14 results found Sort:

satijalab
seurat satijalab
918
2.3k
other
74
R toolkit for single cell genomics
cran human-cell-atlas single-cell-rna-seq single-cell-genomics
Created 2015-05-20
8,541 commits to master branch, last one 6 months ago
scverse
scvi-tools scverse
355
1.3k
bsd-3-clause
26
Deep probabilistic analysis of single-cell and spatial omics data
scverse cite-seq scrna-seq deep-learning human-cell-atlas variational-bayes single-cell-rna-seq single-cell-genomics deep-generative-model variational-autoencoder
Created 2017-09-06
4,101 commits to main branch, last one 3 days ago
theislab
scarches theislab
51
335
bsd-3-clause
12
Reference mapping for single-cell genomics
scrna-seq multiomics single-cell deep-learning batch-correction data-integration human-cell-atlas rna-seq-analysis single-cell-genomics multimodal-deep-learning
Created 2019-08-12
1,175 commits to master branch, last one 5 months ago
spacetx
starfish spacetx
68
228
mit
18
starfish: unified pipelines for image-based transcriptomics
python imaging transcriptomics human-cell-atlas
Created 2017-05-26
1,443 commits to master branch, last one a day ago
iSEE
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
hemberg-lab
SC3 hemberg-lab
55
119
gpl-3.0
11
A tool for the unsupervised clustering of cells from single cell RNA-Seq experiments
human-cell-atlas single-cell-rna-seq bioconductor-package
Created 2016-01-28
363 commits to master branch, last one 4 years ago
stemangiola
CuratedAtlasQueryR stemangiola
7
89
gpl-3.0
5
Tidy R query API for the harmonised and curated CELLxGENE single-cell atlas.
hdf5 duckdb database tidyverse single-cell human-cell-atlas singlecellexperiment
Created 2022-09-12
552 commits to master branch, last one 3 days ago
theislab
cpa theislab
17
88
bsd-3-clause
5
The Compositional Perturbation Autoencoder (CPA) is a deep generative framework to learn effects of perturbations at the single-cell level. CPA performs OOD predictions of unseen combinations of drugs...
scrna-seq human-cell-atlas single-cell-rna-seq single-cell-genomics
Created 2021-10-15
344 commits to main branch, last one 3 months ago
drisso
SingleCellExperiment drisso
18
67
unknown
10
Clone of the Bioconductor repository for the SingleCellExperiment package, see https://bioconductor.org/packages/devel/bioc/html/SingleCellExperiment.html for the official development version.
bioconductor human-cell-atlas single-cell-rna-seq bioconductor-package
Created 2017-08-17
359 commits to master branch, last one 14 days ago
FertigLab
CoGAPS FertigLab
17
66
bsd-3-clause
13
Bayesian MCMC matrix factorization algorithm
bioinformatics human-cell-atlas machine-learning bayesian-inference single-cell-rna-seq non-negative-matrix-factorization
Created 2015-12-18
1,678 commits to master branch, last one 28 days ago
broadinstitute
single_cell_portal_core broadinstitute
26
63
bsd-3-clause
17
Rails/Docker application for the Broad Institute's single cell RNA-seq data portal
human-cell-atlas rna-seq-analysis single-cell-genomics
Created 2016-03-17
12,487 commits to development branch, last one 7 days ago
MarioniLab
DropletUtils MarioniLab
27
56
unknown
12
Clone of the Bioconductor repository for the DropletUtils package.
human-cell-atlas single-cell-rna-seq bioconductor-package
Created 2017-12-18
498 commits to devel branch, last one about a month ago
Teichlab
Genes2Genes Teichlab
5
46
mit
2
Aligning gene expression trajectories of single-cell reference and query systems
python scrna-seq single-cell human-cell-atlas bayesian-inference dynamic-programming trajectory-alignment pseudotime-trajectory minimum-message-length
Created 2022-10-25
135 commits to main branch, last one about a month ago
showteeth
scfetch showteeth
4
34
gpl-3.0
2
Access and Format Single-cell RNA-seq Datasets from Public Resources
bam geo sra fastq zenodo cellxgene panglaodb human-cell-atlas ucsc-cell-browser single-cell-rna-seq format-conversion-tool
Created 2023-07-12
82 commits to main branch, last one 6 months ago