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I am using the windows installed deepLC application. Train with unmodified peptide information from MaxQuant evidence.txt, and test with unmodified peptide gets good results. However, there is the fol…
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I got sequence and retention times from the msms.txt file of a chymotrypsin MaxQuant search result. Use R to select columns, and split them into the following csvs.
test.csv
seq,modifications
AAA…
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- Describe the issue or question:
Dear all,
I have python 3.10 installed on my computer and tried to use library generation with FragPipe. However, this version is not yet completely supported …
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To enable DeepLC calibration and other DeepLC options in fasta2speclib, the fasta2speclib config (from json file) should be passed to the `ms2pip.retention_time` module:
Replace this line:
https:/…
RalfG updated
2 years ago
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Hello,
I have noticed, that when selecting one of the default models (i.e. `--file_model` is not provided) the last one in the list is selected as the best one independently of the performance.
He…
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Hello,
I used to be able to install without issues and now there are various failures because of wxPython and/or gooey. I need to be able to install without ui on virtual machines (i.e. docker) and o…
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Hi,
Thank you for providing such useful tools! Good job!
Something related to https://github.com/compomics/DeepLC/issues/16
Does the docker version support GPU? In specific Tesla A100/V100 series…
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sklearn is missing as a dependency in setup.py and the conda yaml file:
https://github.com/bioconda/bioconda-recipes/blob/master/recipes/deeplc/meta.yaml
The GitHub Actions tests pass, as sklearn …
RalfG updated
2 years ago
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I am using DeepLC through the MS2PIP website along with the intensity predictor for a list of peptides. Many of the peptides are assigned a negative retention time and I am not sure how to interpret t…
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Dear all,
as I have a larger batch of predictions, I wanted to use the MS2PIP_Server.py script (https://github.com/compomics/ms2pip_c/wiki/MS2PIP-Server-API). The idea is to forward the predictions…