RforMassSpectrometry/MetaboAnnotation issues and pull requests

#100 - Issue with addProcessing MatchedSpectra class

Issue - State: closed - Opened by RemyDeB about 1 year ago - 2 comments

#99 - Add possibility to select spectra variable for RT matching in matchSpectra

Pull Request - State: closed - Opened by jorainer over 1 year ago

#98 - Allow to define spectraVariable for RT comparison in MS2 data matching

Issue - State: closed - Opened by michaelwitting over 1 year ago
Labels: enhancement

#97 - Update readme

Pull Request - State: closed - Opened by jorainer over 1 year ago

#96 - docs: require mzR package for vignette

Pull Request - State: closed - Opened by jorainer over 1 year ago

#95 - Error for matchSpectra: "Not implemented for MsBackendMassbankSql."

Issue - State: closed - Opened by YANGJJ93MS over 1 year ago - 13 comments

#94 - Minor performance tweaks and additional documentation

Pull Request - State: closed - Opened by jorainer over 1 year ago - 1 comment

#93 - Performance issue with matching functions

Issue - State: open - Opened by Adafede over 1 year ago - 16 comments
Labels: documentation

#92 - Integrate MetFrag

Issue - State: open - Opened by jorainer over 1 year ago - 1 comment

#91 - No MassBank support in AnnotationHub?

Issue - State: closed - Opened by pratarora over 1 year ago - 3 comments

#90 - scoreVariables function

Pull Request - State: closed - Opened by andreavicini about 2 years ago

#89 - Support matching of spectra against annotation sources

Pull Request - State: closed - Opened by jorainer about 2 years ago

#88 - Matching against several annotation resources

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

#87 - filterMatches, ScoreThresholdParam

Pull Request - State: closed - Opened by andreavicini about 2 years ago - 7 comments

#86 - Additional filterMatched filters

Issue - State: open - Opened by jorainer about 2 years ago

#85 - matchApply

Pull Request - State: closed - Opened by andreavicini over 2 years ago - 1 comment

#84 - matchApply function to allow applying any function to each match

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

#83 - Refactor filterMatches

Pull Request - State: closed - Opened by jorainer over 2 years ago

#82 - Extend `filterMatches` framework

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

#81 - Extend filterMatches framework

Issue - State: closed - Opened by jorainer over 2 years ago - 2 comments
Labels: enhancement

#80 - Support for SummarizedExperiment and QFeatures

Pull Request - State: closed - Opened by andreavicini over 2 years ago

#79 - refactor: improve mirror plot in validateMatchedSpectra

Pull Request - State: closed - Opened by jorainer over 2 years ago

#78 - packages for function validateMatchedSpectra

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

#77 - Error when matching ion modes

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

#76 - Issue #69 fixed.

Pull Request - State: closed - Opened by andreavicini over 2 years ago

#75 - refactor: plotly: use segments instead of bars

Pull Request - State: closed - Opened by jorainer over 2 years ago

#74 - fix: fix issue in selecting target rows (issue #73)

Pull Request - State: closed - Opened by jorainer over 2 years ago

#73 - validateMatchedSpectra crashes

Issue - State: closed - Opened by michaelwitting over 2 years ago - 5 comments

#72 - refactor: refactor validateMatchedSpectra

Pull Request - State: closed - Opened by jorainer over 2 years ago

#71 - Michael shinydevel

Pull Request - State: closed - Opened by michaelwitting over 2 years ago - 1 comment

#70 - fix: small updates in shiny app

Pull Request - State: closed - Opened by jorainer over 2 years ago

#69 - matchedData not working for all result objects

Issue - State: closed - Opened by jorainer over 2 years ago - 1 comment
Labels: bug

#68 - Rename matchMz to matchValues and some doc updates

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

#67 - Support for QFeatures

Issue - State: closed - Opened by michaelwitting over 2 years ago - 11 comments

#66 - matchSpectra -- Error in x$.self$finalize() : attempt to apply non-function

Issue - State: closed - Opened by jmbadia over 2 years ago - 1 comment
Labels: wontfix

#65 - Change matchMz to matchValues

Issue - State: closed - Opened by jorainer over 2 years ago - 1 comment

#64 - matchMz, CompareMassParam

Pull Request - State: closed - Opened by andreavicini over 2 years ago - 11 comments

#63 - feat: add setBackend,MatchedSpectra

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

#62 - update with master

Pull Request - State: closed - Opened by michaelwitting over 2 years ago

#61 - Additional CCS matching?

Issue - State: open - Opened by michaelwitting over 2 years ago - 6 comments

#60 - change in score, score_rt and ppm_error definitions

Pull Request - State: closed - Opened by andreavicini over 2 years ago

#59 - calculation of m/z error in ppm

Pull Request - State: closed - Opened by andreavicini over 2 years ago - 1 comment

#58 - prototype for ion mode matching

Pull Request - State: open - Opened by michaelwitting over 2 years ago - 1 comment

#57 - Jomain

Pull Request - State: closed - Opened by jorainer over 2 years ago

#56 - matchIonMode function?

Issue - State: closed - Opened by michaelwitting over 2 years ago - 19 comments

#55 - Devel michael

Pull Request - State: closed - Opened by michaelwitting over 2 years ago - 7 comments

#54 - update devel_michael

Pull Request - State: closed - Opened by michaelwitting over 2 years ago

#53 - question - not issue, per se

Issue - State: open - Opened by cbroeckl over 2 years ago - 1 comment

#52 - MatchSpectra function

Issue - State: open - Opened by tiwa1125 over 2 years ago - 5 comments

#51 - Report ppm error in matchMz

Issue - State: closed - Opened by jorainer almost 3 years ago - 1 comment

#50 - Add different param object that accept also RI

Issue - State: closed - Opened by michaelwitting almost 3 years ago - 1 comment

#49 - Add matchMz and matchSpectra for CompDb and IonDb

Issue - State: open - Opened by jorainer almost 3 years ago

#48 - RT filter for adducts

Issue - State: open - Opened by LiesaSalzer almost 3 years ago

#47 - Export result as mzTab?

Issue - State: open - Opened by jorainer almost 3 years ago - 1 comment

#46 - Multiple ppm as parameter

Issue - State: open - Opened by bitbarbie almost 3 years ago

#45 - Add sticker to readme

Pull Request - State: closed - Opened by jorainer almost 3 years ago

#44 - fix: fix calculation of rows/columns in plotSpectraMirror

Pull Request - State: closed - Opened by jorainer almost 3 years ago

#43 - Add parameter toleranceRt to CompareSpectraParam

Pull Request - State: closed - Opened by jorainer about 3 years ago - 17 comments

#42 - Support for manually defined adducts in matchMz

Pull Request - State: closed - Opened by andreavicini about 3 years ago

#41 - Support for manually defined adducts in `matchMz`

Issue - State: closed - Opened by jorainer about 3 years ago
Labels: enhancement

#40 - feat: add THRESHFUN_REVERSE (issue #37)

Pull Request - State: closed - Opened by jorainer about 3 years ago

#39 - Updates

Pull Request - State: closed - Opened by jorainer about 3 years ago

#38 - slow performance of matchSpectra

Issue - State: closed - Opened by stanstrup about 3 years ago - 11 comments

#37 - filter based on reverse score in MatchForwardReverseParam?

Issue - State: closed - Opened by stanstrup about 3 years ago - 8 comments

#36 - number of common peaks in @matches

Issue - State: closed - Opened by stanstrup about 3 years ago - 5 comments

#35 - retention time in MatchForwardReverseParam

Issue - State: closed - Opened by stanstrup about 3 years ago - 4 comments

#34 - Tolerance parameter in matchSpectra()

Issue - State: closed - Opened by hvaret about 3 years ago - 3 comments

#33 - matchMz performance improvement and parameter renaming

Pull Request - State: closed - Opened by jorainer about 3 years ago

#32 - Consistency in parameter naming

Issue - State: closed - Opened by jorainer about 3 years ago - 2 comments

#31 - Parameter score in addMatches supports data.frame or numeric

Pull Request - State: closed - Opened by jorainer about 3 years ago

#30 - Updates to documentation and examples

Pull Request - State: closed - Opened by jorainer about 3 years ago

#29 - More flexible score parameter for addMatches

Issue - State: closed - Opened by jorainer about 3 years ago
Labels: enhancement

#28 - matchMz very slow

Issue - State: closed - Opened by jorainer about 3 years ago - 2 comments

#27 - keep/dropMatches

Pull Request - State: closed - Opened by andreavicini about 3 years ago - 2 comments

#26 - Have a way to select or remove specific matches

Issue - State: closed - Opened by jorainer about 3 years ago
Labels: enhancement

#25 - Documentation updates and smaller fixes

Pull Request - State: closed - Opened by jorainer about 3 years ago - 1 comment

#24 - New versions of .dollar and .matchedData

Pull Request - State: closed - Opened by andreavicini about 3 years ago - 1 comment

#23 - add some unit tests for issue #22

Pull Request - State: closed - Opened by jorainer about 3 years ago - 1 comment

#22 - Matched objects don't work if $query_idx and $target_idx are unsorted

Issue - State: closed - Opened by jorainer about 3 years ago - 1 comment
Labels: bug

#21 - matchMz between SummarizedExperiment and data.frame

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

#20 - Implement a Matched object for SummarizedExperiment

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

#19 - Target prefix removed from Param objects

Pull Request - State: closed - Opened by andreavicini over 3 years ago - 1 comment

#18 - Naming of Param objects

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

#17 - Sticker for MetaboAnnotation

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

#16 - Comparing isotope pattern

Issue - State: open - Opened by michaelwitting over 3 years ago - 7 comments

#15 - matchMz updates

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

#14 - match m/z against m/z

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

#13 - match m/z and retention times

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

#12 - Add the Matched object and re-implement the matchMz function

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

#11 - Matched object and matchMz TargetMass2MzParam

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

#10 - matchMz TargetMass2MzParam

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

#9 - Implement a generic `Matched` object

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

#8 - fix: fix warnings and notes from R CMD check

Pull Request - State: closed - Opened by jorainer over 3 years ago - 1 comment

#7 - Devel michael

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

#6 - Add MatchForwardReverseParam

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

#5 - Add spectra matching functionality

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

#4 - Comparison functions for spectral matching

Issue - State: closed - Opened by michaelwitting over 3 years ago - 3 comments
Labels: question

#3 - multiple similarity scores

Issue - State: open - Opened by michaelwitting over 3 years ago - 9 comments

#2 - Mass and m/z matching

Issue - State: closed - Opened by jorainer over 3 years ago - 10 comments

#1 - AnnotatedSpectra or MatchedSpectra

Issue - State: closed - Opened by jorainer over 3 years ago - 21 comments
Labels: question

GitHub / RforMassSpectrometry/MetaboAnnotation issues and pull requests