zinbwave
Clone of the Bioconductor repository for the zinbwave package, see https://bioconductor.org/packages/zinbwave
Science Score: 46.0%
This score indicates how likely this project is to be science-related based on various indicators:
-
○CITATION.cff file
-
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
-
✓Academic publication links
Links to: nature.com -
✓Committers with academic emails
2 of 12 committers (16.7%) from academic institutions -
○Institutional organization owner
-
○JOSS paper metadata
-
○Scientific vocabulary similarity
Low similarity (12.8%) to scientific vocabulary
Keywords from Contributors
Repository
Clone of the Bioconductor repository for the zinbwave package, see https://bioconductor.org/packages/zinbwave
Basic Info
- Host: GitHub
- Owner: drisso
- Language: R
- Default Branch: master
- Size: 649 KB
Statistics
- Stars: 45
- Watchers: 6
- Forks: 10
- Open Issues: 11
- Releases: 0
Metadata Files
README.md
zinbwave
Zero-inflated Negative Binomial based Wanted Variation Extraction (ZINB-WaVE)
This package implements a zero-inflated negative binomial model for single-cell RNA-seq data, with latent factors.
The model is described in details in the paper:
Installation
Since Bioconductor 3.7 the new recommended way to install Bioconductor packages is via the BiocManager package, available on CRAN:
{r}
install.packages("BiocManager")
BiocManager::install("zinbwave")
Note that zinbwave requires R (>=3.4) and Bioconductor (>=3.6).
In virtually all cases, installing from Bioconductor is recommended. However, if you want to install the development version of zinbwave from GitHub, you can do so with the following.
{r}
library(devtools)
install_github("drisso/zinbwave")
Owner
- Name: Davide Risso
- Login: drisso
- Kind: user
- Location: New York, NY
- Company: Weill Cornell Medicine
- Website: drisso.github.io
- Repositories: 23
- Profile: https://github.com/drisso
GitHub Events
Total
- Issues event: 1
- Watch event: 2
Last Year
- Issues event: 1
- Watch event: 2
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Davide Risso | r****e@g****m | 58 |
| Davide Risso | d****2@m****u | 51 |
| Nitesh Turaga | n****a@g****m | 10 |
| Fanny | f****u@b****u | 9 |
| fedeago | f****s@h****t | 3 |
| Szymon M. Kiełbasa | s****a@l****l | 2 |
| Hervé Pagès | h****s@f****g | 2 |
| vobencha | v****a@g****m | 2 |
| vobencha | v****n@r****g | 2 |
| Martin Morgan | m****n@f****g | 1 |
| Kayla-Morrell | k****l@r****g | 1 |
| Leon Fodoulian | 3****n | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 7 months ago
All Time
- Total issues: 67
- Total pull requests: 8
- Average time to close issues: 4 months
- Average time to close pull requests: 2 months
- Total issue authors: 46
- Total pull request authors: 4
- Average comments per issue: 3.1
- Average comments per pull request: 2.75
- Merged pull requests: 8
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 1
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 1
- Pull request authors: 0
- Average comments per issue: 0.0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- drisso (8)
- gbiele (5)
- bio-la (4)
- vincr04 (3)
- yeroslaviz (3)
- eltonjrv (2)
- ktroule (2)
- zji90 (2)
- reubenthomas (1)
- timydaley (1)
- tibo1 (1)
- nbartonicek (1)
- CcYyQq (1)
- giovp (1)
- aditisk (1)
Pull Request Authors
- fperraudeau (4)
- SzMK (2)
- fedeago (1)
- leonfodoulian (1)
Top Labels
Issue Labels
Pull Request Labels
Dependencies
- actions/cache v2 composite
- actions/checkout v2 composite
- actions/upload-artifact master composite
- docker/build-push-action v1 composite
- r-lib/actions/setup-pandoc master composite
- r-lib/actions/setup-r master composite
- R >= 3.4 depends
- SingleCellExperiment * depends
- SummarizedExperiment * depends
- methods * depends
- BiocParallel * imports
- Matrix * imports
- edgeR * imports
- genefilter * imports
- softImpute * imports
- stats * imports
- BiocStyle * suggests
- DESeq2 * suggests
- Rtsne * suggests
- biomaRt * suggests
- ggplot2 * suggests
- knitr * suggests
- magrittr * suggests
- matrixStats * suggests
- rmarkdown * suggests
- scRNAseq * suggests
- testthat * suggests