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https://github.com/csoneson/alevinqc
Create QC and summary reports for Alevin output
https://github.com/csoneson/alevinqc
Last synced: 1 day ago
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Create QC and summary reports for Alevin output
- Host: GitHub
- URL: https://github.com/csoneson/alevinqc
- Owner: csoneson
- License: other
- Created: 2018-11-02T19:55:16.000Z (about 6 years ago)
- Default Branch: devel
- Last Pushed: 2024-12-21T17:45:54.000Z (about 1 month ago)
- Last Synced: 2025-01-14T06:07:06.185Z (9 days ago)
- Language: R
- Homepage: https://csoneson.github.io/alevinQC/
- Size: 14.2 MB
- Stars: 31
- Watchers: 5
- Forks: 6
- Open Issues: 2
-
Metadata Files:
- Readme: README.md
- Changelog: NEWS.md
- License: LICENSE
Awesome Lists containing this project
README
## alevinQC
[](https://codecov.io/github/csoneson/alevinQC)
[](https://github.com/csoneson/alevinQC/actions)
The `alevinQC` R package provides functionality for generating QC reports
summarizing the output of [alevin](https://salmon.readthedocs.io/en/latest/alevin.html)
([Srivastava et al., Genome Biology 20:65 (2019)](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1670-y)). The reports can
be generated in html or pdf format, or as R/Shiny applications.
### Installation:
`alevinQC` is available from
[Bioconductor](https://bioconductor.org/packages/alevinQC/), and can be
installed using the `BiocManager` CRAN package:
```
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("alevinQC")
```
Note that `alevinQC` v 1.1 or newer is required to process output from Salmon version 0.14.0 or newer.
### Example usage:
```
alevinQCReport(baseDir = system.file("extdata/alevin_example_v0.14",
package = "alevinQC"),
sampleId = "testSample",
outputFile = "alevinReport.html",
outputFormat = "html_document",
outputDir = tempdir(), forceOverwrite = TRUE)
```
For more information, we refer to the package vignette.
