From 46b6e0b2d8e20e1a897ee84968e747789a611519 Mon Sep 17 00:00:00 2001 From: Christian Mertes Date: Wed, 27 Jan 2021 22:52:05 +0100 Subject: [PATCH] version bump and cleanup --- DESCRIPTION | 4 ++-- NEWS | 5 +++++ README.md | 9 ++++++--- 3 files changed, 13 insertions(+), 5 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 900bf577..62d249c6 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: FRASER Type: Package Title: Find RAre Splicing Events in RNA-Seq Data -Version: 1.3.0 -Date: 2020-10-15 +Version: 1.3.1 +Date: 2021-01-27 Authors@R: c( person("Christian", "Mertes", role=c("aut", "cre"), email="mertes@in.tum.de"), diff --git a/NEWS b/NEWS index d4b3770d..5603fb13 100644 --- a/NEWS +++ b/NEWS @@ -1,3 +1,8 @@ +CHANGES IN VERSION 1.2.1 + o Add merging of external counts + o Add publication + o Minor bugfixes + CHANGES IN VERSION 1.1.6 ------------------------- o Use proper S3/S4 methods to share functions between packages diff --git a/README.md b/README.md index 8edac3a7..8e9443aa 100644 --- a/README.md +++ b/README.md @@ -1,15 +1,18 @@ # FRASER - Find RAre Splicing Events in RNA-seq -[![Build Status](https://travis-ci.com/c-mertes/FRASER.svg?branch=master)](https://travis-ci.com/c-mertes/FRASER) -[![AppVeyor build status](https://ci.appveyor.com/api/projects/status/371x22cn6fipu7bw/branch/master?svg=true)](https://ci.appveyor.com/project/c-mertes/fraser/branch/master) +[![Build](https://github.com/c-mertes/FRASER/workflows/Build/badge.svg?branch=master)](https://github.com/c-mertes/FRASER/actions?query=workflow%3ABuild) [![Version](https://img.shields.io/github/v/release/c-mertes/FRASER)](https://github.com/c-mertes/FRASER/releases) [![Coverage status](https://codecov.io/gh/c-mertes/FRASER/branch/master/graph/badge.svg)](https://codecov.io/github/c-mertes/FRASER/branch/master) [![License](https://img.shields.io/github/license/mashape/apistatus.svg?maxAge=2592000)](https://github.com/c-mertes/FRASER/blob/master/LICENSE) -FRASER is a tool to detect aberrant splicing events in RNA-seq data. The method is described in a preprint on [bioRxiv](https://www.biorxiv.org/content/10.1101/2019.12.18.866830v1) and available through [Bioconductor](http://bioconductor.org/packages/release/bioc/html/FRASER.html). It is also part of the [Detection of RNA Outlier Pipeline (DROP)](https://github.com/gagneurlab/drop). The DROP pipeline is described [here on Nature's protocol exchange](https://doi.org/10.21203/rs.2.19080/v1). +FRASER is a tool to detect aberrant splicing events in RNA-seq data. The method is described and published in [Nature Communications](https://doi.org/doi:10.1038/s41467-020-20573-7) and available through [Bioconductor](https://doi.org/doi:10.18129/B9.bioc.FRASER). It is also part of the [Detection of RNA Outlier Pipeline (DROP)](https://github.com/gagneurlab/drop). The DROP pipeline is described and published in [Nature Protocols](https://doi.org/doi:10.1038/s41596-020-00462-5). The FRASER framework and workflow aims to assist the diagnostics in the field of rare diseases where RNA-seq is performed to identify aberrant splicing defects. For a short tutorial on how to use FRASER on a dataset please use the [vignette](http://bioconductor.org/packages/release/bioc/vignettes/FRASER/inst/doc/FRASER.pdf) or our Colab tutorial at: [http://tinyurl.com/RNA-ASHG-colab](http://tinyurl.com/RNA-ASHG-colab). The Colab is based on a workshop that we presented at ASHG 2019/2020. +Please cite our method paper if you use it in a publication: + +> Mertes, C., Scheller, I.F., Yépez, V.A. *et al.* Detection of aberrant splicing events in RNA-seq data using FRASER. *Nat Commun* **12**, 529 (2021). https://doi.org/10.1038/s41467-020-20573-7 + ## Installation `FRASER` is an R/Bioconductor software package requiring a running