- implemented a novel approach to scoring that uses measurements from panel-based tests such as RT-qPCR and nanostring
- implemented a function that returns a set of stable genes we have identified in carcinomas and in blood
- fixed bugs in the multiScore function that produced errors when scoring a single sample
- fixed bugs in the generateNull function that produced errors when assessing a single geneset
- fixed bugs in the vignette
- added link to the F1000research published workflow that demonstrates usage of singscore on a real dataset (https://f1000research.com/articles/8-776/v2)
- allow labelling of samples on dispersion plots (
plotDispersion) in a similar manner to landscape plots (projectScoreLandscape)
- allow continous and discrete annotations for
plotDispersionandprojectScoreLandscape. Annotations can now be part of the score data.frame and then specified as a column name - plot themes updated
- citation updated: cite the singscore manuscript
- number of bins for the hexbin plot in
plotLandscapeis determined from the data - fixed bug in calculation of scores. Boundary calculation was previously done with all genes in the gene-set. It should be done with genes present in both the gene-set and the data (i.e. after filtering out those not measured in the data).
- TotalDispersion now estimated as the mean of dispersions from the up- and down-regulated gene sets instead of the sum (previous estimate divided by 2)
- created a website for the package
- added ORCID IDs for authors
- added sticker for package
- remove internal keyword from generateNull
- vectorize getPvals
- make toy_epxr_se
- represent expression data in SummarizedExperiement dataset
- function input checkings
- R code re-organised
- change argument name bidirectional to knownDirection, default as TRUE
- bidirection flag added to simpleScore() function
- optimise generateNull() function
- change GSEABase from import to Depends