APAF-bioinformatics APAFunctions issues

APAF-bioinformatics / APAFunctions

R package of all the functions common to APAF's proteomics analysis code. Intended for install_github("APAF-bioinformatics/APAFunctions")

https://apaf-bioinformatics.github.io/APAFunctions/

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issues

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TMT is broken as APAFunctions::HClust doesn't incorporate a TMT flag

#15 gerisullivan opened 1 year ago
0
Change all instances of exp to experiment as there is an inbuilt R function called exp already and we can't overwrite that in the readInputFiles loop

#14 gerisullivan opened 1 year ago
1
createResultsImages.xlsx can issue Errors if some of the images aren't created

#13 keiran-rowell-mq opened 1 year ago
1
Heatmap colouring

#12 gerisullivan opened 1 year ago
0
APAFunctions could be published as a Bioconductor package

#11 keiran-rowell-mq opened 1 year ago
0
createdClusterDendrogram() should be merged with plotColouredDendrogram()

#10 keiran-rowell-mq closed 1 year ago
1
Functions that have multiple options (SWATH or TMT) or (Prot vs Pep) should use c("Option 1", "Option 2") so in the function argument so the documentation becomes clearer

#9 keiran-rowell-mq closed 1 year ago
1
APAFunctions/tests/testthat() should have descriptive statistics and plotting tests

#8 keiran-rowell-mq opened 1 year ago
0
Move the APAF codebase to R 4

#7 keiran-rowell-mq closed 1 year ago
2
SWATH results and TMT results are using different print[Info|Explaination]Sheet functions

#6 keiran-rowell-mq closed 1 year ago
1
Decide on the highlight colours for cells in the Excel data sheets.

#5 keiran-rowell-mq closed 1 year ago
0
printDataSheetxlsx() should have a Protect = TRUE/FALSE flag

#4 keiran-rowell-mq closed 1 year ago
1
normalize.R should be a wrapper for *any* normalisation applied to APAF data.

#3 keiran-rowell-mq opened 1 year ago
1
APAF plots could use Pokemon colourschemes

#2 keiran-rowell-mq closed 1 year ago
1
APAFunctions documentation can be improved

#1 keiran-rowell-mq opened 1 year ago
0