Search Results - RepositoryStats

awesome-single-cell seandavi

989

3.2k

mit

248

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

Created 2016-06-29

791 commits to master branch, last one 18 days ago

salmon COMBINE-lab

165

780

gpl-3.0

38

🐟 🍣 🍱 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 8 months ago

nichenetr saeyslab

118

493

unknown

14

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 2 months ago

enformer-pytorch lucidrains

82

436

mit

17

Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch

genomics transformer deep-learning dna-sequences gene-expression attention-mechanism artificial-intelligence

Created 2021-10-23

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

Tangram broadinstitute

51

261

bsd-3-clause

13

Spatial alignment of single cell transcriptomic data.

visium scrna-seq snrna-seq spatial-data gene-expression computational-biology

Created 2020-08-21

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

ClusterGVis junjunlab

24

250

mit

4

One-step to Cluster and Visualize Gene Expression Matrix

mfuzz visualization complexheatmap gene-clustering gene-expression

Created 2022-11-19

139 commits to main branch, last one 12 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

3,245 commits to devel branch, last one 2 days ago

pymrmr fbrundu

37

138

mit

2

Python3 binding to mRMR Feature Selection algorithm (currently not maintained)

data-science gene-expression feature-selection mutual-information computational-biology

Created 2017-03-09

228 commits to master branch, last one 3 years ago

dorothea saezlab

27

133

gpl-3.0

15

R package to access DoRothEA's regulons

regulons tf-activities gene-expression functional-analysis bioconductor-package transcription-factor

Created 2017-03-27

282 commits to master branch, last one 9 months ago

awesome-expression-browser federicomarini

38

132

mit

16

😎 A curated list of software and resources for exploring and visualizing (browsing) expression data 😎

atlas awesome-list rna-seq-data bioinformatics humancellatlas gene-expression data-exploration data-visualization expression-browser gene-expression-profiles

Created 2019-03-30

186 commits to main branch, last one 7 months ago

powsimR bvieth

23

105

artistic-2.0

8

Power analysis is essential to optimize the design of RNA-seq experiments and to assess and compare the power to detect differentially expressed genes. PowsimR is a flexible tool to simulate and evalu...

r power rna-seq simulation single-cell power-analysis gene-expression experimental-design simulation-framework

Created 2017-04-16

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

CodonTransformer Adibvafa

4

104

apache-2.0

2

CodonTransformer: The ultimate tool for codon optimization, optimizing DNA sequences for heterologous protein expression across 164 species.

codon biotechnology deep-learning bioinformatics codon-optimizer gene-expression machine-learning synthetic-biology codon-optimization computational-biology

Created 2024-05-24

245 commits to main branch, last one 29 days ago

BASiCS catavallejos

17

84

unknown

7

BASiCS: Bayesian Analysis of Single-Cell Sequencing Data. This is an unstable experimental version. Please see http://bioconductor.org/packages/BASiCS/ for the official release version

r rcpp bayesian scrna-seq single-cell rcpparmadillo gene-expression bioconductor-package

Created 2015-05-19

1,003 commits to devel branch, last one 8 months ago

tf-bind-transformer lucidrains

9

81

mit

8

A repository with exploration into using transformers to predict DNA ↔ transcription factor binding

transformers deep-learning gene-expression attention-mechanism transcription-factors artificial-intelligence transcription-factor-binding

Created 2021-12-08

234 commits to main branch, last one 2 years ago

EPIC GfellerLab

21

76

other

5

Repository for the R package EPIC, to Estimate the Proportion of Immune and Cancer cells from bulk gene expression data.

rna-seq bulk-data cell-type cancer-cells gene-expression

Created 2017-01-18

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

GeneTonic federicomarini

9

76

other

6

Enjoy your transcriptomic data and analysis responsibly - like sipping a cocktail

r gui shiny bioconductor rna-seq-data transcriptome user-friendly gene-expression transcriptomics data-exploration pathway-analysis rna-seq-analysis data-visualization bioconductor-package reproducible-research functional-enrichment-analysis

Created 2019-06-24

1,092 commits to devel branch, last one about a month ago

SCope aertslab

15

68

gpl-3.0

9

Fast visualization tool for large-scale and high dimensional single-cell data

aws grpc loom cloud reactjs single-cell gene-expression gene-regulatory-network large-scale-data-visualization

Created 2018-02-13

1,617 commits to master branch, last one 3 years ago

helical helicalAI

7

66

agpl-3.0

5

This repository contains the python package for Helical

vcf data rnaseq biology rna-seq transformer pre-training deep-learning dna-sequences bioinformatics gene-expression neural-networks foundation-models pre-trained-model artificial-intelligence

Created 2024-04-27

830 commits to release branch, last one 28 days ago

BioBombe greenelab

25

64

bsd-3-clause

6

BioBombe: Sequentially compressed gene expression features enhances biological signatures

tcga hetnet msigdb network biobombe gene-sets autoencoder compression gene-expression

Created 2018-03-22

234 commits to master branch, last one 3 years ago

countToFPKM AAlhendi1707

15

62

gpl-3.0

3

Convert Counts to Fragments per Kilobase of Transcript per Million (FPKM)

rna-seq normalization gene-expression

Created 2019-03-23

172 commits to master branch, last one 3 years ago

MERINGUE JEFworks-Lab

5

61

gpl-3.0

4

characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular densities

rstats single-cell gene-expression spatial-analysis cell-cell-communication spatial-transcriptomics

Created 2018-04-26

184 commits to master branch, last one 2 years ago

terminus COMBINE-lab

3

57

bsd-3-clause

6

This repository has no description...

rna-seq gene-expression transcriptomics

Created 2020-01-30

56 commits to master branch, last one 2 years ago

scNanoGPS gaolabtools

2

40

other

5

Single cell Nanopore sequencing data for Genotype and Phenotype

isoforms single-cell cell-barcode umi-curation demultiplexing gene-expression rna-seq-pipeline long-read-sequencing nanopore-analysis-pipeline single-nucleotide-variation

Created 2022-09-13

34 commits to v1.1 branch, last one 2 months ago

breast-cancer-gene-expression ezgisubasi

4

38

unknown

4

This project aims to predict people who will survive breast cancer using machine learning models with the help of clinical data and gene expression profiles of the patients.

breast-cancer data-analysis gene-expression machine-learning data-visualization breast-cancer-classification

Created 2021-05-30

42 commits to main branch, last one 3 years ago