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peptide-shaker-2.0-issue-tracker
Issue tracker for the beta release of PeptideShaker 2.0
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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
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