Ecosyste.ms: Issues

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GitHub / sneumann/camera issues and pull requests

#81 - pcgroup clarification

Issue - State: closed - Opened by apulvino over 1 year ago - 6 comments

#80 - Understanding how the calculation of adducts works

Issue - State: open - Opened by szfilip over 1 year ago

#78 - Whether the mzabs parameter of findAddct() can be adjusted by the user？

Issue - State: open - Opened by Suyun11 over 1 year ago - 1 comment

#77 - Error in findIsotopesWithValidation function

Issue - State: closed - Opened by chuyaowang almost 2 years ago - 4 comments

#76 - Changed language in desctiption and details for clarification

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

#75 - Several || left where _R_CHECK_LENGTH_1_LOGIC2_ barfs

Issue - State: open - Opened by sneumann about 3 years ago

#74 - Add class1 class2 arguments

Pull Request - State: open - Opened by a-velt about 3 years ago

#73 - Add of class1 and class2 options in the annotateDiffreport function

Issue - State: open - Opened by a-velt about 3 years ago - 2 comments

#72 - fillPeaks(xset_gr) error in xcms

Issue - State: open - Opened by manasonur about 3 years ago - 1 comment

#71 - The larger the isotope number, the larger the m/z error

Issue - State: open - Opened by Annatkachev over 3 years ago - 1 comment

#70 - Unexpected outputs: m/z differences and isotope number

Issue - State: open - Opened by Annatkachev over 3 years ago - 1 comment

#65 - calcIso in annotaeDiffreport not propagated down to groupCorr

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

#64 - False negatives, losing peaks when using xsAnnotate on an xcmsSet

Issue - State: closed - Opened by jmorim almost 4 years ago - 2 comments

#63 - Dependency on deprecated xcmsClusterApply

Issue - State: open - Opened by sneumann about 4 years ago - 4 comments

#62 - Unit test failure: number of annotations changed

Issue - State: closed - Opened by sneumann about 4 years ago - 1 comment

#61 - Update neutraladdition.csv

Pull Request - State: closed - Opened by shutinet about 4 years ago - 2 comments

#60 - misunderstanding between "O" and "0"

Issue - State: closed - Opened by shutinet about 4 years ago - 1 comment

#59 - Wrong molecular mass for neutral addition "CF3COOH"

Issue - State: closed - Opened by shutinet about 4 years ago

#58 - CAMERA Peaklist table is empty

Issue - State: open - Opened by ZandkarimiF over 4 years ago - 4 comments

#56 - Possible bug in `findIsotopesWithValidation`

Issue - State: open - Opened by breidan over 4 years ago - 2 comments

#55 - Fixed Bug in labelling and/or legend of plotEICs

Pull Request - State: open - Opened by jmosl01 over 4 years ago

#54 - Error in fillpeaks after XCMSnExp conversion

Issue - State: open - Opened by ghost over 4 years ago - 3 comments

#54 - Error in fillpeaks after XCMSnExp conversion

Issue - State: open - Opened by ghost over 4 years ago - 3 comments

#53 - Change all messages from cat to message

Issue - State: open - Opened by stanstrup over 4 years ago

#52 - Export core function to identify isotopes

Pull Request - State: open - Opened by jorainer over 4 years ago - 1 comment

#51 - Expose the function to identify isotopes?

Issue - State: open - Opened by jorainer over 4 years ago - 4 comments

#50 - groupCorr cor_exp_th = 0.90 separate two > 0.9995

Issue - State: open - Opened by cbonnefoy over 4 years ago - 6 comments

#49 - use which.max to keep up with latest changes in R 3.6

Pull Request - State: open - Opened by korseby over 4 years ago - 3 comments

#48 - getReducedPeaklist values not reported

Issue - State: closed - Opened by korseby over 4 years ago - 3 comments

#47 - creating custom rule table for CAMERA

Issue - State: open - Opened by vlagani over 4 years ago - 2 comments

#46 - Fix plotPsSpectrum()

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

#44 - failure: length > 1 in coercion to logical

Issue - State: open - Opened by sneumann almost 5 years ago - 1 comment

#43 - Corrected vignette text not being visible due to not wrapping around …

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

#42 - Vignettes: code not visible

Issue - State: closed - Opened by antonwnk almost 5 years ago - 3 comments

#41 - xraw parameter

Issue - State: open - Opened by jsaintvanne about 5 years ago - 2 comments

#40 - Provide option to select intval in findAdducts function within xsAnnotate.R script

Pull Request - State: closed - Opened by sunil20dhakad over 5 years ago - 3 comments

#39 - No option to change intval (intensity type) in findAdducts function

Issue - State: open - Opened by sunil20dhakad over 5 years ago - 2 comments

#38 - Isotopes assigned to different pc groups

Issue - State: open - Opened by shefalilathwal over 5 years ago - 4 comments

#36 - Use MSnbase objects for storing CAMERA annotations

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

#35 - Export PSPectra as annotated spectrum

Issue - State: open - Opened by sneumann over 5 years ago - 1 comment

#34 - CAMERA fails to load from source files

Issue - State: closed - Opened by ldag27 almost 6 years ago - 1 comment

#33 - From XCMS3 - NA values in xcmsSet. Use fillPeaks()

Issue - State: open - Opened by lecorguille over 6 years ago - 19 comments

#32 - Unexpected [M+2]+ isotope annotation

Issue - State: open - Opened by Tomnl over 6 years ago - 1 comment

#31 - getEICs fix

Pull Request - State: open - Opened by trljcl over 6 years ago - 1 comment

#30 - Rcorr fix

Pull Request - State: open - Opened by trljcl over 6 years ago - 3 comments

#29 - Update fct_groupCorr.R to incorporate rt correction

Pull Request - State: open - Opened by trljcl over 6 years ago - 1 comment

#28 - RT correction is not incorporated into groupCorr() EIC extraction functions

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

#27 - findIsotope: subscript out of bound

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

#26 - findIsotopes: Combine isotope cluster bug

Issue - State: open - Opened by cdinter over 6 years ago - 8 comments

#25 - Is there a way to respectively perform findIsotopes to each phenodata class?

Issue - State: closed - Opened by YonghuiDong almost 7 years ago - 3 comments

#24 - Identify all places where CAMERA still uses xcms1 internally

Issue - State: open - Opened by meowcat almost 7 years ago - 2 comments

#23 - sanity check on groupCorr parameters

Pull Request - State: closed - Opened by sneumann almost 7 years ago - 1 comment

#22 - getPeaklist not pulling rownames correctly

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

#21 - Fixed bug in getPeaklist

Pull Request - State: closed - Opened by stanstrup about 7 years ago - 1 comment

#20 - bugfixes to getPeaklist and getReducedPeaklist

Pull Request - State: closed - Opened by korseby about 7 years ago - 3 comments

#19 - error with groupCorr

Issue - State: closed - Opened by MarcNIOZ over 7 years ago - 1 comment

#18 - allow matchedfilter alternative intval in getPeaklist

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

#17 - change nslaves to BPPARAM as in XCMS

Issue - State: open - Opened by stanstrup over 7 years ago - 1 comment

#16 - getReducedPeaklist

Pull Request - State: closed - Opened by korseby over 7 years ago - 1 comment

#15 - intval is not passed from groupcorr to calcCaS

Issue - State: closed - Opened by stanstrup over 7 years ago - 1 comment

#14 - passed intval from Groupcorr to calcCaS

Pull Request - State: closed - Opened by stanstrup over 7 years ago - 1 comment

#12 - WARNING: subdirectory of ‘inst’ also used by R

Issue - State: open - Opened by sneumann about 8 years ago

#11 - 'dimnames' must be a list in Examples

Issue - State: closed - Opened by sneumann about 8 years ago - 2 comments

#10 - New: Added function findIsotopesWithValidation and S4 class compoundQuantiles

Pull Request - State: closed - Opened by Treutler about 8 years ago - 1 comment

#9 - Added function findIsotopesWithValidation and S4 class compoundQuantiles

Pull Request - State: closed - Opened by Treutler about 8 years ago - 4 comments

#8 - Error in plotPsSpectrum(): missing value where TRUE/FALSE needed

Issue - State: open - Opened by sneumann over 8 years ago - 6 comments

#7 - Neutral masses do not match

Issue - State: closed - Opened by mheiser-md over 8 years ago - 3 comments

#6 - R CMD check failure on recent BioC `Error in getPeaks_selection(xs)`

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

#5 - slot neutraladdition can not be empty to use generateRules

Issue - State: closed - Opened by sneumann about 10 years ago

#3 - Failure on windows with SNOW in parallel mode

Issue - State: open - Opened by sneumann about 10 years ago - 1 comment

#2 - Bug in labelling and/or legend of plotEICs

Issue - State: open - Opened by sneumann about 10 years ago - 4 comments

#1 - cor_exp_th was not passed from annotateDiffreport to groupCorr

Pull Request - State: closed - Opened by stanstrup over 10 years ago