Ecosyste.ms: Issues

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

GitHub / topdownproteomics/sdk issues and pull requests

#115 - Monoisotopic mass and m/z on isotopic envelopes

Pull Request - State: closed - Opened by rfellers 3 months ago - 1 comment

#114 - Negative Mode and Charge Carriers

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

#113 - TopPic Proforma Parser

Pull Request - State: closed - Opened by mikehollas123 about 1 year ago - 1 comment

#112 - Proteoform Modification Evidence

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

#111 - Mercury7 High Pruning Limit

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

#110 - Update action versions

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

#109 - Descriptor value for RESID

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

#108 - Fix to RESID ProForma writing

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

#107 - UniProt XML, FASTA parsers?

Issue - State: open - Opened by acesnik almost 2 years ago - 2 comments

#106 - Chemical Formula Improvements

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

#105 - Full v2 Spec + Proteoform Level Implementation by zrolfs

Pull Request - State: closed - Opened by rfellers almost 2 years ago - 10 comments

#104 - Concrete Chemical Formula

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

#103 - test codecov

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

#102 - update codecov stuff

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

#101 - update codecov stuff

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

#100 - Better Fixed Isotope handling

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

#99 - Update codecov uploader

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

#98 - Improve formula and composition writing

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

#97 - Glycan compositions

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

#96 - Dual Target

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

#95 - N-term check, upper Unimod on writing and parsing

Pull Request - State: closed - Opened by joseph-greer almost 3 years ago - 1 comment

#94 - Add codecov step in build

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

#93 - Update release.yml

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

#92 - Update dotnet.yml

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

#91 - Small usability changes

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

#90 - loosens requirement for protein detection protocol

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

#89 - MzIdentML Parser Improvements

Pull Request - State: closed - Opened by mtrobey about 3 years ago

#88 - Fixing nuget push command

Pull Request - State: closed - Opened by acesnik over 3 years ago - 1 comment

#87 - Remove AppVeyor badge & add back changes to release.yml that got lost

Pull Request - State: closed - Opened by acesnik over 3 years ago - 1 comment

#85 - Fixing continuous builds

Issue - State: closed - Opened by acesnik over 3 years ago

#84 - Add Sequence Ambiguity and Proteoform Classification

Pull Request - State: closed - Opened by zrolfs over 3 years ago - 14 comments

#83 - XlMod lookup

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

#82 - Mass Descriptors to standardize on 4 decimal places

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

#81 - Mod Name Lookup + Hash Mass

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

#80 - Handle multiple origins on single PSI-MOD term

Pull Request - State: closed - Opened by rfellers about 4 years ago

#79 - PSI-MOD Remap

Pull Request - State: closed - Opened by rfellers about 4 years ago

#78 - Handle Zeros in Chemical Formulas

Pull Request - State: closed - Opened by rfellers about 4 years ago

#77 - Proteoform Group Ambiguity

Pull Request - State: closed - Opened by rfellers about 4 years ago

#76 - ptmlist parse fix

Pull Request - State: closed - Opened by rfellers about 4 years ago

#75 - Proteoform Hash Changes

Pull Request - State: closed - Opened by rfellers about 4 years ago

#74 - Adds mzIdentML parser

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

#73 - ProForma Writer fixes for v2

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

#72 - Inter-Chain Crosslinks

Issue - State: open - Opened by rfellers over 4 years ago

#71 - Proforma v2 from HUPO-PSI

Pull Request - State: closed - Opened by rfellers over 4 years ago - 6 comments

#70 - OBO based PSI-MOD parser

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

#69 - Formal Charge Mass Calculation

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

#68 - Expanded the scope of the Modification Lookup tests for Unimod and Un…

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

#67 - Removed part of a test that was failing. The functionality is tested…

Pull Request - State: closed - Opened by b-early about 5 years ago

#66 - Isotopes

Pull Request - State: closed - Opened by b-early about 5 years ago

#65 - Fixed a bug in the InMemoryElementProvider and added some tests.

Pull Request - State: closed - Opened by b-early about 5 years ago

#64 - Implemented a chemical proteoform hash, a unique string for a proteof…

Pull Request - State: closed - Opened by b-early about 5 years ago

#63 - Multiple modifications at site

Pull Request - State: closed - Opened by b-early about 5 years ago

#62 - Added indices to modifications in ProteoformGroup.

Pull Request - State: closed - Opened by b-early about 5 years ago

#61 - Fix the empty nuspec file listing

Pull Request - State: closed - Opened by acesnik almost 6 years ago - 1 comment

#60 - Isotope handling

Pull Request - State: closed - Opened by rfellers about 6 years ago

#59 - Improve bracket handling cases

Pull Request - State: closed - Opened by acesnik over 6 years ago

#58 - Tough cases to check

Issue - State: open - Opened by acesnik over 6 years ago

#57 - Add parsing and writing for ambiguity descriptors

Pull Request - State: closed - Opened by acesnik over 6 years ago - 4 comments

#56 - Add Isotope Support

Issue - State: closed - Opened by rfellers over 6 years ago - 3 comments
Labels: Enhancement

#55 - UofW incorporation

Pull Request - State: closed - Opened by rfellers over 6 years ago - 6 comments

#54 - UniProt modification handling

Pull Request - State: closed - Opened by rfellers over 6 years ago
Labels: ProForma Parser

#53 - PSI-MOD handling

Pull Request - State: closed - Opened by rfellers over 6 years ago

#52 - NU code merge

Pull Request - State: closed - Opened by rfellers over 6 years ago - 1 comment

#51 - Add Unimod support

Pull Request - State: closed - Opened by rfellers over 6 years ago

#50 - catch non-amino acid uppercase letters

Pull Request - State: closed - Opened by rmillikin over 6 years ago - 5 comments

#49 - remove some code region annotations

Pull Request - State: closed - Opened by rmillikin over 6 years ago

#48 - added nuspec

Pull Request - State: closed - Opened by acesnik over 6 years ago - 2 comments

#47 - Readme start

Pull Request - State: closed - Opened by rfellers over 6 years ago - 1 comment

#46 - license this thing

Pull Request - State: closed - Opened by rfellers over 6 years ago - 1 comment

#45 - RESID Modification handling

Pull Request - State: closed - Opened by rfellers almost 7 years ago

#44 - PTM likelihoods and scores

Issue - State: open - Opened by acesnik almost 7 years ago - 2 comments
Labels: Question

#43 - Rename hypothesis and add some residue handling

Pull Request - State: closed - Opened by rfellers almost 7 years ago

#42 - Proteoform hypothesis

Pull Request - State: closed - Opened by rfellers almost 7 years ago

#41 - Chemical formula expansion and performance

Issue - State: open - Opened by acesnik almost 7 years ago - 7 comments
Labels: Enhancement, Performance

#40 - Chemical formula api

Pull Request - State: closed - Opened by rfellers almost 7 years ago - 2 comments

#39 - Changed index property name and description

Pull Request - State: closed - Opened by acesnik almost 7 years ago

#38 - Writing prefix tags

Issue - State: open - Opened by acesnik almost 7 years ago - 2 comments
Labels: Enhancement

#37 - ProteoformGroup

Issue - State: open - Opened by acesnik almost 7 years ago - 13 comments
Labels: Question

#36 - Created basic ProForma writer with some tests

Pull Request - State: closed - Opened by rfellers almost 7 years ago

#35 - Trimming white space left of values in parsing?

Issue - State: open - Opened by acesnik almost 7 years ago - 1 comment
Labels: Question

#34 - Biomarker Search

Issue - State: open - Opened by trishorts almost 7 years ago - 4 comments
Labels: Question, Ambiguity of Localization

#33 - Handle 4 best practice proforma sequences

Pull Request - State: closed - Opened by rfellers almost 7 years ago - 1 comment

#32 - Rule 7

Pull Request - State: closed - Opened by rfellers almost 7 years ago

#31 - Reorg project

Pull Request - State: closed - Opened by rfellers almost 7 years ago - 1 comment

#30 - Proteoform lists and line lengths

Issue - State: open - Opened by trishorts almost 7 years ago - 6 comments
Labels: Question

#29 - Starts work on rule 6, need some feedback

Pull Request - State: closed - Opened by rfellers almost 7 years ago - 4 comments

#28 - force strict XML doc standards, add simple documentation where needed

Pull Request - State: closed - Opened by rfellers almost 7 years ago

#26 - Handle incorrect sequence characters

Pull Request - State: closed - Opened by rfellers almost 7 years ago

#25 - Update appveyor badge

Pull Request - State: closed - Opened by stefanks almost 7 years ago

#24 - Create Chemical Formula API to support ProForma

Issue - State: closed - Opened by rfellers almost 7 years ago - 1 comment
Labels: ProForma Parser

#23 - Force documentation on library

Issue - State: closed - Opened by rfellers almost 7 years ago

#22 - Add support for modification names from alternate databases

Issue - State: closed - Opened by acesnik almost 7 years ago - 1 comment
Labels: ProForma Parser

#20 - Testing equivalency of proteoform sequences

Issue - State: open - Opened by acesnik almost 7 years ago - 1 comment
Labels: ProForma Parser

#19 - Validating ProForma

Issue - State: open - Opened by acesnik almost 7 years ago - 2 comments
Labels: ProForma Parser

#18 - Writing ProForma

Issue - State: closed - Opened by acesnik almost 7 years ago - 1 comment
Labels: ProForma Parser

#17 - Ambiguity of PTM localization

Issue - State: open - Opened by acesnik almost 7 years ago - 19 comments
Labels: ProForma Parser, Ambiguity of Localization

#15 - Improve handling of bad input

Issue - State: closed - Opened by rfellers almost 7 years ago
Labels: ProForma Parser

#14 - Add support for terminal modifications (Rule 7)

Issue - State: closed - Opened by rfellers almost 7 years ago - 1 comment
Labels: ProForma Parser