Commits · c75375bf0752cae402404c36b3f6d93626e0a8d7 · Environmental Cheminformatics / RMassBank_by_MaliRemorker

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Jul 08, 2019
- Version bump for S4power · c75375bf
  meowcat authored 5 years ago
  
  c75375bf
Jul 05, 2019

Fixed multiplicity filtering to work identical to 2.3.1 version: removing... · 0fa63c20

meowcat authored 5 years ago

Fixed multiplicity filtering to work identical to 2.3.1 version: removing peaks which fall out due to "refiltering", where formulas may get multiplicity 1. See #219

0fa63c20

Jul 01, 2019
- Fixed filterMultiplicity and reanalyzeFailpeaks for incomplete compounds · fa28a941
  meowcat authored 5 years ago
  
  fa28a941
Jun 28, 2019
- Don't "clean noise" when no spectra are there · 8278c165
  meowcat authored 5 years ago
  
  8278c165
Jun 26, 2019
- Retrieving recalibration from the parent, since it's stored there. Standard vignette builds now · a860e9d2
  meowcat authored 5 years ago
  
  a860e9d2
- Add recalibration into updated workspace · 73f0ba64
  meowcat authored 5 years ago
  
  73f0ba64
- do problematicPeaks spectra-wise, then aggregate. Old workspace now... · d2ca8910
  meowcat authored 5 years ago
  
  do problematicPeaks spectra-wise, then aggregate. Old workspace now successfully loading, but without recalibration models
  d2ca8910
Jun 25, 2019

Fixing loading old workspaces by re-processing aggregation and multiplicity... · a31d91c5

meowcat authored 5 years ago

Fixing loading old workspaces by re-processing aggregation and multiplicity filtering. Currently not yet working: problematic peaks detection

a31d91c5

May 02, 2018
- Backported (or "forward-ported") the column name fix from the main branch · fcfe53db
  Michele Stravs authored 7 years ago
  
  fcfe53db
Sep 07, 2017

Temporary fix for allowing workflow to run, loading old workspaces is... · cb176dea

Michele Stravs authored 7 years ago

Temporary fix for allowing workflow to run, loading old workspaces is currently not working. Fixes to filterPeaksMultiplicity. Currently returns incorrect results

cb176dea

Dec 09, 2016
- Updating how reanalysis and isotope results are added to the spectrum. · 99d7b623
  Michele Stravs authored 8 years ago
  
  New slot "formulaSource" for RmbSpectrum2
  99d7b623
- Merge branch 'master' into s4power · 6f205b27
  Michele Stravs authored 8 years ago
  
  6f205b27
- (Finally) bumped version number · 1907ec24
  Michele Stravs authored 8 years ago
  
  1907ec24
- DIA deconvoluter - first attempt · 668e4bd6
  Michele Stravs authored 8 years ago
  
  668e4bd6
Dec 02, 2016
- Merge branch 'master' into s4power · 9310f46f
  Michele Stravs authored 8 years ago
  
  Conflicts: R/leMsmsRaw.R
  9310f46f
Nov 29, 2016
- fix in xcms workflow (the "standard" case 1 file for each cpdID was incorrect) · 1d861383
  Michele Stravs authored 8 years ago
  
  1d861383
- fixed empty molfile issue (#165), was stray line in createMolfile · 80c90026
  Michele Stravs authored 8 years ago
  
  80c90026
- fixed empty molfile issue (#165), was stray line in createMolfile · 73cb7f35
  Michele Stravs authored 8 years ago
  
  73cb7f35
- added filter for annotation and alternative accession number generation · 0c71d51b
  Michele Stravs authored 8 years ago
  
  0c71d51b
- Update webAccess.R - PubChem has moved to https · eb10244c
  schymane authored 8 years ago
  
  "<!DOCTYPE HTML PUBLIC \"-//IETF//DTD HTML 2.0//EN\">\n<html><head>\n<title>301 Moved Permanently</title>\n</head><body>\n<h1>Moved Permanently</h1>\n<p>The document has moved <a href=\"https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/MXWJVTOOROXGIU-UHFFFAOYSA-N/description/json\">here</a>.</p>\n</body></html>\n" I only tried getPcID, but fixed all http to https. This probably needs to filter through to all BioC versions.
  eb10244c
Nov 18, 2016

Fixes in leMsMs.RAW: enforce polarity for switching-mode files; fixed... · 257748e4

Michele Stravs authored 8 years ago

Fixes in leMsMs.RAW: enforce polarity for switching-mode files; fixed precursor filling bug that failed for MS2 before first MS1 scan

257748e4

Nov 01, 2016
- Adapted Erik's parseMassBank to parse into RmbSpectrum2 objects (retaining all... · 8d1d9178
  Michele Stravs authored 8 years ago
  
  Adapted Erik's parseMassBank to parse into RmbSpectrum2 objects (retaining all information from the record)
  8d1d9178
- Adding option to treat unknown (level 5) masses as "charged" (default) or "neutral", as per #42. · 1567e958
  Michele Stravs authored 8 years ago
  
  Fixing: discard formula-less MS1 masses in recalibration calculation
  1567e958
Sep 30, 2016
- Merge branch 'master' into s4power · 34b0fee0
  Michele Stravs authored 8 years ago
  
  34b0fee0
May 12, 2016
- Merge pull request #164 from sneumann/master · cc71371f
  meowcat authored 8 years ago
  
  Copied code from splashR-0.0.3
  cc71371f
May 10, 2016
- Copied code from splashR-0.0.3 · e3640fa3
  Steffen Neumann authored 8 years ago
  
  e3640fa3
Apr 02, 2016
- Cactus changed their interface to https-only · 431cced1
  ermueller authored 8 years ago
  
  431cced1
Mar 08, 2016
- Reworked isotopic annotation · 7a11f9ac
  ermueller authored 9 years ago
  
  7a11f9ac
Mar 02, 2016
- Fixed SPLASH appearing in PK · 4142038a
  ermueller authored 9 years ago
  
  4142038a
Feb 20, 2016
- Isotopic annotation a bit better · a366bd84
  ermueller authored 9 years ago
  
  a366bd84
Feb 18, 2016
- Removed global variable and modularized isotopic annotation further · 94502bd3
  ermueller authored 9 years ago
  
  94502bd3
Feb 15, 2016
- fix bug · 742de175
  michele authored 9 years ago
  
  742de175
Feb 12, 2016

Fixed bug in Recalibration if more than 1 MS1-peak falls withing the specified m/z ppm boundaries · 95bc68b6
ermueller authored 9 years ago

95bc68b6
Eliminated the _FORMULATAG workaround. Also, time for a version bump :) · bc2aac9a
michele authored 9 years ago

bc2aac9a

Thanks to... · c16f0702

michele authored 9 years ago

Thanks to https://github.com/lgatto/MSnbase/commit/3746a473aa0cdcc1eb7088812534efeb276fda53 polarity is now in Spectrum2 objects. Update to feed the data into there from the acquisition mode (note: even where present, data from mzR is unreliable and often -1)

c16f0702

* Fixes in mb record generation · a13e2506

michele authored 9 years ago

* AC$INSTRUMENT, INSTRUMENT_TYPE moved out of gatherData...() functions into getAnalyticalInfo()
* Minimal "gatherData" functions for the export of spectra not further processed
* SMILES into RmbSpectraSet on step 1 of workflow

a13e2506

Feb 11, 2016
- Merge remote-tracking branch 'origin/master' into s4power · d8586839
  michele authored 9 years ago
  
  Conflicts: R/createMassBank.R
  d8586839
- Support for SMILES in RmbSpectraSet · 56814c2f
  michele authored 9 years ago
  
  56814c2f
- More NULL-tolerance and independence during mbWorkflow. Fix for doublepeaks. · c708d505
  michele authored 9 years ago
  
  Importantly, mz is now taken directly from the compound (RmbSpectraSet) rather than retrieved again. I don't know why I had that. maybe because of the pre-refactoring data structure.
  c708d505
- Another selectPeaks fix · 143f8803
  michele authored 9 years ago
  
  143f8803