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

#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

#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

#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

#743 - Add new plotPrecursorIons function and address issue #742

Pull Request - State: closed - Opened by jorainer 5 months ago - 8 comments

#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

#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

#731 - Update retention times to alkane retention time indices for GC-MS

Issue - State: open - Opened by CLUES-Emory 7 months ago - 5 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

#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

#714 - Update Ubuntu version for System dependency check

Pull Request - State: closed - Opened by sneumann 8 months ago - 1 comment

#709 - Updates and fixes

Pull Request - State: closed - Opened by jorainer 10 months ago - 4 comments

#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

#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

#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