics hacktoberfest bioinformatics dna-sequencing transcriptomics machine-learning hacktoberfest2024 protein-sequences amino-acid-sequence regulatory-elements artificial-intelligence

Created 2022-07-31

1,361 commits to main branch, last one 2 months ago

RNAlysis GuyTeichman

13

129

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

3,398 commits to master branch, last one about a month ago

Pando quadbio

21

111

mit

5

Multiome GRN inference.

epigenomics single-cell transcriptomics

Created 2021-06-08

354 commits to main branch, last one 6 months ago

sg-nex-data GoekeLab

25

111

unknown

7

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

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

Created 2019-02-28

289 commits to master branch, last one 2 months ago

scrattch.hicat AllenInstitute

31

106

other

15

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 5 months ago

scDeepSort ZJUFanLab

18

99

gpl-3.0

6

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

HoneyBADGER JEFworks-Lab

31

96

gpl-3.0

8

HMM-integrated Bayesian approach for detecting CNV and LOH events from single-cell RNA-seq data

hmm bayesian cnv-detection heterogeneity subpopulation bioinformatics transcriptomics single-cell-rna-seq single-cell-analysis

Created 2017-02-24

106 commits to master branch, last one 3 years ago