https://github.com/bioconductor-source/scvir
Science Score: 13.0%
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○CITATION.cff file
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✓codemeta.json file
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○.zenodo.json file
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○Scientific vocabulary similarity
Low similarity (8.6%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: bioconductor-source
- Language: R
- Default Branch: devel
- Size: 9.61 MB
Statistics
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
scviR
The scviR package provides an experimental interface between R and scvi-tools.
Our first release addresses the use of the totalVI model for CITE-seq data.
- The scviR vignette works through a chunk of the colab tutorial for scvi-tools 0.19.0; 0.20.0 employs muon, and this has not been addressed yet.
- scviR defines python infrastructure via the basilisk
discipline; the main python dependencies are declared in
R/basilisk.R. - We have collected a number of intermediate results so that the outputs of totalVI (and other VI procedures) can be explored without taking the time to fit the model. An example in the CITE-seq domain is the anndata instance for the 5k-10k PBMC dataset with representations of the latent space, cluster assignments, and UMAP projection:
```
tot = getTotalVI5k10kAdata() # retrieved on first call from Open Storage Network, cached tot AnnData object with nobs × nvars = 10849 × 4000 obs: 'ngenes', 'percentmito', 'ncounts', 'batch', 'scvilabels', 'scvibatch', 'leidentotalVI' var: 'highlyvariable', 'highlyvariablerank', 'means', 'variances', 'variancesnorm', 'highlyvariablenbatches' uns: 'scvimanageruuid', 'scviuuid', 'hvg', 'leiden', 'log1p', 'neighbors', 'umap' obsm: 'XtotalVI', 'Xumap', 'denoisedprotein', 'proteinexpression', 'proteinforegroundprob' layers: 'counts', 'denoisedrna' obsp: 'connectivities', 'distances' table(tot$obs$batch)
PBMC5k PBMC10k 3994 6855
dim(xx$obsm$get("X_totalVI")) # cell positions in 20 dimensional latent space [1] 10849 20
```
Vignettes in the package show how to populate a Bioconductor SingleCellExperiment with components of this structure to help compare methods employed in the two frameworks.
Owner
- Name: (WIP DEV) Bioconductor Packages
- Login: bioconductor-source
- Kind: organization
- Email: maintainer@bioconductor.org
- Website: https://bioconductor.org
- Repositories: 1
- Profile: https://github.com/bioconductor-source
Source code for packages accepted into Bioconductor