https://github.com/mikelove/alpine

Modeling and correcting fragment sequence bias for RNA-seq
https://github.com/mikelove/alpine

bioconductor rnaseq

Last synced: 19 days ago
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Modeling and correcting fragment sequence bias for RNA-seq

• Host: GitHub
• URL: https://github.com/mikelove/alpine
• Owner: mikelove
• Created: 2013-11-08T20:36:17.000Z (almost 12 years ago)
• Default Branch: master
• Last Pushed: 2024-06-04T22:40:54.000Z (over 1 year ago)
• Last Synced: 2024-12-28T12:25:28.537Z (9 months ago)
• Topics: bioconductor, rnaseq
• Language: R
• Homepage: http://biorxiv.org/content/early/2015/08/28/025767
• Size: 1.29 MB
• Stars: 24
• Watchers: 5
• Forks: 6
• Open Issues: 3
• Metadata Files:
  • Readme: README.md
  • Changelog: NEWS

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README

          
# alpine

![alpine](http://mikelove.nfshost.com/img/alpine.jpg)

(the [Sassolungo](https://en.wikipedia.org/wiki/Langkofel) mountain in the Dolomites)

*alpine* is an R/Bioconductor package for modeling and correcting fragment

sequence bias for RNA-seq transcript abundance estimation. In

particular, it is the first method of its kind to take into account

sample-specific dependence of RNA-seq fragments on their GC content.

An example workflow can be found in `vignettes/alpine.Rmd`, or by typing:

```{r}

vignette("alpine")

```

*alpine* is designed for un-stranded paired-end RNA-seq data.

A paper explaining the *alpine* methods was published in December 2016: