NEWS.md

In DavisLaboratory/singscore: Rank-based single-sample gene set scoring method

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

DavisLaboratory/singscore documentation built on Nov. 21, 2024, 8:17 a.m.