Ecosyste.ms: Issues

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

GitHub / HeldLab/ProteoSushi issues and pull requests

#63 - Re-enable gui by supplying the multithread parameter

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

#62 - Segmentation Fault upon running within the GUI

Issue - State: open - Opened by rseymour1 almost 3 years ago
Labels: bug, help wanted

#61 - Fix queries

Pull Request - State: closed - Opened by rseymour1 almost 3 years ago

#60 - Localization 2

Pull Request - State: closed - Opened by rseymour1 over 3 years ago

#59 - windows problem with uniprot annotation

Issue - State: closed - Opened by rseymour1 over 3 years ago - 2 comments
Labels: bug

#58 - Add troubleshooting information for uniprot annotations in documentation

Issue - State: open - Opened by rseymour1 over 3 years ago
Labels: documentation

#57 - mention the alternate `python` command for windows

Issue - State: open - Opened by rseymour1 over 3 years ago
Labels: documentation

#56 - Clearly explain how to run example files in the documentation

Issue - State: open - Opened by rseymour1 over 3 years ago
Labels: documentation

#55 - Annotate domain from uniprot

Issue - State: open - Opened by rseymour1 over 3 years ago
Labels: enhancement

#54 - Min cleave adj

Pull Request - State: closed - Opened by rseymour1 over 3 years ago

#53 - Some sites 1 behind in mascot output in windows

Issue - State: closed - Opened by rseymour1 over 3 years ago - 2 comments
Labels: bug

#52 - Add length of sequence if blank and Range_of_Interest isn't

Issue - State: closed - Opened by rseymour1 over 3 years ago - 1 comment
Labels: enhancement

#51 - KeyError: 'Subcellular location ID' on Windows with Maxquant annotation

Issue - State: closed - Opened by rseymour1 over 3 years ago
Labels: bug

#50 - GUI retains filepath of input even after search engine is changed

Issue - State: closed - Opened by rseymour1 over 3 years ago - 1 comment
Labels: bug, low priority

#49 - Occasionally adds a site that is off by one along with correct one

Issue - State: closed - Opened by rseymour1 over 3 years ago - 3 comments
Labels: bug

#48 - Output results may have <5 length peptides

Issue - State: closed - Opened by rseymour1 over 3 years ago - 2 comments
Labels: bug, low priority

#47 - Make documentation explain output better

Issue - State: closed - Opened by rseymour1 over 3 years ago - 2 comments
Labels: documentation

#46 - Incorrect site assignment for loc threshold sites

Issue - State: closed - Opened by rseymour1 over 3 years ago - 1 comment
Labels: bug

#45 - PS may be omitting genes that shouldn't be

Issue - State: closed - Opened by rseymour1 over 3 years ago - 1 comment
Labels: bug

#44 - PS uses | symbol for pepdict file which fails in windows

Issue - State: closed - Opened by rseymour1 over 3 years ago - 1 comment
Labels: bug

#43 - Reduce ram

Pull Request - State: closed - Opened by rseymour1 almost 4 years ago

#42 - Localization

Pull Request - State: closed - Opened by rseymour1 almost 4 years ago

#41 - Remove the target genes header when it isn't being used

Issue - State: closed - Opened by rseymour1 almost 4 years ago - 1 comment
Labels: enhancement

#40 - import error when using github directly with run_proteosushi.py

Issue - State: closed - Opened by rseymour1 almost 4 years ago - 2 comments
Labels: bug

#39 - Reduce memory requirement for uniprot annotation

Issue - State: closed - Opened by rseymour1 almost 4 years ago - 1 comment
Labels: enhancement

#37 - Miss-cleaved peptides are not used in intensity values

Issue - State: closed - Opened by rseymour1 almost 4 years ago

#36 - Change documentation to say that peptide length must be between 5 and 55 to be rolled up and annotated

Issue - State: closed - Opened by rseymour1 almost 4 years ago - 1 comment
Labels: documentation

#34 - b2.1.0 Fixed columns and documentation

Pull Request - State: closed - Opened by rseymour1 about 4 years ago
Labels: bug, enhancement

#33 - Separate the code folder from the working folder

Issue - State: closed - Opened by rseymour1 about 4 years ago
Labels: enhancement, wontfix, low priority

#32 - Multi-threading update

Pull Request - State: closed - Opened by rseymour1 about 4 years ago
Labels: enhancement

#31 - Change the output file chooser button from "Save"

Issue - State: open - Opened by rseymour1 about 4 years ago
Labels: enhancement, low priority

#30 - Add a column for localization score?

Issue - State: closed - Opened by rseymour1 about 4 years ago - 2 comments
Labels: enhancement

#29 - Integrate ProteoSushi with Perseus

Issue - State: open - Opened by rseymour1 about 4 years ago
Labels: low priority

#28 - Have ProteoSushi indicate whether an Intensity Column is summed or averaged

Issue - State: closed - Opened by rseymour1 about 4 years ago - 1 comment
Labels: enhancement

#27 - ProteoSushi doesn't allow [+IAC/NEM] for Skyline

Issue - State: closed - Opened by rseymour1 about 4 years ago - 1 comment

#26 - Maxquant files do not currently rollup some sites that differ by a PTM not of interest

Issue - State: closed - Opened by rseymour1 about 4 years ago - 2 comments
Labels: bug

#25 - Make a new row for each gene when there is more than 1 associated gene for a site

Issue - State: closed - Opened by rseymour1 about 4 years ago - 1 comment
Labels: enhancement

#24 - Add sequence similarities from the Uniprot entry

Issue - State: open - Opened by rseymour1 about 4 years ago
Labels: enhancement

#23 - Add GO info from Uniprot page

Issue - State: open - Opened by rseymour1 about 4 years ago
Labels: enhancement

#22 - Add info from Keywords section on Uniprot page

Issue - State: open - Opened by rseymour1 about 4 years ago - 1 comment
Labels: enhancement

#21 - Add option to choose output folder to the GUI

Issue - State: closed - Opened by rseymour1 about 4 years ago - 1 comment
Labels: enhancement, low priority

#20 - Add secondary structure to the uniprot annotations

Issue - State: open - Opened by rseymour1 about 4 years ago - 1 comment
Labels: enhancement

#19 - Add a protein name column in the results

Issue - State: closed - Opened by rseymour1 about 4 years ago - 1 comment
Labels: enhancement

#18 - Make the rhea column of the uniprot annotations more human readable

Issue - State: closed - Opened by rseymour1 about 4 years ago - 1 comment
Labels: enhancement

#17 - Add a column for annotation score in the results

Issue - State: closed - Opened by rseymour1 about 4 years ago - 1 comment
Labels: enhancement

#16 - ProteoSushi does not annotate all sites

Issue - State: closed - Opened by rseymour1 over 4 years ago - 1 comment
Labels: bug, wontfix

#15 - ProteoSushi does not combine peptides with differing sites not of interest

Issue - State: closed - Opened by rseymour1 over 4 years ago - 1 comment
Labels: bug

#14 - Maxquant doesn't grab all "intensity" columns

Issue - State: closed - Opened by rseymour1 over 4 years ago - 1 comment
Labels: bug, enhancement

#13 - Fix dependencies on pandas and request

Issue - State: closed - Opened by rseymour1 over 4 years ago
Labels: enhancement, wontfix, low priority

#12 - Add tooltip to clarify that threshold can be left blank

Issue - State: closed - Opened by rseymour1 over 4 years ago
Labels: enhancement

#11 - For some proteome fasta files, ProteoSushi puts words (e.g. Homo Sapiens) in the Species ID

Issue - State: closed - Opened by rseymour1 over 4 years ago - 1 comment
Labels: bug

#10 - Update ProteoSushi docs to recommend newest version of MaxQuant

Issue - State: closed - Opened by rseymour1 over 4 years ago - 1 comment
Labels: documentation

#9 - ProteoSushi does not work after completing an analysis

Issue - State: closed - Opened by rseymour1 over 4 years ago - 2 comments
Labels: bug, wontfix, low priority

#8 - ProteoSushi crashes when I click cancel on the file chooser

Issue - State: closed - Opened by rseymour1 over 4 years ago - 1 comment
Labels: bug

#7 - GUI layout is set at the bottom

Issue - State: open - Opened by rseymour1 over 4 years ago - 1 comment
Labels: enhancement, low priority

#6 - Use multiple threads for ProteoSushi GUI and backend

Issue - State: closed - Opened by rseymour1 over 4 years ago - 2 comments
Labels: enhancement, low priority

#5 - ProteoSushi creates rows for PTM sites that weren't selected

Issue - State: closed - Opened by rseymour1 over 4 years ago - 1 comment
Labels: bug

#4 - Write mascot output parameters in the documentation

Issue - State: closed - Opened by rseymour1 over 4 years ago - 1 comment
Labels: documentation

#3 - Mascot no intensity values error

Issue - State: closed - Opened by rseymour1 over 4 years ago - 1 comment
Labels: bug

#2 - ProteoSushi crashes for some errors

Issue - State: closed - Opened by rseymour1 over 4 years ago - 2 comments
Labels: bug

#1 - pepdict is not saved, but deleted each time

Issue - State: closed - Opened by rseymour1 over 4 years ago - 1 comment