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NEWS
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NEWS
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CHANGES IN VERSION 1.8.0 (2020-04-22)
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o implemented a novel approach to scoring that uses measurements from panel-based tests such as RT-qPCR and nanostring
o implemented a function that returns a set of stable genes we have identified in carcinomas and in blood
o fixed bugs in the multiScore function that produced errors when scoring a single sample
o fixed bugs in the generateNull function that produced errors when assessing a single geneset
o fixed bugs in the vignette
CHANGES IN VERSION 1.5.1 (2019-10-03)
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o added link to the F1000research published workflow that demonstrates usage of singscore on a real dataset (https://f1000research.com/articles/8-776/v2)
o allow labelling of samples on dispersion plots (`plotDispersion`) in a similar manner to landscape plots (`projectScoreLandscape`)
CHANGES IN VERSION 1.3.2
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o 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
o plot themes updated
o citation updated: cite the singscore manuscript
o number of bins for the hexbin plot in `plotLandscape` is determined from the data
o 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).
o 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)
CHANGES IN VERSION 1.2.2
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o created a website for the package
o added ORCID IDs for authors
o added sticker for package
CHANGES IN VERSION 0.99.9
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o remove internal keyword from generateNull
CHANGES IN VERSION 0.99.8
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o vectorize getPvals
o make toy_epxr_se
CHANGES IN VERSION 0.99.5
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o represent expression data in SummarizedExperiement dataset
o function input checkings
o R code re-organised
CHANGES IN VERSION 0.99.3
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o change argument name bidirectional to knownDirection, default as TRUE
CHANGES IN VERSION 0.99.2
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o bidirection flag added to simpleScore() function
o optimise generateNull() function
o change GSEABase from import to Depends