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 We have a big error with LFQ data: ``` nf-core/quantms execution completed unsuccessfully! The exit status of the task that caused the workflow execution to...
### Description of the bug @daichengxin I have reanalyzed again the dataset PXD014414, if you see the volcano plots almost no proteins are differentially expressed. I was checking the notebooks...
### Description of the bug Project URL: http://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/proteomes/proteogenomics/benchmakrs/7a81c7b0dd0465b49b39b743bc8d0a/ ### Command used and terminal output _No response_ ### Relevant files _No response_ ### System information _No response_
### Description of the bug URL of the working file: http://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/proteomes/proteogenomics/benchmakrs/15acadc82868c799e567dd1b219b44/ ``` nf-core/quantms execution completed unsuccessfully! The exit status of the task that caused the workflow execution to fail was:...
### Description of feature @jpfeuffer and @ypriverol discussed that it would be great to have 2 full datasets, LFQ and TMT for the AWS tests. We need to find from...
### Description of feature I'm aiming to integrate the MSFragger search engine into the QuantMS workflow. It should be included as an option for the closed search, alongside a completely...
### Description of feature FLR is the current method Luciphor has to compute the statistics around the phospho sites. However, Luciphor needs 50 PSMs by each charge state to compute...
### Description of feature We probably need to do this to put them into nf-core anyway. E.g. - [x] add containers everywhere, even if it just uses bash - [x]...
### Description of feature Hi @jpfeuffer : At some point, we need to update this figure to reflect the steps of the DIANN pipeline. Even if DIANN is used alone...
### Description of feature MSstats scripts for TMT, LFQ and LFQ-DIA shares multiple steps. We should have only one script containing both logics.