Ecosyste.ms: Issues

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

GitHub / smith-chem-wisc/mzLib issues and pull requests

#785 - [WIP] Edited FlashLFQ to include option for verbose peaks

Pull Request - State: open - Opened by Alexander-Sol about 1 month ago - 1 comment

#784 - Revert intensity pairs pr765

Pull Request - State: closed - Opened by trishorts about 1 month ago - 1 comment
Labels: bug, Maintenance, ready for review

#783 - Update nearly all nuget packages and .Net to 8.0

Pull Request - State: closed - Opened by trishorts about 1 month ago - 3 comments
Labels: Maintenance, ready for review

#782 - Sam

Pull Request - State: open - Opened by trishorts about 2 months ago

#781 - .NET 8 transition?

Issue - State: closed - Opened by acesnik about 2 months ago - 2 comments

#780 - Allow multiple custom fragmentations

Pull Request - State: closed - Opened by nbollis about 2 months ago - 1 comment
Labels: bug, enhancement, ready for review

#779 - FlashLFQ now enables selection of peptides to be quantified

Pull Request - State: closed - Opened by Alexander-Sol 2 months ago - 1 comment

#778 - Update dotnet.yml

Pull Request - State: closed - Opened by Alexander-Sol 3 months ago - 1 comment
Labels: Maintenance

#777 - Mbr part1

Pull Request - State: open - Opened by Alexander-Sol 3 months ago - 1 comment
Labels: enhancement, ready for review

#776 - Tims tof reader

Pull Request - State: open - Opened by Alexander-Sol 3 months ago - 1 comment
Labels: WIP

#775 - MsPathFinderT result reading

Pull Request - State: open - Opened by nbollis 3 months ago - 2 comments
Labels: ready for review, New Feature

#774 - Added support for crux output

Pull Request - State: open - Opened by nbollis 3 months ago - 1 comment
Labels: ready for review, New Feature

#773 - Allow SSRCalc to be called from just base sequence without constructing PeptideWithSetModifications

Pull Request - State: closed - Opened by nbollis 3 months ago - 1 comment
Labels: ready for review

#772 - PSI-MOD download certificate error

Issue - State: open - Opened by acesnik 3 months ago

#771 - Added IClonable implementation to MsDataScan

Pull Request - State: closed - Opened by nbollis 4 months ago - 1 comment
Labels: enhancement

#770 - Fragger Result reading

Pull Request - State: closed - Opened by nbollis 4 months ago - 1 comment
Labels: ready for review, New Feature

#769 - Pwsm target decoy

Pull Request - State: open - Opened by Alexander-Sol 4 months ago - 1 comment

#768 - Changed PWSM GetHashCode and Equals methods

Pull Request - State: closed - Opened by Alexander-Sol 4 months ago - 1 comment

#767 - Update dotnet.yml

Pull Request - State: closed - Opened by Alexander-Sol 4 months ago - 1 comment
Labels: Maintenance, ready for final review / merge

#766 - Spectrum similarity bug fix

Pull Request - State: closed - Opened by trishorts 4 months ago
Labels: bug, ready for review

#765 - Improved intensity pairs trying to make spectrum library comparisons faster

Pull Request - State: closed - Opened by trishorts 4 months ago - 1 comment
Labels: Performance, ready for review

#764 - Test fixed mod gptmd mod competition during digestion

Pull Request - State: closed - Opened by trishorts 5 months ago
Labels: Documentation, Discussion, ready for review

#763 - Handled edge case with digestion product having a null parent

Pull Request - State: closed - Opened by nbollis 5 months ago - 1 comment
Labels: bug, ready for review

#762 - Peptide with set mods no protein parent

Pull Request - State: closed - Opened by trishorts 5 months ago
Labels: bug

#761 - Chronologer Retention Time model predictor

Pull Request - State: open - Opened by elaboy 5 months ago - 1 comment
Labels: New Feature

#760 - Changed Deconvoluter to have a static call

Pull Request - State: closed - Opened by nbollis 5 months ago - 1 comment
Labels: bug, enhancement, ready for review

#759 - Add leucine to chymo cleavage motif

Pull Request - State: closed - Opened by trishorts 5 months ago
Labels: bug, ready for review

#758 - Mbr refactor

Pull Request - State: closed - Opened by Alexander-Sol 5 months ago - 1 comment

#757 - Nucleotide, Rnase, Digestion Params Clone Method, and Interface Modificaiton

Pull Request - State: closed - Opened by nbollis 6 months ago - 1 comment
Labels: enhancement, ready for review, New Feature

#756 - Changed behavior of masked members in Digestionparams

Pull Request - State: closed - Opened by nbollis 6 months ago - 1 comment
Labels: bug, ready for review

#755 - Usi downloader

Pull Request - State: open - Opened by Alexander-Sol 6 months ago - 1 comment

#754 - Retriever of Pride Data

Pull Request - State: open - Opened by YulingDai 6 months ago - 1 comment

#753 - Proteomics repository retriever

Pull Request - State: open - Opened by trishorts 6 months ago

#752 - Mz spectrum weighted merge within mz tolerance

Pull Request - State: open - Opened by trishorts 6 months ago - 1 comment

#751 - Edited the MatchedFramgentIon Equals method

Pull Request - State: closed - Opened by Alexander-Sol 7 months ago - 1 comment
Labels: ready for final review / merge

#750 - Update uniprot comment

Pull Request - State: closed - Opened by trishorts 7 months ago - 1 comment

#749 - Eliminate extra tab from chromatographic peak

Pull Request - State: closed - Opened by trishorts 7 months ago - 1 comment
Labels: bug

#748 - Removed extra tab from peptide output in FlashLFQ

Pull Request - State: closed - Opened by Alexander-Sol 7 months ago

#747 - Eliminate extra tab from chromatographic peak

Pull Request - State: closed - Opened by trishorts 7 months ago - 1 comment
Labels: bug

#746 - Machine learning project module

Pull Request - State: open - Opened by elaboy 7 months ago - 1 comment

#745 - Including a Machine learning project for ML/DL and the Chronologer Model

Pull Request - State: closed - Opened by elaboy 7 months ago - 1 comment
Labels: WIP

#744 - [WIP] Transciptomics: Digestion, Fragmentaiton, Decoy Generation

Pull Request - State: closed - Opened by nbollis 7 months ago - 1 comment

#743 - Rearranging classes to fit within the Transcriptomics Structure

Pull Request - State: closed - Opened by nbollis 7 months ago - 1 comment
Labels: enhancement, ready for review

#742 - Create CONTRIBUTING.md

Pull Request - State: closed - Opened by trishorts 7 months ago

#741 - Create CODE_OF_CONDUCT.md

Pull Request - State: closed - Opened by trishorts 7 months ago

#740 - [Do not merge] Incorporating Chronologer

Pull Request - State: open - Opened by elaboy 8 months ago - 1 comment
Labels: enhancement

#739 - Above Averaging Algorithm Rework and Crash Fix

Pull Request - State: closed - Opened by nbollis 8 months ago - 1 comment
Labels: bug, ready for review

#738 - IGNORE Chronologer tensor

Pull Request - State: open - Opened by trishorts 8 months ago

#737 - PsmFromTsv Reader that also will work for RNA

Pull Request - State: closed - Opened by trishorts 8 months ago - 1 comment
Labels: Maintenance, ready for review

#736 - Allowed reading of scan descriptions from Raw Files

Pull Request - State: closed - Opened by nbollis 9 months ago - 1 comment
Labels: enhancement, ready for review

#735 - Toppic search result reading

Pull Request - State: closed - Opened by nbollis 9 months ago - 1 comment
Labels: enhancement, ready for review

#734 - From Private to Protected, allows control from inherited classes

Pull Request - State: open - Opened by elaboy 9 months ago
Labels: enhancement, WIP

#733 - Public method for replacing dictionary of mods in PeptideWithSetModifications

Pull Request - State: closed - Opened by elaboy 9 months ago - 1 comment
Labels: Performance, WIP

#732 - snip those raw files

Pull Request - State: open - Opened by trishorts 10 months ago

#731 - Disabled Development Tests from Running Automatically

Pull Request - State: closed - Opened by nbollis 10 months ago
Labels: Maintenance, ready for review

#730 - EncyclopeDIA amodified peptides format mass shift

Pull Request - State: closed - Opened by trishorts 10 months ago - 1 comment

#728 - Semi colon in protein group explanation

Pull Request - State: closed - Opened by trishorts 10 months ago
Labels: Documentation, ready for final review / merge

#727 - Reduced compexity of GetOneBasedScan from O(logN) to O(1)

Pull Request - State: closed - Opened by nbollis 11 months ago - 1 comment

#726 - Encyclopedia formated peptide full sequence including mass shift in brackets

Pull Request - State: closed - Opened by trishorts 11 months ago - 1 comment
Labels: enhancement, ready for review

#725 - Uniprot legacy comment update

Pull Request - State: closed - Opened by trishorts 11 months ago
Labels: Maintenance, ready for review

#724 - Legacy comment update

Issue - State: open - Opened by acesnik 11 months ago - 1 comment
Labels: Documentation

#723 - Added support for negative mode deconvolution

Pull Request - State: closed - Opened by nbollis 12 months ago - 1 comment
Labels: ready for review

#722 - Added method to check valid base sequences to AminoAcidPolymerExtensions

Pull Request - State: closed - Opened by Alexander-Sol 12 months ago - 1 comment

#721 - Flash lfq robust to funny peptide sequence

Pull Request - State: closed - Opened by trishorts 12 months ago - 1 comment
Labels: bug

#720 - [WIP] Indexed ion decon not working

Pull Request - State: open - Opened by trishorts 12 months ago

#719 - Fixed bug in GetClosestIndex for arrays of length 1 or 2

Pull Request - State: closed - Opened by Alexander-Sol 12 months ago - 3 comments

#718 - [DO NOT MERGE] Base Implementation of Transcriptomics Project

Pull Request - State: closed - Opened by nbollis 12 months ago - 1 comment
Labels: ready for review

#717 - Binary search extension

Pull Request - State: closed - Opened by Alexander-Sol about 1 year ago - 1 comment

#716 - GetClosestOneBasedSpectrumNumber using Binary Search instead of for loop

Pull Request - State: closed - Opened by elaboy about 1 year ago - 2 comments
Labels: Performance, Maintenance

#715 - fix gz decompress so that we get the complete xml database

Pull Request - State: closed - Opened by trishorts about 1 year ago - 1 comment
Labels: bug, WIP

#714 - Added comments to FlashLFQ

Pull Request - State: closed - Opened by Alexander-Sol about 1 year ago - 1 comment

#713 - Isobar indexing

Pull Request - State: open - Opened by Alexander-Sol about 1 year ago
Labels: WIP

#712 - UnimodLoader throws KeyNotFoundException

Issue - State: open - Opened by Alexander-Sol about 1 year ago - 1 comment

#711 - External Software File Reading

Pull Request - State: closed - Opened by nbollis about 1 year ago - 1 comment
Labels: enhancement, ready for review

#710 - Binary search related bug in MzSpectrum.Extract

Issue - State: open - Opened by avcarr2 about 1 year ago - 2 comments

#709 - Raw file connection not closing

Pull Request - State: closed - Opened by elaboy about 1 year ago - 2 comments
Labels: bug, ready for review

#708 - Update Loaders.cs

Pull Request - State: closed - Opened by elaboy about 1 year ago - 1 comment
Labels: bug, ready for review

#707 - Fixed bug where pwsm.ChemicalFormula threw null reference exception

Pull Request - State: closed - Opened by Alexander-Sol about 1 year ago - 1 comment
Labels: bug, ready for review

#706 - Null ChemicalFormula throws NullReferenceException

Issue - State: closed - Opened by Alexander-Sol about 1 year ago

#705 - removed the zero-equivalent intensity filtering from mzMl

Pull Request - State: closed - Opened by avcarr2 about 1 year ago - 5 comments
Labels: bug, WIP

#703 - Calculated number of averagines is only 1500

Issue - State: open - Opened by avcarr2 about 1 year ago

#702 - Bruker support

Pull Request - State: closed - Opened by avcarr2 about 1 year ago - 3 comments
Labels: ready for review

#700 - Added option to quantify ambiguous peptides in FlashLFQ

Pull Request - State: closed - Opened by Alexander-Sol about 1 year ago - 1 comment

#699 - Prepare Release - Readers backward compatibility improvement && Remove Develpment Dependency

Pull Request - State: closed - Opened by nbollis about 1 year ago - 1 comment
Labels: Maintenance, ready for review

#698 - Reader refactoring, take 2

Pull Request - State: closed - Opened by avcarr2 over 1 year ago - 1 comment
Labels: enhancement, ready for review

#697 - Fix add chemical formula with negative values

Pull Request - State: closed - Opened by trishorts over 1 year ago - 3 comments
Labels: bug, ready for review

#696 - Bug in ChemicalFormula.

Pull Request - State: closed - Opened by avcarr2 over 1 year ago - 7 comments
Labels: bug, WIP

#695 - Zero column effects result in identical intensity values

Pull Request - State: closed - Opened by Alexander-Sol over 1 year ago - 4 comments

#693 - weighted mean polish

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

#692 - Bruker support

Pull Request - State: closed - Opened by avcarr2 over 1 year ago
Labels: WIP

#691 - Test Median Polish

Pull Request - State: closed - Opened by trishorts over 1 year ago - 1 comment
Labels: Maintenance, ready for review

#690 - Deconvolution Testing Environment

Pull Request - State: closed - Opened by nbollis over 1 year ago - 1 comment
Labels: ready for review

#689 - 688

Pull Request - State: closed - Opened by trishorts over 1 year ago - 2 comments

#688 - Fix random tests failing after HTTP request fails

Pull Request - State: closed - Opened by nbollis over 1 year ago - 1 comment
Labels: bug, ready for review

#687 - Fixing namespaces

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

#686 - Deconvolution Development

Pull Request - State: closed - Opened by nbollis over 1 year ago - 1 comment
Labels: ready for review

#685 - Simulated data

Pull Request - State: closed - Opened by avcarr2 over 1 year ago - 1 comment
Labels: WIP