Ecosyste.ms: Issues

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GitHub / lgatto/synapter issues and pull requests

#100 - problem with making master

Issue - State: closed - Opened by pavel-shliaha over 9 years ago
Labels: bug

#99 - Should we create sample names automatically?

Issue - State: closed - Opened by sgibb over 9 years ago - 1 comment
Labels: question

#98 - MSnBase complains

Issue - State: closed - Opened by pavel-shliaha over 9 years ago - 5 comments
Labels: question

#97 - question about memory allocation

Issue - State: closed - Opened by pavel-shliaha over 9 years ago - 28 comments
Labels: question, wontfix

#96 - bug in new synapter while reading pep3D

Issue - State: closed - Opened by pavel-shliaha over 9 years ago - 3 comments
Labels: bug

#95 - Are the "light" variants of writeMergedPeptides/writeMatchedEMRTs still needed?

Issue - State: closed - Opened by sgibb over 9 years ago
Labels: question

#94 - Confusing names

Issue - State: closed - Opened by pavel-shliaha over 9 years ago - 2 comments
Labels: Important, TODO

#93 - perform rescue after transfer

Issue - State: closed - Opened by pavel-shliaha over 9 years ago - 7 comments
Labels: bug

#92 - Code chunk plotcxseq in fragmentmatching vigette fails

Issue - State: closed - Opened by lgatto over 9 years ago - 6 comments
Labels: bug

#91 - Error when compiling fragmentmatching vignette

Issue - State: closed - Opened by lgatto over 9 years ago - 2 comments
Labels: bug

#90 - synapter bug

Issue - State: closed - Opened by pavel-shliaha over 9 years ago - 1 comment
Labels: bug

#89 - export Fragments/Spectra to MGF

Issue - State: closed - Opened by sgibb over 9 years ago - 3 comments
Labels: TODO

#88 - Implement unit tests for synapter

Issue - State: open - Opened by lgatto over 9 years ago - 2 comments
Labels: TODO

#87 - useless columns?

Issue - State: closed - Opened by sgibb over 9 years ago - 1 comment
Labels: question

#86 - synapter warning

Issue - State: closed - Opened by lgatto almost 10 years ago - 1 comment

#85 - `filterUniqueMatches` needs to remove Pep3D data

Issue - State: closed - Opened by sgibb about 10 years ago - 4 comments
Labels: Important, FragmentMatching

#84 - test whether filterNonUniqueMatches reintroduces Pep3D data correctly

Issue - State: closed - Opened by sgibb about 10 years ago - 1 comment
Labels: Important, TODO, FragmentMatching

#83 - Update fragmentmatching vignette

Issue - State: closed - Opened by sgibb about 10 years ago - 3 comments
Labels: Important, FragmentMatching

#82 - RT alignment reference

Issue - State: open - Opened by lgatto about 10 years ago - 3 comments

#81 - Adapt `synergise` to new 3D grid search

Issue - State: closed - Opened by sgibb about 10 years ago - 4 comments
Labels: bug, Important

#80 - Status of ion mobility

Issue - State: closed - Opened by lgatto about 10 years ago - 2 comments
Labels: question

#79 - Cleanup NEWS file.

Issue - State: closed - Opened by sgibb about 10 years ago - 3 comments
Labels: TODO

#78 - Replace `Version` slot by `ClassVersion` slot.

Issue - State: closed - Opened by sgibb about 10 years ago - 1 comment
Labels: TODO

#77 - promote `validObject` in manuals and vignettes

Issue - State: open - Opened by sgibb about 10 years ago
Labels: TODO

#76 - add more useful tests to `validObject`

Issue - State: open - Opened by sgibb about 10 years ago
Labels: TODO

#75 - Provide a sufficient updater method for old `Synapter` objects.

Issue - State: closed - Opened by sgibb about 10 years ago
Labels: Important

#74 - Store fragment library as MSnExp in master

Issue - State: closed - Opened by sgibb over 10 years ago - 3 comments
Labels: Important

#73 - How to handle false positives produced by the grid search?

Issue - State: closed - Opened by sgibb over 10 years ago - 20 comments
Labels: Important

#72 - Reduce crossmatching to ident fragment vs quant spectrum comparison

Issue - State: closed - Opened by sgibb over 10 years ago - 6 comments
Labels: question

#71 - Do masterPeptides need two master data.frames?

Issue - State: closed - Opened by sgibb over 10 years ago - 2 comments
Labels: question, wontfix

#69 - centroided spectra in synobj2

Issue - State: closed - Opened by lgatto over 10 years ago - 5 comments

#68 - 3D grid search

Pull Request - State: closed - Opened by sgibb over 10 years ago - 12 comments
Labels: ready

#67 - misleading names

Issue - State: closed - Opened by pavel-shliaha over 10 years ago - 1 comment
Labels: Important, TODO

#66 - Adapt ionmobility.Rnw to new HDMSE dataset

Issue - State: closed - Opened by sgibb over 10 years ago
Labels: TODO

#65 - introduce filterFragments and plotCumulativeNumberOfFragments

Pull Request - State: closed - Opened by sgibb almost 11 years ago

#64 - cross matching performance plots

Pull Request - State: closed - Opened by sgibb almost 11 years ago

#63 - fragment library

Issue - State: closed - Opened by pavel-shliaha almost 11 years ago
Labels: Important

#62 - add removePrecursor/tolerance argument to load{SpectrumXml,FragmentCsv}Files

Pull Request - State: closed - Opened by sgibb almost 11 years ago

#61 - add argument ILequal to dbUniquePeptideSet; closes #60

Pull Request - State: closed - Opened by sgibb almost 11 years ago - 3 comments

#60 - treat L,I as identical in dbUniquePeptideSet

Issue - State: closed - Opened by sgibb almost 11 years ago

#59 - remove precursor ions from spectrum.xml and fragment.csv data

Issue - State: closed - Opened by sgibb almost 11 years ago

#58 - summary plot for ion mobility

Pull Request - State: closed - Opened by sgibb almost 11 years ago - 3 comments

#57 - emulate PLGS' peptide cleavage; close #53

Pull Request - State: closed - Opened by sgibb almost 11 years ago - 4 comments

#56 - fragment matching

Pull Request - State: closed - Opened by sgibb almost 11 years ago - 4 comments

#55 - not performing database digestion every time analysis is run

Issue - State: closed - Opened by pavel-shliaha almost 11 years ago - 4 comments
Labels: enhancement

#54 - add progress bar to estimateMasterFdr

Issue - State: closed - Opened by pavel-shliaha almost 11 years ago - 2 comments
Labels: enhancement

#53 - Special missed cleavage handling

Issue - State: closed - Opened by pavel-shliaha almost 11 years ago - 3 comments
Labels: enhancement

#52 - change separator in GridDetails' names to :

Pull Request - State: closed - Opened by sgibb almost 11 years ago

#51 - change default value of grid.ppm.from to 2 (was 5 before)

Pull Request - State: closed - Opened by sgibb almost 11 years ago

#50 - Optimize gridSearch2 (and fix a bug in the calculation of non unique matches)

Pull Request - State: closed - Opened by sgibb almost 11 years ago

#49 - Modification of findMSeEMRTs to speed up searchGrid

Pull Request - State: closed - Opened by sgibb almost 11 years ago - 1 comment

#48 - fix some typos in the Synapter manual page

Pull Request - State: closed - Opened by sgibb almost 11 years ago

#46 - fix little typo in the vignette

Pull Request - State: closed - Opened by sgibb almost 11 years ago

#45 - 2DRP_realignment

Issue - State: open - Opened by pavel-shliaha over 11 years ago
Labels: enhancement

#44 - LOPIMS bug

Issue - State: closed - Opened by pavel-shliaha over 11 years ago - 1 comment
Labels: bug

#43 - checking isotopic distribution for matched EMRT

Issue - State: closed - Opened by pavel-shliaha over 11 years ago - 1 comment
Labels: enhancement

#42 - checking correspondance between pep3D and final_peptide files

Issue - State: closed - Opened by pavel-shliaha almost 12 years ago - 8 comments
Labels: enhancement

#41 - missreporting number of non-proteotypic peptides

Issue - State: closed - Opened by pavel-shliaha almost 12 years ago - 1 comment
Labels: bug

#40 - 2DRP master

Issue - State: open - Opened by pavel-shliaha about 12 years ago - 4 comments

#39 - Correct saturation by only quantifying on unsaturated isotopes in all samples under comparison

Issue - State: closed - Opened by pavel-shliaha about 12 years ago - 75 comments
Labels: enhancement

#38 - Not transferring ids for identified peptides

Issue - State: closed - Opened by pavel-shliaha about 12 years ago
Labels: bug, Important

#37 - Adressing detector saturation in HDMSE by isotope correction

Issue - State: closed - Opened by pavel-shliaha over 12 years ago - 2 comments
Labels: enhancement

#36 - Add quick-guide and summary function table in vignette

Issue - State: closed - Opened by lgatto over 12 years ago
Labels: enhancement

#35 - Different retention time alignment methods.

Issue - State: closed - Opened by pavel-shliaha over 12 years ago

#34 - Transfering ids, rather than adding ids while master construction

Issue - State: open - Opened by pavel-shliaha over 12 years ago
Labels: enhancement

#33 - 3D matching for HDMSE runs

Issue - State: closed - Opened by pavel-shliaha over 12 years ago
Labels: enhancement, Important

#32 - Update GUI screen shots

Issue - State: closed - Opened by lgatto over 12 years ago
Labels: bug

#31 - Use unique pep sequences for id stats calculation

Issue - State: open - Opened by lgatto over 12 years ago

#30 - New filter on peptide length

Issue - State: closed - Opened by lgatto over 12 years ago - 1 comment

#29 - Proportional and determinstic masters

Issue - State: closed - Opened by lgatto over 12 years ago

#28 - Non proteoptypic peptides in complex proteomes

Issue - State: open - Opened by lgatto over 12 years ago

#26 - GUI does not show up properly

Issue - State: closed - Opened by lgatto over 12 years ago - 5 comments

#25 - Synapter GUI grid search: change "to" to "by"

Issue - State: closed - Opened by lgatto over 12 years ago - 1 comment

#24 - bug in PLGS

Issue - State: closed - Opened by lgatto over 12 years ago

#23 - merging uniqueness filters

Issue - State: closed - Opened by lgatto over 12 years ago

#22 - Investigate effect of span/parameter selection/subset

Issue - State: closed - Opened by lgatto over 12 years ago - 1 comment

#21 - Peptide Score FDR adjustment

Issue - State: closed - Opened by lgatto over 12 years ago - 1 comment

#20 - making filter for uniqueness in the final_peptide file optional

Issue - State: closed - Opened by lgatto over 12 years ago - 1 comment

#19 - Fixing LOESS span at 0.02 produces error in some datasets

Issue - State: closed - Opened by lgatto over 12 years ago

#18 - best parameters selection

Issue - State: closed - Opened by lgatto over 12 years ago

#17 - Revise peptide FDR filtering

Issue - State: closed - Opened by lgatto over 12 years ago - 1 comment

#16 - making filtering on uniqueness optional

Issue - State: closed - Opened by lgatto over 12 years ago - 1 comment

#15 - performing grid search on a specified number of merged peptides

Issue - State: closed - Opened by lgatto over 12 years ago

#14 - bug MSE and HDMSE final_peptide files are swapped

Issue - State: closed - Opened by lgatto over 12 years ago

#13 - synapter vignette

Issue - State: closed - Opened by lgatto over 12 years ago

#12 - getGrid(xx) returns very low value for percent total

Issue - State: closed - Opened by lgatto over 12 years ago

#11 - performance

Issue - State: closed - Opened by lgatto over 12 years ago

#10 - PLGS manual

Issue - State: closed - Opened by lgatto over 12 years ago - 1 comment

#9 - Use grid details to set best parameters

Issue - State: closed - Opened by lgatto over 12 years ago - 1 comment

#8 - Grid search documentation

Issue - State: closed - Opened by lgatto over 12 years ago

#7 - filtering non-unique peptides

Issue - State: closed - Opened by lgatto over 12 years ago - 5 comments

#6 - performanave function does not work

Issue - State: closed - Opened by lgatto over 12 years ago - 1 comment

#5 - no grid search results in synapter 0.4.6.

Issue - State: closed - Opened by lgatto over 12 years ago

#4 - export of MSE and HDMSE data before merging

Issue - State: closed - Opened by lgatto over 12 years ago - 1 comment

#3 - Check license compatibilities

Issue - State: closed - Opened by lgatto over 12 years ago - 1 comment

#2 - export Synapter notes log as a txt file

Issue - State: closed - Opened by lgatto over 12 years ago - 1 comment

#1 - synapter performance evaluation

Issue - State: closed - Opened by lgatto over 12 years ago - 1 comment