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Change chunk injection #8

Merged
merged 37 commits into from
May 1, 2023
Merged

Change chunk injection #8

merged 37 commits into from
May 1, 2023

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csoneson
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@csoneson csoneson commented May 1, 2023

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@csoneson
Version bump
d9f9cc0
@csoneson
Change Rmd text injection to avoid need for duplicating escapes
539a99f
@csoneson
Adapt run scripts to new way of injecting values into the Rmd files
759f07e
@csoneson
Add argument to set the colour column in doPCA
7cc9742
@csoneson
Collapse list of comparisons and group compositions also in PTM workflow
171c0ea
@csoneson
Use einprotLabel instead of pid for labeling in peptide vs protein lo…
febcbab 
…gFC plot
@csoneson
Fix CHECK notes
21cd583
@csoneson
Include extra columns in output from runPTMTest
7a2fc9c
@csoneson
Add FragPipe example data
d35ff49
@csoneson
Add tests for FragPipe run functions
647040d
@csoneson
Expand unit tests
83daf8c
@csoneson
Fix tidyselect warnings
3c57118
@csoneson
Allow '^Abundance.' iColPattern
d9abdf0
@csoneson
Fix PDTMT argument check
ace55c2
@csoneson
Suggest closest iColPattern if the provided one is invalid
eb0d3fc
@csoneson
Add test for identical sample weights
51707e2
@csoneson
Display sample weights in html
90aaf40
@csoneson
Add more unit tests
4230512
@csoneson
Add scale and subset_row arguments to doPCA
6264c38
@csoneson
Move definition of feature IDs after the filtering
049d3f7
@csoneson
Version bump
f84481e
@csoneson
Extract FragPipe decoy pattern from config file
173e0d9
@csoneson
Remove features with too few non-imputed values before doing PCA
55fe663
@csoneson
Retain a few more rowData columns for MaxQuant
a502ea7
@csoneson
Fix extraction of fixed modifications from MQ XML file
6e85ce1
@csoneson
Read also min peptide length and max peptide mass from MQ XML
83459da
@csoneson
Add Top3 to the valid assays
b37285b
@csoneson
Add also Top3 abundances to MQ test result output
a0c013b
@csoneson
Allow more than one abundanceColPat in plotVolcano
8d1dd79
@csoneson
Specify assay to use for iSEE heatmaps
e08546b
@csoneson csoneson merged commit f1e5580 into main May 1, 2023
@csoneson csoneson deleted the change-chunk-injection branch May 1, 2023 08:16
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@csoneson