Noble-Lab/casanovo issues and pull requests

#191 - KeyError

Issue - State: closed - Opened by javamng over 1 year ago - 1 comment
Labels: bug

#190 - Casanovo-3.3.0 validation_step is not updated

Issue - State: closed - Opened by r00bit over 1 year ago - 10 comments
Labels: bug

#189 - About the trainning data of CasaNovo published in ICML 2022

Issue - State: closed - Opened by wuwo007 over 1 year ago - 1 comment
Labels: question

#188 - Casanovo skipping spectra unexpectedly

Issue - State: closed - Opened by temana-short over 1 year ago - 17 comments
Labels: bug

#187 - Remove lightning_logs

Issue - State: closed - Opened by wsnoble over 1 year ago
Labels: enhancement

#186 - NaN output from model with some weights

Issue - State: closed - Opened by melihyilmaz over 1 year ago - 6 comments
Labels: bug

#185 - No output with n_beams=1

Issue - State: closed - Opened by melihyilmaz over 1 year ago - 5 comments
Labels: bug

#184 - CLI revamp

Pull Request - State: closed - Opened by wfondrie over 1 year ago - 6 comments

#183 - Error with Casanovo

Issue - State: closed - Opened by BenSamy2020 over 1 year ago - 1 comment
Labels: question

#182 - assembly cutoff

Issue - State: closed - Opened by biocc over 1 year ago - 1 comment
Labels: question

#181 - Preprocess spectra in depthcharge

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

#180 - charge state issues

Issue - State: closed - Opened by wsnoble over 1 year ago - 1 comment
Labels: bug

#179 - Question: Mztab score meanings

Issue - State: closed - Opened by Nkts007 over 1 year ago - 3 comments
Labels: question

#178 - Key error by running example

Issue - State: closed - Opened by PMDekker over 1 year ago - 5 comments
Labels: bug

#177 - Multiprocessing bug when using CPU only

Issue - State: closed - Opened by sampie over 1 year ago - 13 comments
Labels: bug

#176 - Fix CPU bug, overhaul model runner, and update to lightning >=2.0

Pull Request - State: closed - Opened by wfondrie over 1 year ago - 6 comments

#175 - Avoid uninformative warnings

Pull Request - State: closed - Opened by bittremieux over 1 year ago - 3 comments

#174 - Investigate various warnings

Issue - State: closed - Opened by wsnoble over 1 year ago - 4 comments
Labels: enhancement

#173 - Add num_gpus config parameter

Issue - State: closed - Opened by wsnoble over 1 year ago - 4 comments
Labels: enhancement

#172 - Issue a warning when skipping spectra with no charge

Issue - State: closed - Opened by wsnoble over 1 year ago
Labels: enhancement

#171 - Only split off known extensions from output filename

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

#170 - FDR scoring mzTab output

Issue - State: closed - Opened by patrick-willems over 1 year ago - 1 comment
Labels: question

#169 - Suppress distracting warnings

Issue - State: closed - Opened by wsnoble over 1 year ago - 1 comment
Labels: enhancement

#168 - Always use full file paths

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

#167 - KeyError in denovo mode

Issue - State: closed - Opened by wsnoble over 1 year ago
Labels: bug

#166 - Minor refactoring + issue fix

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

#165 - Add validation frequency option

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

#164 - Fix validation step

Pull Request - State: closed - Opened by melihyilmaz over 1 year ago
Labels: bug

#163 - Fix link to sample MGF

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

#162 - Prepare for release v3.3.0

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

#161 - ModuleNotFoundError: No module named 'pytorch_lightning.lite'

Issue - State: closed - Opened by rostkick over 1 year ago - 1 comment
Labels: bug

#160 - Upgrade depthcharge

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

#159 - Including SCANS or TITLE attribute in mztab file

Issue - State: closed - Opened by cguetot over 1 year ago - 1 comment
Labels: enhancement

#158 - KeyError: 'A+42.011'

Issue - State: closed - Opened by cguetot over 1 year ago - 1 comment
Labels: bug

#157 - Replace the `--mode` argument with subcommands

Issue - State: closed - Opened by wfondrie over 1 year ago - 1 comment
Labels: enhancement

#156 - Include model instance arguements with weights

Issue - State: closed - Opened by wfondrie over 1 year ago
Labels: enhancement

#155 - Casanovo Mztab file confirmation

Issue - State: closed - Opened by Nkts007 over 1 year ago - 9 comments
Labels: bug

#154 - Getting top-k candidates

Issue - State: closed - Opened by cguetot over 1 year ago - 1 comment
Labels: enhancement

#153 - Migrate to pyproject.toml and restrict depthcharge version

Pull Request - State: closed - Opened by wfondrie over 1 year ago - 3 comments

#152 - run error when using casanovo_massivekb_v3_0_0.ckpt

Issue - State: closed - Opened by yanshu20220502 over 1 year ago - 4 comments
Labels: bug

#151 - Modularize configuration code

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

#150 - Multiple warnings when running de novo, and doesn't complete

Issue - State: closed - Opened by neely over 1 year ago - 3 comments
Labels: question

#149 - Clarify dependencies

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

#148 - Running Issue: Module Error

Issue - State: closed - Opened by Nkts007 over 1 year ago - 8 comments
Labels: bug

#147 - Install error using "Getting Started" directions

Issue - State: closed - Opened by neely over 1 year ago - 4 comments
Labels: question

#146 - annotating MGFs for training

Issue - State: closed - Opened by yc386 over 1 year ago - 2 comments
Labels: question

#145 - The difference between paper accepted by ISBM2022 and code in this project

Issue - State: closed - Opened by qiyueliuhuo23 over 1 year ago - 9 comments
Labels: question

#144 - Disable multithreading for MPS backend

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

#143 - Numpy errors

Issue - State: closed - Opened by treitpeter over 1 year ago - 3 comments
Labels: bug

#142 - Track scan numbers in MGF files

Issue - State: open - Opened by wsnoble over 1 year ago
Labels: enhancement

#141 - Note that inference should only use a single GPU

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

#140 - Multi-GPU is broken

Issue - State: closed - Opened by seantur almost 2 years ago - 1 comment
Labels: bug

#139 - Export multiple PSMs per spectrum

Pull Request - State: closed - Opened by bittremieux almost 2 years ago - 5 comments

#138 - Discard beams that include multiple N-terminal modifications

Issue - State: closed - Opened by melihyilmaz almost 2 years ago
Labels: enhancement

#137 - No module named 'tensorboard

Issue - State: closed - Opened by yingluoqiao almost 2 years ago - 2 comments
Labels: bug

#136 - Don't predict short peptides

Pull Request - State: closed - Opened by bittremieux almost 2 years ago - 3 comments

#135 - How did Casanovo deal with variable peaks in the encoder ?

Issue - State: closed - Opened by alifare almost 2 years ago - 3 comments
Labels: question

#134 - Replace list comprehension with slicing

Pull Request - State: closed - Opened by seantur almost 2 years ago - 1 comment

#133 - Questions about comparing de novo methods

Issue - State: closed - Opened by wsnoble almost 2 years ago - 3 comments
Labels: question

#132 - Add training data information

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

#131 - Availability of MassIVE-KB dataset

Issue - State: closed - Opened by irleader almost 2 years ago - 6 comments
Labels: question

#130 - First Casanovo DB Search Iteration

Pull Request - State: closed - Opened by VarunAnanth2003 almost 2 years ago - 1 comment
Labels: enhancement

#129 - Casanovo Assigning Multiple Modifications to Single AA

Issue - State: closed - Opened by kostrouc almost 2 years ago - 3 comments
Labels: question

#128 - Freeze / hangup with multiple GPUs

Issue - State: closed - Opened by douweschulte almost 2 years ago - 5 comments
Labels: bug

#127 - Add documentation for config.yaml

Pull Request - State: closed - Opened by melihyilmaz almost 2 years ago - 1 comment

#126 - Align printed metrics with published terminology

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

#125 - Modifications and their representations in revised 9-species benchmark

Issue - State: closed - Opened by irleader almost 2 years ago - 13 comments
Labels: question

#124 - Fix changelog

Pull Request - State: closed - Opened by bittremieux almost 2 years ago - 1 comment

#123 - Check for stop token

Pull Request - State: closed - Opened by bittremieux almost 2 years ago - 1 comment

#122 - Inconsistent metrics result between eval and denovo mode, and possible reason

Issue - State: closed - Opened by irleader almost 2 years ago - 17 comments
Labels: bug

#121 - Calculate AA scores as mean AA scores and peptide score

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

#120 - Document config file

Issue - State: closed - Opened by wsnoble almost 2 years ago - 1 comment
Labels: documentation

#119 - Casanovo nonenzymatic model

Issue - State: closed - Opened by piroman999 almost 2 years ago - 1 comment
Labels: question

#118 - Casanovo Denovo Error

Issue - State: closed - Opened by kostrouc almost 2 years ago - 2 comments
Labels: bug

#117 - Fix unit tests

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

#116 - Describe which model weights file to use

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

#115 - Refuse to predict peptides that are too short

Issue - State: closed - Opened by wsnoble almost 2 years ago
Labels: enhancement

#114 - train a new model

Issue - State: closed - Opened by biocc almost 2 years ago - 1 comment
Labels: question

#113 - Preprint info

Pull Request - State: closed - Opened by bittremieux almost 2 years ago - 1 comment

#112 - Change printed output to reflect terminology in the paper

Issue - State: closed - Opened by melihyilmaz almost 2 years ago
Labels: enhancement

#111 - Inconsistent performance between from provided pretrained model weights and published results

Issue - State: closed - Opened by irleader almost 2 years ago - 11 comments
Labels: question

#110 - How to run as scripts?

Issue - State: closed - Opened by feiluoo almost 2 years ago - 1 comment
Labels: question

#109 - CPUAccelerator devices should be an int > 0

Issue - State: closed - Opened by tempoche1 almost 2 years ago - 3 comments
Labels: bug

#108 - Allow specifying different model weights from GitHub Assets

Issue - State: closed - Opened by bittremieux almost 2 years ago
Labels: enhancement

#107 - Casanovo confidently predicts short peptide sequences (< 5 aa)

Issue - State: closed - Opened by RowanNelson almost 2 years ago - 7 comments
Labels: bug

#106 - Integration test fails on no-GPU machine

Issue - State: closed - Opened by melihyilmaz almost 2 years ago - 1 comment
Labels: bug

#105 - Change PSM ID with identifier in peak file

Pull Request - State: closed - Opened by melihyilmaz almost 2 years ago - 6 comments

#104 - Update README.md

Pull Request - State: closed - Opened by wsnoble almost 2 years ago - 1 comment

#103 - OSError: [Errno 28] Can't write data (file write failed: time = Wed Nov 30 22:27:02 2022

Issue - State: closed - Opened by BenSamy2020 almost 2 years ago - 4 comments
Labels: question

#102 - Assign the mean of AA score and peptide score to each amino acid

Issue - State: closed - Opened by melihyilmaz almost 2 years ago
Labels: enhancement

#101 - Casanovo with GPU engagement

Issue - State: closed - Opened by BenSamy2020 almost 2 years ago - 5 comments
Labels: question

#100 - Release 3.2.0

Pull Request - State: closed - Opened by bittremieux about 2 years ago - 1 comment

#96 - Add multi-PSM output

Issue - State: closed - Opened by melihyilmaz about 2 years ago
Labels: enhancement

#95 - Defining Output Terminology

Issue - State: closed - Opened by kostrouc about 2 years ago - 3 comments
Labels: question

#93 - Running Casanovo in Linux Env

Issue - State: closed - Opened by kostrouc about 2 years ago - 10 comments
Labels: bug

#87 - Add beam search peptide decoding

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

#85 - Adding .csv generation to eval mode of Casanovo

Pull Request - State: closed - Opened by VarunAnanth2003 about 2 years ago - 8 comments
Labels: enhancement

#84 - By default, Casanovo should do precursor filtering

Issue - State: closed - Opened by wsnoble about 2 years ago - 6 comments
Labels: duplicate, enhancement

#70 - Track input spectra origin

Issue - State: closed - Opened by bittremieux about 2 years ago
Labels: enhancement

#56 - Casanovo predicts for invalid spectra

Issue - State: open - Opened by bittremieux over 2 years ago - 3 comments
Labels: bug

GitHub / Noble-Lab/casanovo issues and pull requests