diff --git a/DESCRIPTION b/DESCRIPTION index bdd10bd..02586b8 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: rnaseqDTU Title: RNA-seq workflow for differential transcript usage following Salmon quantification -Version: 0.99.16 +Version: 0.99.17 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 cd012ae..aecda58 100644 --- a/vignettes/bibliography.bib +++ b/vignettes/bibliography.bib @@ -203,18 +203,6 @@ @article{Yi2018Gene publisher={BioMed Central} } -@article{Anders2012DEXSeq, - title={{Detecting differential usage of exons from RNA-seq data}}, - author={Anders, Simon and Reyes, Alejandro and Huber, Wolfgang}, - journal={{Genome Research}}, - volume={22}, - number={10}, - pages={2008--2017}, - year={2012}, - publisher={Cold Spring Harbor Lab} -} - - @article{Love2014Moderated, author = {Love, Michael I. and Huber, Wolfgang and Anders, Simon}, journal = {Genome Biology}, diff --git a/vignettes/rnaseqDTU.Rmd b/vignettes/rnaseqDTU.Rmd index a5fb2bd..2fd4499 100644 --- a/vignettes/rnaseqDTU.Rmd +++ b/vignettes/rnaseqDTU.Rmd @@ -64,7 +64,7 @@ opts_chunk$set(message=TRUE, warning=FALSE, error=FALSE, RNA-seq experiments can be analyzed to detect differences across groups of samples in total gene expression -- the total expression produced by all isoforms of a gene -- and additionally differences in -transcript usage within a gene. If the amount of expression +transcript isoform usage within a gene. If the amount of expression switches among two or more isoforms of a gene, then the total gene expression may not change by a detectable amount, but the differential transcript usage (DTU) is nevertheless biologically relevant. @@ -75,8 +75,8 @@ tissue-specific isoforms [@Reyes2018]. DTU may produce functionally different gene products through alternative splicing and changes to the coding sequence of the transcript, and DTU may result in transcripts with different untranslated regions on the 5' or 3' end of -the transcript, which may affect recognition sites of RNA binding -proteins. [@Reyes2018] found that the later case, alternative usage +the transcript, which may affect binding sites of RNA binding +proteins. [@Reyes2018] found that the later case, alternative usage of transcription start and termination sites, was a more common event than alternative splicing when examining DTU events across tissues in GTEx. Specific patterns of DTU have been identified in a number of @@ -84,7 +84,7 @@ diseases, including cancer, retinal diseases, and neurological disorders, among others [@Scotti2018]. Large-scale analyses of cancer transcriptomic data, comparing tumor to normal samples, have identified that protein domain losses are a common feature of DTU in -cancers, including domains involved in protein-protein interactions +cancer, including domains involved in protein-protein interactions [@Vitting2017;@Climente2017]. While many tutorials and workflows in the @@ -814,7 +814,7 @@ to controlling its FDR and OFDR in the evaluations, after using the ## DEXSeq The *DEXSeq* package was originally designed for detecting -differential exon usage [@Anders2012DEXSeq], but can also be adapted +differential exon usage [@Anders2012Detecting], but can also be adapted to run on estimated transcript counts, in order to detect DTU. Using *DEXSeq* on transcript counts was evaluated by @Soneson2016Isoform, showing the benefits in FDR control from @@ -873,7 +873,7 @@ have already conducted filtering via *DRIMSeq* functions). We compute a per-gene adjusted p-value, using the *perGeneQValue* function, which aggregates evidence from multiple tests within a gene to a single p-value for the gene and then corrects for multiple testing across -genes [@Anders2012DEXSeq]. Other methods for aggregative evidence from the +genes [@Anders2012Detecting]. Other methods for aggregative evidence from the multiple tests within genes have been discussed in a recent publication and may be substituted at this step [@Yi2018Gene]. Finally, we build a simple results table with the @@ -939,7 +939,7 @@ head(dex.padj) ## Citing methods in published research This concludes the DTU section of the workflow. If you use *DRIMSeq* -[@Nowicka2016DRIMSeq], *DEXSeq* [@Anders2012DEXSeq], +[@Nowicka2016DRIMSeq], *DEXSeq* [@Anders2012Detecting], *stageR* [@Van2017StageR], *tximport* [@Soneson2015Differential], or *Salmon* [@Patro2017Salmon] in published research, please cite the relevant methods publications,