https://github.com/lpantano/degreport

Create a cromphensive report of DEG list coming from any analysis of RNAseq data
https://github.com/lpantano/degreport

bioconductor differential-expression qc r report rna-seq smallrna

Last synced: 12 days ago
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Create a cromphensive report of DEG list coming from any analysis of RNAseq data

• Host: GitHub
• URL: https://github.com/lpantano/degreport
• Owner: lpantano
• License: mit
• Created: 2014-03-13T13:06:49.000Z (over 10 years ago)
• Default Branch: main
• Last Pushed: 2024-02-27T23:03:53.000Z (8 months ago)
• Last Synced: 2024-10-14T15:26:01.484Z (24 days ago)
• Topics: bioconductor, differential-expression, qc, r, report, rna-seq, smallrna
• Language: R
• Homepage: http://lpantano.github.io/DEGreport/
• Size: 51.7 MB
• Stars: 23
• Watchers: 5
• Forks: 16
• Open Issues: 16
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# DEGreport



[![Build status](https://secure.travis-ci.org/lpantano/DEGreport.png)](https://travis-ci.org/lpantano/DEGreport)

[![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)

[![BioC Downloads](http://bioconductor.org//shields/downloads/DEGreport.svg)](http://bioconductor.org/packages/3.6/bioc/html/DEGreport.html)

[![coverage](https://img.shields.io/codecov/c/github/lpantano/DEGreport/master.svg)](https://codecov.io/github/lpantano/DEGreport?branch=master)

[![Support this project by running your production jobs at BatchX](https://images.batchx.io/gh-badge-logo.svg)](https://platform.batchx.io/lpantano-team/tools/degreport%2Fdeg-patterns "Support this project by running your production jobs at BatchX")

QCs, figures and analyses after differential expression with DESeq2 or other similar tool.

Pantano L (2017). DEGreport: Report of DEG analysis. R package version 1.13.8. 

DOI: [10.18129/B9.bioc.DEGreport](https://doi.org/doi:10.18129/B9.bioc.DEGreport)

## Installation

This is an [R][] package.

### [Bioconductor][] stable version

```r

if (!requireNamespace("BiocManager", quietly=TRUE))

    install.packages("BiocManager")

BiocManager::install("DEGreport")

```

### [Bioconductor][] latest version

```r

devtools::install_git("https://[email protected]/packages/DEGreport")

```

### [devtools][] unstable version

```r

install.packages("devtools")

devtools::install_github("lpantano/DEGreport")

```

Load the package and learn what to do:

`browseVignettes("DEGreport")`

Here is the last devel [vignette](https://bioconductor.org/packages/devel/bioc/vignettes/DEGreport/inst/doc/DEGreport.pdf).

[Bioconductor]: https://bioconductor.org

[bcbio-nextgen]: https://github.com/chapmanb/bcbio-nextgen

[devtools]: https://cran.r-project.org/package=devtools

[R]: https://www.r-project.org