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how_to:start [2012/01/23 14:08] 132.168.72.130 |
how_to:start [2013/01/28 08:09] (current) 132.168.72.131 |
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===== Visualization ===== | ===== Visualization ===== | ||
- | * [[browseContextProtGroups|browse context's protein groups]] | + | * [[browseContextProtGroups|Browse all context's protein groups]] |
* [[peptideView|visualize all context's peptides]] | * [[peptideView|visualize all context's peptides]] | ||
* [[viewProtgroups|visualize protein groups ]] information details | * [[viewProtgroups|visualize protein groups ]] information details | ||
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* [[editIdentificationInfos|view and edit identification informations (general information ans run/sample)]] | * [[editIdentificationInfos|view and edit identification informations (general information ans run/sample)]] | ||
* [[accessspectralcountdata|run and/or view spectral count data]] | * [[accessspectralcountdata|run and/or view spectral count data]] | ||
+ | * :!: **New** [[accessadjustedspectralcountdata|run and/or view adjusted spectral count data]] | ||
* [[accessProperties|access object properties, show/hide columns in a tree view, filter columns in a tree view]] | * [[accessProperties|access object properties, show/hide columns in a tree view, filter columns in a tree view]] | ||
- | ===== Save and export ===== | + | ===== Save, import and export ===== |
* [[exportContext|export identified proteins & peptides from a context]] | * [[exportContext|export identified proteins & peptides from a context]] | ||
* [[exportComparison|export a comparison result]] | * [[exportComparison|export a comparison result]] | ||
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* [[spectrumMatchFeeder|populate MSI database with spectra]] | * [[spectrumMatchFeeder|populate MSI database with spectra]] | ||
* [[generateAMTdb|[AMT] generate a new AMT database from a context]] | * [[generateAMTdb|[AMT] generate a new AMT database from a context]] | ||
- | * [[includeUmcInAmtDb|[AMT] include UMCs in AMTdb]] | + | * <del>[[includeUmcInAmtDb|[AMT] include UMCs in AMTdb]]</del> (see Import UMCs into MSIdb) |
* [[exportPride|[PRIDE] export context to PRIDE XML format]] | * [[exportPride|[PRIDE] export context to PRIDE XML format]] | ||
* [[exportPrideLog|[PRIDE] view PRIDE log]] | * [[exportPrideLog|[PRIDE] view PRIDE log]] | ||
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* [[exportadhocexport_ppmswleaves|[Ad-hoc export] export Protein Groups, Peptides and Leaves]] | * [[exportadhocexport_ppmswleaves|[Ad-hoc export] export Protein Groups, Peptides and Leaves]] | ||
* [[exportAdHocExport_N15|[Ad-hoc export, N15] export 15N data]] | * [[exportAdHocExport_N15|[Ad-hoc export, N15] export 15N data]] | ||
+ | * [[importUmcToMsiDb|[AMT] Import UMCs into MSIdb]] | ||
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* [[alignRetentionTime|[AMT] align retention time]] | * [[alignRetentionTime|[AMT] align retention time]] | ||
* [[recomputeRetentionTime|[AMT] recompute retention time]] | * [[recomputeRetentionTime|[AMT] recompute retention time]] | ||
- | * make [[batchProcessing|batch processing]] | + | * [[batchProcessing| make batch processing]] |
+ | * [[computeFalsePositiveRate|Compute False Positive Rate]] |