compomics peptide-shaker-2.0-issue-tracker issues

compomics / peptide-shaker-2.0-issue-tracker

Issue tracker for the beta release of PeptideShaker 2.0

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issues

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Creating mzIdentML file fails

#63 InduKhatri closed 3 years ago
1
Large database memory usage

#62 andrewjmc closed 3 years ago
2
PeptideShakerCLI: java.lang.IllegalArgumentException: Not enough representative modification sites found.

#61 shengbokw closed 4 years ago
9
java.lang.RuntimeException

#60 VladimirRoudko closed 3 years ago
7
PeptideShaker going into endless loop

#59 CarlaCristinaUranga closed 3 years ago
5
Protein count alternates

#58 dominik-kopczynski closed 4 years ago
4
Extend documentation

#57 mvaudel opened 4 years ago
0
Fix sorting of PSMs in the Spectrum IDs tab

#56 hbarsnes closed 4 years ago
1
Missing merge during peptide modification alignment

#55 mvaudel opened 4 years ago
0
ReportCLI not functioning

#54 CarlaCristinaUranga closed 4 years ago
39
Error double insertion

#53 CarlaCristinaUranga closed 4 years ago
9
Export data as fractions

#52 hanne-hox closed 4 years ago
5
Null pointer when trying to run PeptideShakerCLI

#51 ohickl closed 4 years ago
17
Problems running Comet and Andromeda in 4.0.0 beta on Linux server

#50 ohickl closed 4 years ago
4
DirecTag results can only be loaded on their own

#49 hbarsnes closed 4 years ago
1
Many PSMs passing the FDR filter (=0.01) have PeptideShaker scores = 0 - according to exported MzIdentML file.

#48 MarcIsak closed 4 years ago
5
Cannot reopen saved PeptideShaker projects

#47 MarcIsak closed 4 years ago
11
Null pointer in the protein inference due to custom FASTA headers

#46 tivdnbos closed 4 years ago
14
Improve the docs for spectrum counting normalization

#45 mvaudel opened 4 years ago
1
Not enough representative modification sites found

#44 MarcIsak opened 4 years ago
8
IdentiPy

#43 chrishuges closed 4 years ago
2
Problem with dataset and Protein reports (normal and non-validated matches)

#42 CarlosHorro closed 4 years ago
5
Reports crashing: possible lack of precission with long variable peptideKey?

#41 CarlosHorro closed 5 years ago
2
Support the peptide and PSM project modes in the GUI

#40 hbarsnes closed 4 years ago
1
getPossibleModificationSites fails on PTM patterns longer than one residue

#39 hbarsnes closed 4 years ago
1
Reintroduce the Database Details dialog

#38 hbarsnes closed 5 years ago
1
Check the default spectrum annotation level

#37 hbarsnes closed 4 years ago
1
Two modifications at the same site

#36 hbarsnes opened 5 years ago
4
The Copy to File options for the tables have to be reimplemented

#35 hbarsnes closed 4 years ago
1
The precursor mass deviation filter is unstable

#34 hbarsnes closed 5 years ago
1
PTM mapping can result in a null pointer

#33 hbarsnes closed 5 years ago
1
The possible sequence coverage values ought to be checked

#32 hbarsnes closed 4 years ago
2
Peptides with the same set of PTMs are not merged

#31 hbarsnes closed 4 years ago
1
Protein inference graph results in null pointer

#30 hbarsnes closed 5 years ago
1
Peptide sequence search not working

#29 hbarsnes closed 5 years ago
1
Weird error with streams in CommandParameter.isInList

#28 CarlosHorro closed 5 years ago
2
Peptides go missing from protein groups

#27 hbarsnes closed 5 years ago
4
FM indexes are not updated if the parsing rules change

#26 hbarsnes closed 5 years ago
3
PeptideShaker GUI frozen when creating/opening a project having another one already opened

#25 CarlosHorro closed 5 years ago
1
Follow up analysis pepXML export fails

#24 hbarsnes closed 5 years ago
3
Follow up analysis: "Export accession numbers" and "Export sequences" fails

#23 hbarsnes closed 5 years ago
3
The Default PSM report with non-validated matches and the Extended PSM report fails

#22 hbarsnes closed 5 years ago
1
Wrong visualization in Protein inference dialog

#21 dominik-kopczynski closed 5 years ago
1
The mzid export from the command line fails

#20 hbarsnes closed 5 years ago
1
The Default Peptide Report fails from the command line

#19 hbarsnes closed 5 years ago
1
The Default Protein Report export fails from the command line

#18 hbarsnes closed 5 years ago
1
The Default Peptide and PSM Report fails (both CLI and GUI)

#17 hbarsnes closed 5 years ago
2
The Default Protein Report export fails (both CLI and GUI)

#16 hbarsnes closed 5 years ago
2
Best hit not found in the Spectrum IDs tab

#15 hbarsnes closed 5 years ago
1
Validation status "No Validation" in the Spectrum IDs tab

#14 hbarsnes closed 5 years ago
13