ISA-tools/Risa

Risa allows to access metadata/data in ISA-tab format and builds Bioconductor data structures. Apart from parsing ISA-tab files, the package also provides functionality to save the ISA-tab dataset, or each of its individual files. Additionally, it is also possible to update assay files. Currently, metadata associated to proteomics and metabolomics-based assays (i.e. mass spectrometry) can be processed into an xcmsSet object (from the xcms R package).

Issues

Risa package missing from Bioconductor 3.19
#40 opened 6 months ago by rkjulian
0
Example getExpressionSet
#38 opened 7 years ago by mverouden
1
Warning: Undocumented S4 methods
#35 opened 8 years ago by sneumann
7
Assay Missing
#29 opened 10 years ago by pietrofranceschi
6
A ‘vignettes’ directory is required as from R 3.1.0
#28 opened 10 years ago by sneumann
0
Risa chokes in the presence of editor backup files like "i_Investigation~"
#27 opened 10 years ago by sneumann
0
Warning about Class "C++Object" when running R CMD INSTALL
#4 opened 12 years ago by agbeltran
1
Fails to open Investigations with filenames like a_creinhardtii_metabolite profiling_mass spectrometry.txt
#23 opened 11 years ago by sneumann
1
Risa 1.2.0 and 1.3.0 fail on BioC
#18 opened 12 years ago by sneumann
2
readISAtab fails for MTBLS25
#11 opened 12 years ago by sneumann
3
Use all factors as phenoData for XCMS
#12 opened 12 years ago by sneumann
1
Process mass spectrometry assays
#5 opened 12 years ago by agbeltran
0
Parse complete ISATab dataset
#3 opened 12 years ago by agbeltran
2
creating xcmsSet only works from within unzipped ISA directory
#2 opened 13 years ago by sneumann
0