https://github.com/sa-lee/fluentgenomics
plyranges and tximeta case study
https://github.com/sa-lee/fluentgenomics
atac-seq bioconductor genomics rna-seq workflow
Last synced: 5 months ago
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plyranges and tximeta case study
- Host: GitHub
- URL: https://github.com/sa-lee/fluentgenomics
- Owner: sa-lee
- License: other
- Created: 2019-11-22T01:20:41.000Z (over 6 years ago)
- Default Branch: master
- Last Pushed: 2023-07-02T08:09:14.000Z (almost 3 years ago)
- Last Synced: 2025-01-22T08:14:38.237Z (over 1 year ago)
- Topics: atac-seq, bioconductor, genomics, rna-seq, workflow
- Language: TeX
- Homepage: https://sa-lee.github.io/fluentGenomics/
- Size: 21.9 MB
- Stars: 7
- Watchers: 4
- Forks: 3
- Open Issues: 4
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# Fluent genomics with plyranges and tximeta
[](https://github.com/sa-lee/fluentGenomics/actions)
In *fluentGenomics* we explore the use of the Bioconductor packages plyranges and tximeta through integrating results from an experiment using RNA-seq and ATAC-seq data. Readers will learn how to perform genomic range based operations in a principled way using *plyranges* and how to cleanly import quantification and differential expression data into R using *tximeta*.
## Installation
The `fluentGenomics` package is available on Bioconductor:
```r
# install.packages("BiocManager")
BiocManager::install('fluentGenomics')
```
To install `fluentGenomics` from github with associated dependencies use
``` r
BiocManager::install('sa-lee/fluentGenomics',
build_vignettes = TRUE,
dependencies = TRUE)
```
To install `fluentGenomics` from Bioconductor's devel branch use:
``` r
BiocManager::install('fluentGenomics', version = 'devel')
```
## Workflow
Once the package has been installed, you can work through
the vignette directly from R/Rstudio with:
``` r
vignette("fluentGenomics")
```
Or you can read it online
[here](https://bioconductor.org/packages/devel/workflows/vignettes/fluentGenomics/inst/doc/fluentGenomics.html)
## Course
You can use the package as course material directly with the `usethis`
package:
```{r}
usethis::use_course("sa-lee/fluentGenomics")
```