github.com/OpenMS/OpenMS issues | Ecosyste.ms: OpenCollective

Support Mztab in FileInfo tool

cbielow opened this pull request 4 months ago

TOPPView: show prefix ion (usually b1) when creating theoretical spectra

cbielow opened this pull request 4 months ago

fix displaying an empty path on the console during first cmake call

cbielow opened this pull request 4 months ago

Enable Subset Neighbor Search (FDR)

cbielow opened this pull request 4 months ago

Question: UNASSIGNEDPEPTIDE in tsv output of TextExporter(consensusXML)

jonasscheid opened this issue 5 months ago

Automatic FWHM estimation in FeatureFinderMetabo

YasinEl opened this issue 5 months ago

Configure so that TOPPAS documentation is accessible from help tutorial menu

lopippo opened this issue 5 months ago

Not an issue: new 'keywords' field in .desktop files, sugggestions

lopippo opened this issue 5 months ago

Extending OpenMS for compress support

ypriverol opened this issue 5 months ago

Update the following tools to the latest versions COMET, MSGF+, SAGE and Percolator

ypriverol opened this issue 5 months ago

Use before define ?

lopippo opened this issue 5 months ago

Logic of directory functions and naming

lopippo opened this issue 5 months ago

Plugin installation directory

lopippo opened this issue 5 months ago

Tutorials missing from doc/ for release 3.0.0

lopippo opened this issue 5 months ago

Support "non-existing" amino acids BJXZ

fcyu opened this issue 5 months ago

Update openms_ci_matrix_full.yml

poshul opened this pull request 5 months ago

Cmake doesnt check for lzma support

poshul opened this issue 5 months ago

(nightly) Docs still not uploading

jpfeuffer opened this issue 5 months ago

support initializer lists for creating MS spectra

cbielow opened this pull request 5 months ago

TOPPView: fix glitches in 1D view and layer names

cbielow opened this pull request 5 months ago

Building pyopenms on a Mac with M3 chip for Docker deployment

JohannesvKL opened this issue 5 months ago

up minimal boost version to 1.74

cbielow opened this pull request 5 months ago

[FIX] OpenSwath: error in PASEF window determination

jcharkow opened this pull request 5 months ago

Bump src/pyOpenMS/pyopenms-docs from `9875a9e` to `7628c88`

dependabot[bot] opened this pull request 6 months ago

msstats_converter won't process a metabolomcs consensus file (only accepts protein data)

Massmz opened this issue 6 months ago

CometAdapter & neutral loss

rolivella opened this issue 6 months ago

require boost 1.78?

cbielow opened this issue 6 months ago

IDFilter: new default values ('nan') for filtering by score

cbielow opened this pull request 6 months ago

CometAdapter fix for Comet 2024.01.0

cbielow opened this pull request 6 months ago

Build PyOpenMS with numpy2

poshul opened this pull request 6 months ago

Update authors since 3.1.0

mr-c opened this pull request 6 months ago

convert CHANGELOG_PARAMS to markdown table

mr-c opened this issue 6 months ago

test numpy2

poshul opened this pull request 6 months ago

move to changelog params

timosachsenberg opened this pull request 6 months ago

add html in selectversion.js

JKVISION1101 opened this pull request 6 months ago

Update changelog with the help of tools/changelog_helper.sh

mr-c opened this pull request 6 months ago

[ByGHAction] Updated OpenMS package version numbers

github-actions[bot] opened this pull request 6 months ago

Comet v2024.01.0 gives empty results

cbielow opened this issue 6 months ago

IDFilter: filtering for FDR=0 is impossible/hard

cbielow opened this issue 6 months ago

Add zip option for packaging

t0mdavid-m opened this pull request 6 months ago

Trouble copying MSVC runtime libraries as part of build / package process

timosachsenberg opened this issue 6 months ago

KNIME Plugin needs update

cbielow opened this issue 6 months ago

Filtering by Scan Number not working as intended?

pesavent opened this issue 6 months ago

Porting from Qt5 to Qt6

cbielow opened this pull request 6 months ago

Deprecate XTandemAdapter.cpp

cbielow opened this pull request 6 months ago

Update CHANGELOG

timosachsenberg opened this pull request 6 months ago

Pypifixes

poshul opened this pull request 6 months ago

Correct name of pyopenms-wheels-and-packages

poshul opened this pull request 6 months ago

Update openms_ci_matrix_full.yml to properly set source archive name

timosachsenberg opened this pull request 6 months ago

Update pyopenms test actions

matteopilz opened this pull request 6 months ago

use contrib from github

timosachsenberg opened this pull request 6 months ago

Fix install numpy <=1.26.4

matteopilz opened this pull request 6 months ago

Numpy install 1.26.4 or earlier

matteopilz opened this pull request 6 months ago

Set pyopenms numpy install<2.0

matteopilz opened this pull request 6 months ago

Revert "Update test_pyopenms.yml"

timosachsenberg opened this pull request 6 months ago

Update test_pyopenms.yml

timosachsenberg opened this pull request 6 months ago

fix etcid encoding with supplemental cv term

timosachsenberg opened this pull request 6 months ago

Support or avoid numpy 2.0 in pyopenms

timosachsenberg opened this issue 6 months ago

update PSI ontology

timosachsenberg opened this pull request 6 months ago

OpenSwathWorkflow command not found in Singularity

HFan11 opened this issue 6 months ago

parse relationship as xref

timosachsenberg opened this pull request 6 months ago

TOPPAS & SageAdapter

TheB1307 opened this issue 6 months ago

update PSI-MS.obo

timosachsenberg opened this pull request 6 months ago

Revert "Update psi-ms.obo"

timosachsenberg opened this pull request 6 months ago

remove deprecated doxygen \includedoc

poshul opened this pull request 6 months ago

Build pyopenmswheels nightly

poshul opened this pull request 6 months ago

always install doxygen

timosachsenberg opened this pull request 6 months ago

Nightly build questions

jpfeuffer opened this issue 6 months ago

Update psi-ms.obo

timosachsenberg opened this pull request 6 months ago

How to select ETCID activation for a TRFP mzML file?

rolivella opened this issue 6 months ago

Update percolator

timosachsenberg opened this issue 7 months ago

Support output directories for TOPP tools and TOPPAS

cbielow opened this pull request 7 months ago

Bump THIRDPARTY from `12eb8d3` to `d6594eb`

dependabot[bot] opened this pull request 7 months ago

Wrong retention time values

luca-annecchino opened this issue 7 months ago

What IDE do you recommend for developing and building openMS(C++) under macOS

suhande opened this issue 7 months ago

Update update_nightly.yml

poshul opened this pull request 7 months ago

make more parameters advanced in MetaProSIP

timosachsenberg opened this pull request 7 months ago

Wrap getvalidstrings

poshul opened this pull request 7 months ago

make IonName(s) consistent. remove old fragmentselectioncode

timosachsenberg opened this pull request 7 months ago

[Feature] Export ion annotations for MSSpectrum DataFrame

axelwalter opened this pull request 7 months ago

Bump src/pyOpenMS/pyopenms-docs from `df06fc8` to `9875a9e`

dependabot[bot] opened this pull request 8 months ago

Comet search engines update.

ypriverol opened this issue 8 months ago

Added support for RNAse4 digestion of RNA. Fixed buggy regex for prot…

poshul opened this pull request 8 months ago

Use macos-13 runner as it's the last x86 mac one

poshul opened this pull request 8 months ago

fix compile warnings

timosachsenberg opened this pull request 8 months ago

update citations

timosachsenberg opened this pull request 8 months ago

Move contrib from abibuilder to GitHub

t0mdavid-m opened this pull request 8 months ago

[Feature] DataFrame export for MSSpectrum and MSChromatogram

axelwalter opened this pull request 8 months ago

Bump THIRDPARTY from `947b56a` to `12eb8d3`

dependabot[bot] opened this pull request 8 months ago

Bump contrib from `f2053b2` to `b786ca3`

dependabot[bot] opened this pull request 8 months ago

Update codium-pr-agent.yml

timosachsenberg opened this pull request 8 months ago

Bump contrib from `5545518` to `f2053b2`

dependabot[bot] opened this pull request 8 months ago

remove some old files, script for unused test files

timosachsenberg opened this pull request 8 months ago

Pyopenms build fails due to recent refactors

jpfeuffer opened this issue 8 months ago

[refactor] merge some ff centroided classes into one file. remove FeatureFinderMRM

timosachsenberg opened this pull request 8 months ago

[refactor] Move deisotoping

timosachsenberg opened this pull request 8 months ago

[refactor] rename FILTERING to PROCESSING

timosachsenberg opened this pull request 8 months ago

[refactor] Move spectramerging

timosachsenberg opened this pull request 8 months ago

[refactor] Move scaling

timosachsenberg opened this pull request 8 months ago

[refactor] move resampling code to separate folder

timosachsenberg opened this pull request 8 months ago