Science Score: 36.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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○Academic publication links
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✓Committers with academic emails
20 of 122 committers (16.4%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (9.7%) to scientific vocabulary
Keywords
cran
human-cell-atlas
single-cell-genomics
single-cell-rna-seq
Keywords from Contributors
bioinformatics
transcriptomics
bioconductor
single-cell
anndata
scanpy
scverse
genomics
visualize-data
dna
Last synced: 6 months ago
·
JSON representation
Repository
R toolkit for single cell genomics
Basic Info
- Host: GitHub
- Owner: satijalab
- License: other
- Language: R
- Default Branch: main
- Homepage: http://www.satijalab.org/seurat
- Size: 78.3 MB
Statistics
- Stars: 2,500
- Watchers: 76
- Forks: 961
- Open Issues: 351
- Releases: 44
Topics
cran
human-cell-atlas
single-cell-genomics
single-cell-rna-seq
Created almost 11 years ago
· Last pushed 6 months ago
Metadata Files
Readme
Changelog
License
Code of conduct
README.md
Seurat v5
Seurat is an R toolkit for single cell genomics, developed and maintained by the Satija Lab at NYGC.
We are excited to release Seurat v5! This updates introduces new functionality for spatial, multimodal, and scalable single-cell analysis.
Seurat v5 is backwards-compatible with previous versions, so that users will continue to be able to re-run existing workflows.
Instructions, documentation, and tutorials can be found at:
- https://satijalab.org/seurat
Seurat is also hosted on GitHub, you can view and clone the repository at
- https://github.com/satijalab/seurat
Seurat has been successfully installed on Mac OS X, Linux, and Windows, using the devtools package to install directly from GitHub
Improvements and new features will be added on a regular basis, please post on the github page with any questions or if you would like to contribute
For a version history/changelog, please see the NEWS file.
Owner
- Name: satijalab
- Login: satijalab
- Kind: organization
- Website: https://satijalab.org
- Twitter: satijalab
- Repositories: 12
- Profile: https://github.com/satijalab
Committers
Last synced: 7 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Andrew Butler | a****3@g****m | 1,739 |
| Paul Hoffman | m****e | 938 |
| Paul Hoffman | p****n@n****g | 771 |
| yuhanH | y****0@n****u | 724 |
| David Collins | d****s@n****g | 463 |
| Saket Choudhary | s****c@g****m | 283 |
| Rahul Satija | r****a@n****g | 281 |
| timoast | 4****t | 255 |
| AustinHartman | h****9@g****m | 166 |
| Gesmira | g****a@g****m | 143 |
| Christoph Hafemeister | c****r@n****g | 124 |
| Madeline Kowalski | m****i@g****m | 71 |
| Efthymia Papalexi | e****9@n****u | 68 |
| samuel-marsh | s****h@c****u | 63 |
| Jaison Jain | j****8@g****m | 49 |
| Charlotte Darby | c****y@n****g | 47 |
| Shiwei Zheng | s****g@n****g | 33 |
| zskylarli | z****6@c****u | 32 |
| Izzy Grabski | i****g@i****g | 29 |
| Leon Fodoulian | 3****n | 27 |
| adyzh | j****3@c****u | 25 |
| rsatija | s****l@g****m | 23 |
| TomKellyGenetics | t****s@g****m | 20 |
| Nigel Delaney | n****l@g****m | 20 |
| Jordan Sicherman | j****n@1****m | 19 |
| Jaison Jain | j****j@s****g | 18 |
| Scott Gigante | s****e@g****m | 17 |
| Stephen Williams | s****s@1****m | 16 |
| Paul Hoffman | m****e@u****m | 12 |
| rharao | 1****o | 12 |
| and 92 more... | ||
Committer Domains (Top 20 + Academic)
nygenome.org: 7
nyu.edu: 3
broadinstitute.org: 3
10xgenomics.com: 3
satijalab05.nygenome.org: 2
columbia.edu: 2
izzys-air.nygenome.org: 1
satijalab04.nygenome.org: 1
user.noreply.github.com: 1
strad.nygenome.org: 1
mdc-berlin.de: 1
yale.edu: 1
soe.ucsc.edu: 1
lundbeck.com: 1
bcm.edu: 1
epfl.ch: 1
tgen.org: 1
childrens.harvard.edu: 1
gmx.de: 1
ebi.ac.uk: 1
molgen.mpg.de: 1
mail.huji.ac.il: 1
genetics.med.harvard.edu: 1
email.unc.edu: 1
stats.ox.ac.uk: 1
stonybrook.edu: 1
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 2,324
- Total pull requests: 275
- Average time to close issues: 2 months
- Average time to close pull requests: 5 months
- Total issue authors: 1,613
- Total pull request authors: 74
- Average comments per issue: 2.61
- Average comments per pull request: 1.36
- Merged pull requests: 119
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 450
- Pull requests: 157
- Average time to close issues: 29 days
- Average time to close pull requests: 11 days
- Issue authors: 350
- Pull request authors: 24
- Average comments per issue: 1.02
- Average comments per pull request: 0.73
- Merged pull requests: 74
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- denvercal1234GitHub (21)
- Flu09 (18)
- BenjaminDEMAILLE (13)
- LeaLe88 (12)
- yulchen810 (11)
- Dario-Rocha (10)
- levinhein (10)
- chrkuo (9)
- lucygarner (8)
- AAA-3 (8)
- nick-youngblut (7)
- chungsai (7)
- grimwoo (7)
- vertesy (7)
- cathalgking (7)
Pull Request Authors
- dcollins15 (86)
- samuel-marsh (28)
- YoukaiFromAccounting (12)
- kew24 (6)
- rharao (6)
- dkcoxie (5)
- stephenwilliams22 (5)
- Sandman-1 (4)
- Liripo (4)
- attja (4)
- mojaveazure (4)
- AustinHartman (4)
- zskylarli (4)
- roi-meir (4)
- jsicherman (3)
Top Labels
Issue Labels
bug (643)
enhancement (96)
documentation (81)
more-information-needed (73)
Analysis Question (13)
duplicate (7)
Installation Help (1)
installation-help (1)
Pull Request Labels
bug (6)
Packages
- Total packages: 2
-
Total downloads:
- cran 53,057 last-month
- Total docker downloads: 158,929
-
Total dependent packages: 65
(may contain duplicates) -
Total dependent repositories: 446
(may contain duplicates) - Total versions: 65
- Total maintainers: 1
cran.r-project.org: Seurat
Tools for Single Cell Genomics
- Homepage: https://satijalab.org/seurat
- Documentation: http://cran.r-project.org/web/packages/Seurat/Seurat.pdf
- License: MIT + file LICENSE
-
Latest release: 5.3.0
published 10 months ago
Rankings
Forks count: 0.1%
Stargazers count: 0.1%
Dependent repos count: 0.7%
Dependent packages count: 1.4%
Downloads: 1.8%
Average: 3.6%
Docker downloads count: 17.3%
Maintainers (1)
Last synced:
6 months ago
conda-forge.org: r-seurat
- Homepage: https://satijalab.org/seurat
- License: MIT
-
Latest release: 4.2.1
published over 3 years ago
Rankings
Forks count: 5.7%
Stargazers count: 9.5%
Dependent repos count: 9.7%
Average: 11.1%
Dependent packages count: 19.6%
Last synced:
6 months ago
Dependencies
.github/workflows/R_CMD_check.yaml
actions
- actions/checkout v2 composite
- actions/upload-artifact master composite
DESCRIPTION
cran
- R >= 4.0.0 depends
- methods * depends
- KernSmooth * imports
- MASS * imports
- Matrix >= 1.5 imports
- RANN * imports
- RColorBrewer * imports
- ROCR * imports
- Rcpp >= 1.0.7 imports
- RcppAnnoy >= 0.0.18 imports
- Rtsne * imports
- SeuratObject >= 4.1.3 imports
- cluster * imports
- cowplot * imports
- fitdistrplus * imports
- future * imports
- future.apply * imports
- ggplot2 >= 3.3.0 imports
- ggrepel * imports
- ggridges * imports
- grDevices * imports
- graphics * imports
- grid * imports
- httr * imports
- ica * imports
- igraph * imports
- irlba * imports
- jsonlite * imports
- leiden >= 0.3.1 imports
- lmtest * imports
- matrixStats * imports
- miniUI * imports
- patchwork * imports
- pbapply * imports
- plotly >= 4.9.0 imports
- png * imports
- progressr * imports
- reticulate * imports
- rlang * imports
- scales * imports
- scattermore >= 0.7 imports
- sctransform >= 0.3.5 imports
- shiny * imports
- spatstat.explore * imports
- spatstat.geom * imports
- stats * imports
- tibble * imports
- tools * imports
- utils * imports
- uwot >= 0.1.14 imports
- Biobase * suggests
- BiocGenerics * suggests
- DESeq2 * suggests
- GenomeInfoDb * suggests
- GenomicRanges * suggests
- IRanges * suggests
- MAST * suggests
- R.utils * suggests
- Rfast2 * suggests
- S4Vectors * suggests
- SingleCellExperiment * suggests
- SummarizedExperiment * suggests
- VGAM * suggests
- ape * suggests
- data.table * suggests
- enrichR * suggests
- ggrastr * suggests
- hdf5r * suggests
- limma * suggests
- metap * suggests
- mixtools * suggests
- monocle * suggests
- rsvd * suggests
- rtracklayer * suggests
- testthat * suggests