Ecosyste.ms: Issues
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GitHub / sneumann/xcms issues and pull requests
#765 - Peak mz values when running findChromPeaks on XChromatograms object
Issue -
State: closed - Opened by CLUES-Emory 26 days ago
- 1 comment
#764 - Error in running the tutorial
Issue -
State: open - Opened by Tina9 30 days ago
#763 - Is there any way to map the corresponding MS1 and its isotope information to the MS2 data extracted with spectrum?
Issue -
State: open - Opened by GAOJianguo66 about 1 month ago
#762 - fix: issue #755 for the RELEASE_3_19 branch
Pull Request -
State: closed - Opened by jorainer about 2 months ago
#761 - Some updates and bug fixes
Pull Request -
State: closed - Opened by jorainer about 2 months ago
#760 - Can't use quantify to get result into summarizedexperiment
Issue -
State: closed - Opened by pablovgd 2 months ago
- 2 comments
#759 - There's something wrong with maxo's calculations.
Issue -
State: open - Opened by dongdongdong7 2 months ago
- 5 comments
#758 - small fixes
Pull Request -
State: closed - Opened by philouail 3 months ago
#757 - refactor: dump all data export functionality from xcms
Pull Request -
State: closed - Opened by jorainer 3 months ago
- 2 comments
#756 - ppm paramenter for ChromPeakAreaParam
Issue -
State: open - Opened by stanstrup 3 months ago
- 1 comment
#755 - Chromatograms of MS1 data with two different scan events per file
Issue -
State: closed - Opened by breidan 3 months ago
- 6 comments
#754 - Regarding the steps of operating FillChromPeaksParam
Issue -
State: open - Opened by v-v1150n 4 months ago
- 3 comments
#753 - refactor: updates of documentation and extension of unit tests
Pull Request -
State: closed - Opened by jorainer 4 months ago
- 3 comments
#752 - Add a function to coerce from XcmsExperiment to XCMSnExp
Issue -
State: open - Opened by jorainer 4 months ago
Labels: enhancement
#751 - fillChromPeaks: for MS2 chrom peaks: ensure data is integrated from spectra of the correct isolation window
Issue -
State: open - Opened by jorainer 4 months ago
Labels: swath
#750 - Duplicate values created by fillChromPeaks
Issue -
State: open - Opened by frankyWk 4 months ago
- 1 comment
#749 - refactor: add storeResults/loadResults for Spectra etc
Pull Request -
State: closed - Opened by jorainer 4 months ago
#748 - Setter for filepath in XcmsExperiment
Issue -
State: closed - Opened by jmorim 4 months ago
- 3 comments
#747 - Retention time alignment using a combination of LamaParama and subset-based alignment
Issue -
State: open - Opened by CLUES-Emory 4 months ago
- 2 comments
#746 - Import methods
Pull Request -
State: closed - Opened by philouail 4 months ago
- 6 comments
#745 - fix: ensure dropFeatureDefinitions correctly drops filled peaks
Pull Request -
State: closed - Opened by jorainer 5 months ago
- 2 comments
#744 - Visualize, use plotSpectraMirror function to draw spectrum matching results
Issue -
State: open - Opened by v-v1150n 5 months ago
- 2 comments
#743 - Add new plotPrecursorIons function and address issue #742
Pull Request -
State: closed - Opened by jorainer 5 months ago
- 8 comments
#742 - Support excluding samples for PeakDensity correspondence
Issue -
State: open - Opened by jorainer 5 months ago
#741 - fix: filtering MsLevel for xic plot
Pull Request -
State: closed - Opened by NorStorz 6 months ago
- 1 comment
#740 - fix: add parameter rtimeDifferenceThreshold for ObiwarpParam
Pull Request -
State: closed - Opened by jorainer 6 months ago
- 1 comment
#739 - Waters data problems with Obiwarp
Issue -
State: closed - Opened by parasitetwin 6 months ago
- 9 comments
#738 - Best way to deconvolute metabolite data
Issue -
State: open - Opened by JasonBason 6 months ago
- 1 comment
#737 - Ways to extract all MS2 peaks?
Issue -
State: open - Opened by jzhou19 6 months ago
- 3 comments
#736 - After I perform chromatographic peak detection, how do I confirm the quality of my peaks?
Issue -
State: open - Opened by v-v1150n 6 months ago
- 1 comment
#735 - Best way to document additional XCMS object processing steps in the ProcessHistory slot?
Issue -
State: open - Opened by wkumler 6 months ago
- 3 comments
#734 - Error for XIC plot of timsTof data
Issue -
State: open - Opened by NorStorz 6 months ago
- 3 comments
#733 - The error message encountered when using the "IPO" package
Issue -
State: closed - Opened by v-v1150n 7 months ago
- 10 comments
#732 - `LamaParama` implementation for `AdjustRtime()`: correcting alignment based on external dataset.
Pull Request -
State: closed - Opened by philouail 7 months ago
- 1 comment
#731 - Update retention times to alkane retention time indices for GC-MS
Issue -
State: open - Opened by CLUES-Emory 7 months ago
- 5 comments
#730 - xset crashes on MAC OS 14.3 R 4.3.3 , BiocManager 1.30.22 and xcms 4.0.2
Issue -
State: open - Opened by AndreasReinecke 7 months ago
- 6 comments
#729 - R CMD check problems
Issue -
State: closed - Opened by jorainer 7 months ago
- 5 comments
#728 - Trouble plotting XChromatograms
Issue -
State: closed - Opened by JasonBason 7 months ago
- 5 comments
#727 - fillChromPeaks error
Issue -
State: closed - Opened by JasonBason 7 months ago
- 2 comments
#726 - precusor charge for each features
Issue -
State: open - Opened by 13479776 7 months ago
- 3 comments
#725 - msLevel=2L chromatograms (MRM or SRM) not working with MsExperiment interface
Issue -
State: closed - Opened by jmorim 7 months ago
- 1 comment
#724 - Bad practices with peak merging
Issue -
State: closed - Opened by jmorim 7 months ago
- 2 comments
#723 - Filter MsExperiment object by spectraData filterString
Issue -
State: closed - Opened by breidan 7 months ago
- 16 comments
#722 - Ensure backward compatibility for Parameter classes that gained new slots
Pull Request -
State: closed - Opened by jorainer 7 months ago
- 2 comments
#721 - reconstructChromPeakSpectra
Issue -
State: open - Opened by Slycopersicum 8 months ago
- 1 comment
#720 - Suggested starting parameters for GC-MS data
Issue -
State: closed - Opened by ckeeling 8 months ago
- 3 comments
#719 - fix issue #716 in XcmsExperiment-functions.R
Pull Request -
State: closed - Opened by pablovgd 8 months ago
- 10 comments
#718 - Addition of MzTabParam for export in .mztab format
Pull Request -
State: open - Opened by philouail 8 months ago
- 1 comment
#717 - Seeking advices about data importing
Issue -
State: open - Opened by Babyfaceout 8 months ago
- 5 comments
#716 - Trouble extracting chromatogram plots after manualChromPeaks()
Issue -
State: closed - Opened by pablovgd 8 months ago
- 5 comments
#715 - Retention time alignment using PeakGroupsParam's peakGroupsMatrix parameter renders error
Issue -
State: closed - Opened by pablovgd 8 months ago
- 10 comments
#714 - Update Ubuntu version for System dependency check
Pull Request -
State: closed - Opened by sneumann 8 months ago
- 1 comment
#713 - Addition of method to filter features based on quality assessment
Pull Request -
State: closed - Opened by philouail 8 months ago
#712 - Add possibility to perform peak density correspondence considering m/z dependent margins
Pull Request -
State: closed - Opened by jorainer 9 months ago
- 2 comments
#711 - why do_groupChromPeaks_density processing peaks with fixed size of the overlapping slices in mz dimension
Issue -
State: closed - Opened by WallFacerLR 9 months ago
- 17 comments
#710 - Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘findChromPeaks’ for signature ‘"XMLDocument", "MatchedFilterParam"’
Issue -
State: closed - Opened by RbWick 9 months ago
- 2 comments
#709 - Updates and fixes
Pull Request -
State: closed - Opened by jorainer 10 months ago
- 4 comments
#708 - How would a larger peak width vs smaller peak width affect m/z of features detected?
Issue -
State: open - Opened by Pembs 10 months ago
- 1 comment
#707 - negative subsetting removes chromPeaks
Issue -
State: closed - Opened by philouail 10 months ago
Labels: bug
#706 - Add tests for some ion mobility files
Issue -
State: open - Opened by sneumann 10 months ago
- 1 comment
Labels: enhancement
#705 - Add a function that calculates peak quality metrics for detected peaks
Issue -
State: open - Opened by jorainer 10 months ago
- 10 comments
Labels: enhancement
#704 - Vignette: avoid "data" as object name
Issue -
State: closed - Opened by sneumann 10 months ago
- 2 comments
#703 - Fix issue with subset-based peakGroups alignment and other updates
Pull Request -
State: closed - Opened by jorainer 10 months ago
- 2 comments
#702 - Definition of anchor peaks for subset-based peakGroups alignment not correct
Issue -
State: closed - Opened by jorainer 10 months ago
- 1 comment
Labels: bug
#701 - Batch effect correction without QC sample
Issue -
State: open - Opened by Kotchani 10 months ago
- 1 comment
#700 - xcmsSet interface gives errors
Issue -
State: open - Opened by rickhelmus 11 months ago
- 13 comments
#699 - Addition of PlainTextParam to the storeResults generic function
Pull Request -
State: closed - Opened by philouail 11 months ago
- 6 comments
#698 - feat: creation of new generic function so save XcmsExperiment object
Pull Request -
State: closed - Opened by philouail 11 months ago
- 4 comments
Labels: enhancement
#697 - fix: add method to coerce XcmsExperiment to xcmsSet
Pull Request -
State: closed - Opened by jorainer 12 months ago
#696 - No method to convert XcmsExperiment to xcmsSet - Version 3.99.5
Issue -
State: closed - Opened by CollinStark 12 months ago
- 1 comment
#695 - findChromPeaks finds duplicate peaks
Issue -
State: open - Opened by Pascallio 12 months ago
- 1 comment
#694 - do_findChromPeaks_centWave returns wrong maxo and int* values
Issue -
State: open - Opened by Pascallio 12 months ago
- 3 comments
#693 - Properly serialize an xcms result object to disk/files
Issue -
State: open - Opened by jorainer 12 months ago
- 21 comments
#692 - Build failure on arm/Linux
Issue -
State: closed - Opened by sneumann 12 months ago
- 2 comments
#691 - refactor: chromatogram,XcmsExperiment with only mz or rt defined
Pull Request -
State: closed - Opened by jorainer 12 months ago
#690 - Build error invalid class "MsBackendMzR" object: slots not in object: "peaksVariables"
Issue -
State: closed - Opened by sneumann about 1 year ago
- 2 comments
#689 - Small final updates
Pull Request -
State: closed - Opened by jorainer about 1 year ago
- 1 comment
#688 - Need all chromatograms in particular sample
Issue -
State: open - Opened by 13479776 about 1 year ago
- 1 comment
#687 - Error in writeMSData
Issue -
State: open - Opened by lshyun0415 about 1 year ago
- 1 comment
#686 - Polarity cannot be extracted
Issue -
State: open - Opened by crestre about 1 year ago
- 3 comments
#685 - Adding new peak quality metrics to findChromPeaks for CentWave
Pull Request -
State: closed - Opened by wkumler about 1 year ago
- 31 comments
#684 - return EIC with peak detection output
Issue -
State: open - Opened by cbroeckl about 1 year ago
- 1 comment
Labels: enhancement
#683 - xcmsRaw - error
Issue -
State: open - Opened by crestre about 1 year ago
- 6 comments
#682 - combineSpectra of a feature
Issue -
State: closed - Opened by ricoderks about 1 year ago
- 3 comments
#681 - Added link to changelog to README
Pull Request -
State: closed - Opened by hechth about 1 year ago
#680 - Introduce a changelog
Issue -
State: closed - Opened by hechth over 1 year ago
- 1 comment
#679 - Add XCMS object as data to EDAM Ontology
Issue -
State: open - Opened by hechth over 1 year ago
- 4 comments
#678 - How are features obtained if you don’t specify any class information for grouping?
Issue -
State: open - Opened by Pembs over 1 year ago
- 1 comment
#677 - Why does fill peaks with XCMSnExp object result in considerably less features than fill peaks with XCMSset?
Issue -
State: closed - Opened by Pembs over 1 year ago
- 6 comments
#676 - ERROR: Dimensions of profile matrices do not match !
Issue -
State: open - Opened by zhengjxj over 1 year ago
- 1 comment
#675 - Does minSamples override minFraction when grouping?
Issue -
State: closed - Opened by Pembs over 1 year ago
- 2 comments
#674 - Two overlapping peaks with the same m/z detected as one
Issue -
State: closed - Opened by MonicaCalSan over 1 year ago
- 2 comments
#673 - fix: fix for issue #511
Pull Request -
State: closed - Opened by jorainer over 1 year ago
- 1 comment
#672 - Move multtest from Suggests to Imports in dependencies
Pull Request -
State: closed - Opened by sneumann over 1 year ago
#671 - Handling multtest dependency (BioC build error)
Issue -
State: closed - Opened by sneumann over 1 year ago
- 3 comments
#670 - Error Invalid cvParam accession "1003293"
Issue -
State: closed - Opened by RemyDeB over 1 year ago
- 1 comment
#669 - Centwave error with converted .wiff files.
Issue -
State: open - Opened by jsimpso1 over 1 year ago
- 1 comment
#668 - adjustRtime() Error
Issue -
State: closed - Opened by zinuo-H over 1 year ago
- 8 comments
#667 - tests: fix longtests
Pull Request -
State: closed - Opened by jorainer over 1 year ago
#666 - xcms 4: native support for MsExperiment and Spectra
Pull Request -
State: closed - Opened by jorainer over 1 year ago
- 2 comments