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 the bug see: https://app.readthedocs.org/projects/quantms/ Apparently the configuration file is missing or was removed?
Hi, Thank you for your hard work. This is an interesting project. When I was trying to test the pipeline with a custom TSV following the OpenMS experimental design format...
### Description of the bug My SDRF file has two digestion enzymes (two columns comment[cleavage agent details]). But only one is input in CometAdapter. Implement a --second_enzyme that will take...
Hi, I experience major issues running 14 different PDC studies. For all runs I use the same database; the human proteome (uniprot9606) fasta file. And I run this command: ```...
### Description of the bug I try to run quantms with a premade sdrf file, but it does not download the files using file uri. The download link works with...
### Description of feature The current DIA workflow does not support the Conda platform. Only the ID, DDA-LFQ, and DDA-TMT can be run in the three platforms Conda, Docker, and...
### Description of feature Dear team, First of all, thank you all very much for helping me with configuring DIANN for DIA profiling data. Now, I hope to extend my...
### Description of feature Before integrating into quantms, the phospho scoring algorithm based on AScore should be optimised. This issue should work to track all the issues with the algorithm.
### Description of feature We have multiple issues related to msstats and the lack of response when the data does not fit any model. This includes inhouse quantms projects but...
### Description of the bug Greetings! We want to use quantms on a computing cluster in a Docker virtual environment. We installed it according to the instructions in documentatiob. In...
