Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / compomics/DeepLC issues and pull requests

#80 - Update test.yml

Pull Request - State: closed - Opened by RobbinBouwmeester about 2 months ago

#79 - Update to tf 2.15 >

Pull Request - State: closed - Opened by RobbinBouwmeester about 2 months ago

#78 - Documentation or reference for missing models

Issue - State: open - Opened by vrkosk 2 months ago - 2 comments

#77 - Datasets

Issue - State: open - Opened by xiaosiruwei 2 months ago - 1 comment

#75 - Tons of warnings when using iTRAQ4plex or iTRAQ8plex

Issue - State: open - Opened by vrkosk 3 months ago - 3 comments

#73 - Documentation: table of peptide properties of training data sets

Issue - State: closed - Opened by vrkosk 4 months ago - 2 comments

#72 - Fix GUI publish workflow

Pull Request - State: closed - Opened by RalfG 6 months ago

#71 - GUI DeepLC errors

Issue - State: closed - Opened by MassambaNdiaye 6 months ago - 3 comments

#70 - data set

Issue - State: closed - Opened by HR-RH 7 months ago

#69 - Update CI workflows

Pull Request - State: closed - Opened by RalfG 8 months ago

#68 - Avoid some dependencies

Pull Request - State: closed - Opened by RalfG 8 months ago

#67 - How can I get the PSI-MS format for the 'modifications' column?

Issue - State: closed - Opened by ec-ho-ra-mos 11 months ago - 12 comments

#65 - change pypi to token

Pull Request - State: closed - Opened by RobbinBouwmeester about 1 year ago

#64 - Minor tweaks

Pull Request - State: closed - Opened by RalfG about 1 year ago

#63 - Training new models

Issue - State: closed - Opened by KarlClauser about 1 year ago - 3 comments

#62 - How to configure support for selenocysteine in its carbamidomethylated form?

Issue - State: closed - Opened by KarlClauser about 1 year ago - 2 comments

#61 - Minor tweaks to plotting code, fix missing entry in manifest

Pull Request - State: closed - Opened by RalfG about 1 year ago
Labels: bug, enhancement

#60 - Fix memory leak due to repeatedly calling model.predict(...)

Pull Request - State: closed - Opened by markmipt about 1 year ago

#59 - Pygam calibration is the only option in the latest version

Issue - State: closed - Opened by markmipt about 1 year ago - 5 comments

#58 - batch_num is not used anymore in the resent versions

Issue - State: closed - Opened by markmipt about 1 year ago - 3 comments

#57 - deeplc gui

Issue - State: closed - Opened by HR-RH about 1 year ago - 4 comments

#56 - Error during calibration using modified peptides

Issue - State: closed - Opened by steffenlem over 1 year ago - 4 comments

#55 - I cannot run it on website when my file getting bigger

Issue - State: closed - Opened by hetaofan over 1 year ago - 2 comments

#54 - Low prediction accuracy for versions 2.0.4+

Issue - State: closed - Opened by markmipt over 1 year ago - 3 comments

#53 - error using GUI to predict rt

Issue - State: closed - Opened by sehooni over 1 year ago - 3 comments

#52 - Fix Streamlit web server

Pull Request - State: closed - Opened by RalfG over 1 year ago

#51 - Psm utils integration

Pull Request - State: closed - Opened by RobbinBouwmeester over 1 year ago

#50 - fix load model

Pull Request - State: closed - Opened by ArthurDeclercq over 1 year ago

#49 - Optimized library usage (~85% reduce in DeepLC prediction time)

Pull Request - State: closed - Opened by markmipt almost 2 years ago

#48 - Error when using unmodified peptide to train and using modified peptides to test

Issue - State: closed - Opened by WeiqiangChen almost 2 years ago - 7 comments

#47 - psm_utils integration and code refactoring

Pull Request - State: closed - Opened by RalfG almost 2 years ago

#46 - error using https://iomics.ugent.be/deeplc/

Issue - State: closed - Opened by WeiqiangChen about 2 years ago - 3 comments

#45 - psm_utils integration and code refract

Pull Request - State: closed - Opened by RobbinBouwmeester about 2 years ago

#44 - How to convert peptide modifications of maxquant output file to MS2PIP-style

Issue - State: closed - Opened by lbwfff about 2 years ago - 5 comments

#43 - Make `gooey` an optional dependency

Pull Request - State: closed - Opened by RalfG over 2 years ago
Labels: GUI

#42 - New GUI using Gooey, PyInstaller, and Inno Setup

Pull Request - State: closed - Opened by RalfG over 2 years ago
Labels: enhancement, GUI

#41 - Fix default model selection

Pull Request - State: closed - Opened by caetera over 2 years ago

#40 - The last of default models is selected as the best one

Issue - State: closed - Opened by caetera over 2 years ago - 4 comments

#39 - pip install on Python 3.10 not working correctly

Issue - State: closed - Opened by levitsky over 2 years ago - 9 comments

#38 - add scikit-learn dependency

Pull Request - State: closed - Opened by paretje over 2 years ago

#37 - scikit-learn / sklearn missing from dependency list

Issue - State: closed - Opened by RalfG over 2 years ago - 2 comments
Labels: dependencies

#36 - Deeplc docker GPU support

Issue - State: closed - Opened by Hendricks27 over 2 years ago - 2 comments

#35 - Use importlib to get installed version

Pull Request - State: closed - Opened by RalfG almost 3 years ago

#34 - negative retention times

Issue - State: closed - Opened by Seb-Leb almost 3 years ago - 4 comments

#33 - Streamlit webapp updates

Pull Request - State: closed - Opened by RalfG about 3 years ago
Labels: Streamlit Web Server

#32 - use logger instead of logging

Pull Request - State: closed - Opened by paretje over 3 years ago

#31 - Predictions are slow when library is not full

Issue - State: closed - Opened by markmipt over 3 years ago - 3 comments

#30 - Fix Streamlit container tags yaml formatting

Pull Request - State: closed - Opened by RalfG over 3 years ago
Labels: bug, packaging, Streamlit Web Server

#29 - Support Python 3.9

Pull Request - State: closed - Opened by paretje over 3 years ago

#28 - Bump commons-io from 2.6 to 2.7 in /deeplc_gui

Pull Request - State: closed - Opened by dependabot[bot] over 3 years ago
Labels: dependencies

#27 - Add link to web application to README.md

Pull Request - State: closed - Opened by RalfG over 3 years ago

#26 - Minor updates to streamlit web server

Pull Request - State: closed - Opened by RalfG over 3 years ago
Labels: enhancement, Streamlit Web Server

#25 - Minor improvements and fixes to streamlit webserver

Pull Request - State: closed - Opened by RalfG over 3 years ago
Labels: enhancement, Streamlit Web Server

#24 - Streamlit webserver improvements and deployment fixes

Pull Request - State: closed - Opened by RalfG over 3 years ago
Labels: enhancement, packaging, Streamlit Web Server

#23 - First fully functional web server version

Pull Request - State: closed - Opened by RalfG over 3 years ago - 1 comment
Labels: enhancement, packaging, Streamlit Web Server

#22 - Initial streamlit webserver implementation

Pull Request - State: closed - Opened by RalfG over 3 years ago
Labels: enhancement, packaging, Streamlit Web Server

#21 - What is the unit of tr: retention time (only required for calibration)?

Issue - State: closed - Opened by chinmayaNK22 over 3 years ago - 2 comments

#20 - DeepLC CPU vs GPU performance

Issue - State: closed - Opened by markmipt over 3 years ago - 5 comments

#19 - DeepLC (tensorflow) does not seem to obey num_jobs

Issue - State: closed - Opened by RalfG over 3 years ago - 2 comments

#18 - Unpin/relax tensorflow/scipy/numpy requirements

Pull Request - State: closed - Opened by RalfG over 3 years ago
Labels: packaging

#17 - Bioconda package autobump has some issues

Issue - State: closed - Opened by RalfG over 3 years ago - 1 comment
Labels: packaging

#16 - DeepLC as a docker image

Issue - State: closed - Opened by MarcIsak almost 4 years ago - 2 comments
Labels: question

#14 - Skipping calibration step?

Issue - State: closed - Opened by MarcIsak about 4 years ago - 4 comments

#13 - Drop restriction on python 3.8

Pull Request - State: closed - Opened by paretje over 4 years ago - 1 comment

#12 - Possibility to retrain a model

Issue - State: closed - Opened by cctsou over 4 years ago - 1 comment

#10 - Blank spot after calibration

Issue - State: closed - Opened by courcelm over 4 years ago - 8 comments

#9 - Python 3.8 compatibility

Issue - State: closed - Opened by paretje over 4 years ago - 3 comments

#8 - Update README.md

Pull Request - State: closed - Opened by RalfG over 4 years ago

#7 - Allow pandas v1

Pull Request - State: closed - Opened by RalfG over 4 years ago

#6 - Fix running DeepLC from multiprocessing environment

Pull Request - State: closed - Opened by paretje over 4 years ago

#5 - New version - fixed no models passed

Pull Request - State: closed - Opened by RobbinBouwmeester over 4 years ago

#4 - Ensemble support

Pull Request - State: closed - Opened by RobbinBouwmeester over 4 years ago

#3 - Move to Pypi package structure

Pull Request - State: closed - Opened by RalfG almost 5 years ago

#2 - Small fixes for external usage

Pull Request - State: closed - Opened by RalfG almost 5 years ago

#1 - Gui

Pull Request - State: closed - Opened by RobbinBouwmeester almost 5 years ago