OpenMS/Tutorials issues and pull requests

#205 - Archive/Rename OpenMS/Tutorials repository?

Issue - State: open - Opened by tapaswenipathak over 2 years ago - 5 comments

#204 - QC_with_OpenMS R View fails on linux when given absolute path

Issue - State: open - Opened by poshul over 3 years ago - 2 comments

#203 - [FIX] Metabolite_DeNovoID WF

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

#202 - Remove deprecated Excel writers

Issue - State: open - Opened by jpfeuffer over 3 years ago

#201 - Split collection column missing for Molecule Type Cast

Issue - State: open - Opened by jpfeuffer over 3 years ago - 2 comments
Labels: documentation

#200 - Updated workflows for OpenMS 2.7

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

#199 - Necessary split collection column missing in almost all Metabo WFs and pictures

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

#198 - Update outdated figures

Issue - State: open - Opened by oliveralka over 3 years ago - 1 comment
Labels: documentation

#197 - ProteomicsLFQ

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

#196 - SIRIUSAdapter + HighResPrecursorMassCorrector

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

#195 - [FIX] minted float env

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

#194 - Placement of code examples via minted

Issue - State: closed - Opened by oliveralka over 3 years ago - 1 comment

#193 - [FIX] OSW Metabolomics

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

#192 - [ADD] tutorial-ci

Pull Request - State: closed - Opened by oliveralka over 3 years ago - 2 comments

#191 - [ADD] tutorial-ci

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

#190 - Improve PyOpenMS Tutorial

Issue - State: open - Opened by oliveralka over 3 years ago - 5 comments
Labels: documentation

#189 - TODOs for HTML version

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

#188 - [Feature] html version with tex4ht

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

#187 - OpenMS 2.7: Update WF related to Sirius

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

#186 - OpenSWATH for Metabolomics - DIAMetAlyzer

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

#185 - [Update] PhosphoID

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

#184 - Fixing bugs in Phosphoproteomics ID workflow

Pull Request - State: closed - Opened by JeeH-K about 4 years ago - 1 comment

#183 - Phosphoproteomics_ID

Issue - State: open - Opened by oliveralka about 4 years ago
Labels: Hacktoberfest

#182 - Release/2.6.0

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

#181 - Some of the OpenMS FileConverter requirements might be missing.

Issue - State: closed - Opened by sorenwacker over 4 years ago - 2 comments

#180 - Update handout with ThermoRawFileParser

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

#179 - simple Phospho ID

Pull Request - State: closed - Opened by timosachsenberg over 4 years ago - 2 comments

#178 - update OpenSwath.knwf for 2.6.0 release

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

#177 - exporting results of identification and quantitation as a table

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

#176 - [DRAFT] OpenSWATH for Metabolomics

Pull Request - State: closed - Opened by oliveralka over 4 years ago - 7 comments

#175 - Draft version of an ID only Phosphoproteomics workflow

Pull Request - State: closed - Opened by timosachsenberg almost 5 years ago - 1 comment

#174 - proteomics lfq workflow with MSStats

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

#173 - [DRAFT] ProteomicsLFQ, current with lfq_spikein_dilution

Pull Request - State: closed - Opened by oliveralka almost 5 years ago - 1 comment

#172 - update Versions

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

#171 - fil missing in example data

Issue - State: closed - Opened by johanneswellmann about 5 years ago - 2 comments

#170 - [FIX] general

Pull Request - State: closed - Opened by oliveralka about 5 years ago - 1 comment

#169 - Update handout.tex

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

#168 - GCB 2019

Issue - State: closed - Opened by jpfeuffer over 5 years ago

#167 - File missing in example data

Issue - State: closed - Opened by jylanwhu over 5 years ago - 3 comments

#166 - Workflow for isobaric analysis (untested)

Pull Request - State: closed - Opened by oliveralka over 5 years ago - 38 comments

#165 - Identification / Quantification

Pull Request - State: closed - Opened by oliveralka over 5 years ago - 8 comments

#164 - [Feature] Test Workflow-relative paths

Pull Request - State: closed - Opened by jpfeuffer over 5 years ago

#163 - Boston19: retention time column not present after mzTabExporter in MetaboSpectrumMatcher workflow

Issue - State: open - Opened by jpfeuffer over 5 years ago

#162 - Boston19: CometAdapter has problems with Temp files on Windows (with spaces in path?)

Issue - State: open - Opened by jpfeuffer over 5 years ago - 6 comments

#161 - Boston19: XTandem scores cannot be fitted in consensus ID workflow

Issue - State: open - Opened by jpfeuffer over 5 years ago

#160 - Boston 2019: joiner can't join list of retention times with retention time in metabolomics workflow

Issue - State: closed - Opened by timosachsenberg over 5 years ago - 1 comment

#159 - Metabolomics

Issue - State: open - Opened by oliveralka over 5 years ago

#158 - Boston 2019: map aligner pose clustering crashes

Issue - State: closed - Opened by timosachsenberg over 5 years ago

#157 - remove consensusmap normalizer from iprg

Issue - State: open - Opened by timosachsenberg over 5 years ago

#156 - Boston 2019

Issue - State: open - Opened by timosachsenberg over 5 years ago
Labels: documentation

#155 - [Update] SiriusAdapter

Pull Request - State: closed - Opened by oliveralka almost 6 years ago

#154 - KNIME R Home issue (Linux, MacOS)

Issue - State: open - Opened by oliveralka about 6 years ago
Labels: documentation

#153 - Identification view: add how to save single spectrum in mzML

Issue - State: open - Opened by timosachsenberg about 6 years ago
Labels: documentation

#152 - pyopenms dir and help

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

#151 - [UPDATE] First changes EuBIC2019

Pull Request - State: closed - Opened by oliveralka about 6 years ago - 16 comments

#150 - Add date to handout

Issue - State: closed - Opened by oliveralka over 6 years ago

#149 - Update metabolomics.tex

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

#148 - Update gettingstarted.tex

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

#147 - [ADD] MAD

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

#146 - Feature/um2018

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

#145 - Update metabo KNIME workflow

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

#144 - initialized default values for new parameters

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

#143 - Escape underscores

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

#142 - General fixes

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

#141 - [Update] metabolomics workflows 2.4.0

Pull Request - State: closed - Opened by oliveralka over 6 years ago - 7 comments

#140 - Updated proteomics WFs to 2.4

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

#139 - [DRAFT] Add SiriusAdapter (metabolomics)

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

#138 - Feature/boston2018

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

#137 - [FIX] update figure 13 and ref

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

#136 - Fix/pwizard image

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

#135 - add Proteomics megaworkflow; remove old subworkflows

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

#134 - OMSAA 10 ppm to 5 ppm

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

#133 - Metabo KNIME workflow picture is outdated

Issue - State: closed - Opened by jpfeuffer over 6 years ago - 10 comments

#132 - Loading MSStats missing

Issue - State: closed - Opened by jpfeuffer over 6 years ago - 5 comments
Labels: bug

#131 - Figure 13 wrong naming of input ports

Issue - State: closed - Opened by timosachsenberg over 6 years ago - 3 comments

#130 - Update msConvert image

Issue - State: closed - Opened by timosachsenberg over 6 years ago - 7 comments

#129 - Boston18stuff

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

#128 - Changes Tutorial iPRG

Pull Request - State: closed - Opened by oliveralka over 6 years ago - 3 comments

#127 - R installation instructions at more sensible place

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

#126 - very long nightly path needs more space -> deitemize

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

#125 - PCA replace ggbiplot to ggfortify -> update import

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

#124 - Draft for MSstats iPRG tutorial

Pull Request - State: closed - Opened by oliveralka almost 7 years ago - 13 comments

#123 - MSstats installation

Pull Request - State: closed - Opened by mrurik almost 7 years ago - 6 comments

#118 - Mention that you have to double-click a workflow after you import it

Issue - State: closed - Opened by jpfeuffer about 7 years ago

#117 - Remove part where one needs to copy the spectral library in the plugin folder.

Issue - State: closed - Opened by timosachsenberg about 7 years ago

#116 - Better explain the manual validation of Matched Metabo spectra

Issue - State: closed - Opened by jpfeuffer about 7 years ago

#115 - Add column header to Excel Writer

Issue - State: closed - Opened by jpfeuffer about 7 years ago

#114 - Joining of columns node should be better explained

Issue - State: closed - Opened by timosachsenberg about 7 years ago

#113 - Metabo Workflow more tipps on how to inspect consensusXML

Issue - State: open - Opened by timosachsenberg about 7 years ago

#111 - Rephrase task 3) in 3.3.2

Issue - State: closed - Opened by jpfeuffer about 7 years ago - 5 comments

#110 - Advanced parameters are grey in table - some thought it is disabled

Issue - State: closed - Opened by timosachsenberg about 7 years ago

#109 - Highlight in FeatureFinderMetabo settings that some parameters are advanced

Issue - State: closed - Opened by timosachsenberg about 7 years ago

#108 - Mark topics like smiles & RDKit as "Digression"

Issue - State: closed - Opened by timosachsenberg about 7 years ago - 1 comment

#107 - Catch-up points

Issue - State: open - Opened by timosachsenberg about 7 years ago - 2 comments

#105 - gplots in Metabo workflow not compatible with shipped R bins on Win

Issue - State: open - Opened by jpfeuffer about 7 years ago - 1 comment
Labels: bug

#96 - Programmer tutorial

Issue - State: closed - Opened by hroest over 7 years ago - 12 comments

#95 - Add reference for visualization of structures (RDKIT) - Metabolomics workflow

Issue - State: closed - Opened by oliveralka over 7 years ago

#66 - Better explain settings of Joiner node in Metabo WF

Issue - State: closed - Opened by jpfeuffer almost 8 years ago

#62 - Run your pipeline and inspect your results... on p.30

Issue - State: closed - Opened by timosachsenberg over 8 years ago

#27 - Java version check possibly errornous

Issue - State: closed - Opened by timosachsenberg over 9 years ago - 1 comment

GitHub / OpenMS/Tutorials issues and pull requests