diff --git a/DESCRIPTION b/DESCRIPTION index 02586b8..b1c5f9c 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: rnaseqDTU Title: RNA-seq workflow for differential transcript usage following Salmon quantification -Version: 0.99.17 +Version: 0.99.18 Date: 2018-06-27 Authors@R: c(person(role=c("aut", "cre"), "Michael", "Love", email = "michaelisaiahlove@gmail.com"), person(role=c("aut"), "Charlotte", "Soneson"), diff --git a/vignettes/bibliography.bib b/vignettes/bibliography.bib index aecda58..075c539 100644 --- a/vignettes/bibliography.bib +++ b/vignettes/bibliography.bib @@ -108,6 +108,13 @@ @article{Vitting2017 number = 9 } +@article{Vitting2018, + title = {{IsoformSwitchAnalyzeR: Analysis of changes in genome-wide patterns of alternative splicing and its functional consequences}}, + author = {Vitting-Seerup, Kristoffer and Sandelin, Albin}, + year = 2018, + journal = {bioRxiv} +} + @article{Di2017Nextflow, title={Nextflow enables reproducible computational workflows}, author={Di Tommaso, Paolo and Chatzou, Maria and Floden, Evan W and Barja, Pablo Prieto and Palumbo, Emilio and Notredame, Cedric}, diff --git a/vignettes/rnaseqDTU.Rmd b/vignettes/rnaseqDTU.Rmd index 2fd4499..49748b9 100644 --- a/vignettes/rnaseqDTU.Rmd +++ b/vignettes/rnaseqDTU.Rmd @@ -99,7 +99,7 @@ functions that can be used for statistical analysis of DTU include *DRIMSeq* [@Nowicka2016DRIMSeq]. Other Bioconductor packages which are designed around a DTU analysis include *stageR* [@Van2017StageR], *SGSeq* [@Goldstein2016SGSeq], and -*IsoformSwitchAnalyzeR* [@Vitting2017]. +*IsoformSwitchAnalyzeR* [@Vitting2018]. *stageR* can be used for post-processing of transcript- and gene-level p-values from DTU detection methods, and will be discussed in this workflow. *SGSeq* can be used to visualize