GeoDiff
GeoDiff, an R package for count generating models for analyzing Geomx RNA data. Note that this version of the package is still under development, undergoing submission process to Bioconductor 3.14 release and still needs to complete NanoString internal verification process.
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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○Academic publication links
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○Scientific vocabulary similarity
Low similarity (8.5%) to scientific vocabulary
Repository
GeoDiff, an R package for count generating models for analyzing Geomx RNA data. Note that this version of the package is still under development, undergoing submission process to Bioconductor 3.14 release and still needs to complete NanoString internal verification process.
Basic Info
Statistics
- Stars: 8
- Watchers: 5
- Forks: 6
- Open Issues: 8
- Releases: 1
Metadata Files
README.md
GeoDiff
Overview
We present GeoDiff, an R package for count generating models for analyzing Geomx RNA data, demonstrated by example data analysis pipeline vignette. The package provides a series of statistical models using count generating distributions for fundamental tasks including background modelling, target and sample QC, normalization and differential expression analysis. The new methods are shown to be more suitable for these tasks in real examples than some conventional methods.
It contains the definition of the NanoStringGeoMxSet class which inherits from Biobase’s ExpressionSet class and NanoStringRCCSet class.
Installation
Install the development version from GitHub
r
install.packages("devtools")
library("devtools")
devtools::install_github("Nanostring-Biostats/GeoDiff", ref = "dev")
License
This project is licensed under the MIT license.
Owner
- Name: NanoString Technologies, Inc.
- Login: Nanostring-Biostats
- Kind: organization
- Email: support@nanostring.com
- Website: https://nanostring.com
- Twitter: nanostringtech
- Repositories: 14
- Profile: https://github.com/Nanostring-Biostats
GitHub Events
Total
- Issues event: 1
- Watch event: 1
- Issue comment event: 1
- Push event: 1
Last Year
- Issues event: 1
- Watch event: 1
- Issue comment event: 1
- Push event: 1
Committers
Last synced: almost 3 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Zhi Yang | z****g@n****m | 20 |
| Lei Yang | l****g@n****m | 16 |
| zhiiiyang | z****5@g****m | 13 |
| Maddy Griswold | 4****z | 7 |
| Nicole Ortogero | n****o@n****m | 7 |
| NicoleEO | N****o@g****m | 6 |
| Nitesh Turaga | n****a@g****m | 2 |
| maddygriz | m****d@n****m | 2 |
Committer Domains (Top 20 + Academic)
Packages
- Total packages: 1
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Total downloads:
- bioconductor 7,620 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 5
- Total maintainers: 1
bioconductor.org: GeoDiff
Count model based differential expression and normalization on GeoMx RNA data
- Homepage: https://github.com/Nanostring-Biostats/GeoDiff
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/GeoDiff/inst/doc/GeoDiff.pdf
- License: MIT + file LICENSE
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Latest release: 1.14.0
published over 1 year ago
Rankings
Maintainers (1)
Dependencies
- Biobase * depends
- R >= 4.1.0 depends
- GeomxTools * imports
- Matrix * imports
- NanoStringNCTools * imports
- Rcpp >= 1.0.4.6 imports
- graphics * imports
- lme4 * imports
- methods * imports
- plyr * imports
- robust * imports
- stats * imports
- testthat * imports
- withr * imports
- dplyr * suggests
- knitr * suggests
- rmarkdown * suggests
- EddieHubCommunity/gh-action-community/src/welcome main composite