Changelog

Source: NEWS.md

singscore 1.8.0

  • 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

singscore 1.5.1

  • 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)

singscore 1.3.2

  • allow continous and discrete annotations for plotDispersion and projectScoreLandscape. 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 plotLandscape is 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)

singscore 1.2.2

  • created a website for the package
  • added ORCID IDs for authors
  • added sticker for package

singscore 0.99.9

  • remove internal keyword from generateNull

singscore 0.99.8

  • vectorize getPvals
  • make toy_epxr_se

singscore 0.99.5

  • represent expression data in SummarizedExperiement dataset
  • function input checkings
  • R code re-organised

singscore 0.99.3

  • change argument name bidirectional to knownDirection, default as TRUE

version 0.99.2

  • bidirection flag added to simpleScore() function
  • optimise generateNull() function
  • change GSEABase from import to Depends