From 569391f447276f7c1036483d408c9b1d88bc1098 Mon Sep 17 00:00:00 2001 From: Christian Mertes Date: Thu, 27 Aug 2020 12:00:03 -0700 Subject: [PATCH] Bump FRASER version 1.1.2 -> 1.1.3 --- DESCRIPTION | 4 ++-- NEWS | 10 ++++++++++ README.md | 9 ++++----- 3 files changed, 16 insertions(+), 7 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 95d4b906..9c755390 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: FRASER Type: Package Title: Find RAre Splicing Events in RNA-Seq Data -Version: 1.1.2 -Date: 2020-06-08 +Version: 1.1.3 +Date: 2020-08-27 Authors@R: c( person("Christian", "Mertes", role=c("aut", "cre"), email="mertes@in.tum.de"), diff --git a/NEWS b/NEWS index c9376c61..a763b678 100644 --- a/NEWS +++ b/NEWS @@ -1,3 +1,13 @@ +CHANGES IN VERSION 1.1.3 +------------------------- + + o Update and adjust injectOutlier and hyperParameter functions + o Option to compute z scores in logit space or not + o Add cap value [0.01,0.99] to logit function + o Use pairedEnd counting with Rsubread + o Correct assayName pajd -> padj + o Minor bugfixes + CHANGES IN VERSION 1.1.2 ------------------------- diff --git a/README.md b/README.md index a35e8799..dca99c9e 100644 --- a/README.md +++ b/README.md @@ -2,12 +2,11 @@ [![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) -[![Version](https://img.shields.io/badge/Version-1.1.2-green.svg)](https://github.com/gagneurlab/FRASER/tree/master) -[![Coverage status](https://codecov.io/gh/c-mertes/FRASER/branch/master/graph/badge.svg)](https://codecov.io/github/c-mertes/FRASERbranch=master) +[![Version](https://img.shields.io/badge/Version-1.1.3-green.svg)](https://github.com/c-mertes/FRASER/tree/master) +[![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/gagneurlab/OUTRIDER/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). - +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). 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. @@ -37,7 +36,7 @@ if (!requireNamespace("devtools", quietly=TRUE)) devtools::install_github('gagneurlab/FRASER', dependencies=TRUE) # or a specific version of FRASER (search for tags on github) -devtools::install_github('gagneurlab/FRASER', ref='1.1.2', dependencies=TRUE) +devtools::install_github('gagneurlab/FRASER', ref='1.1.3', dependencies=TRUE) ``` If you have dependency issues while installing any package, please have a look