quantms
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bigbio
Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Isobaric and DIA-LFQ quantification.
### Description of feature I just ran quantms with the argument '--add-decoy' instead of '--add-decoys' and it ran compute intensive steps until percolator failed and the computations had to be...
The sdrf file check for 'sdrf' in the filename seems arbitrary: https://github.com/bigbio/quantms/blob/e516ddca04a2ff9eedae1df951995b8793c82c62/subworkflows/local/input_check/main.nf#L15 This means the input file name without 'sdrf' fails, even when the file is a valid SDRF file....
### Description of feature When running the simplest nextflow command with quantms, the error is quite cryptic. I believe it should point to some resources and give a useful help...
### Description of the bug There are appears to be a bug in the msstats_tmt.R function, which is executed by the process MSSTATS_TMT module. Specifically, in the parse_contrasts function. The...
### Description of feature We have the protein groups in quantms.io representation here the section https://io.quantms.org/#protein. For all our datasets, Im producing quantms.io using the library. We can now produce...
### Description of feature Hi all: First benchmark against #quantms, claiming they are better on merging multiple search engines!!! Really nice to see quantms getting compare with other tools. Here...