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how_to:start [2013/01/15 11:47] 132.168.72.131 |
how_to:start [2013/01/28 08:09] (current) 132.168.72.131 |
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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]] | ||
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===== Save, import and export ===== | ===== Save, import and export ===== | ||
* [[exportContext|export identified proteins & peptides from a context]] | * [[exportContext|export identified proteins & peptides from a context]] | ||
- | * **Changed** :!: [[exportComparison|export a comparison result]] | + | * [[exportComparison|export a comparison result]] |
* [[saveComparison|save/load a comparison result]] | * [[saveComparison|save/load a comparison result]] | ||
* [[saveToMSIdb|save modifications back to the MSIdb]] | * [[saveToMSIdb|save modifications back to the MSIdb]] | ||
* [[exportSqlResult|export an SQL result to a file]] | * [[exportSqlResult|export an SQL result to a file]] | ||
* [[spectrumMatchFeeder|populate MSI database with spectra]] | * [[spectrumMatchFeeder|populate MSI database with spectra]] | ||
- | * **Changed** :!: [[generateAMTdb|[AMT] generate a new AMT database from a context]] | + | * [[generateAMTdb|[AMT] generate a new AMT database from a context]] |
* <del>[[includeUmcInAmtDb|[AMT] include UMCs in AMTdb]]</del> (see Import UMCs into MSIdb) | * <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]] | ||
* [[exportAdHocExport|[Ad-hoc export] on-demand exports]] | * [[exportAdHocExport|[Ad-hoc export] on-demand exports]] | ||
- | * **Changed** :!: [[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]] | ||
- | * **New** :!: [[importUmcToMsiDb|[AMT] Import UMCs into MSIdb]] | + | * [[importUmcToMsiDb|[AMT] Import UMCs into MSIdb]] |
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* [[proteinFiltering|filter proteins or protein groups]] | * [[proteinFiltering|filter proteins or protein groups]] | ||
* [[resetProteinFiltering|reset protein/protein group filter]] | * [[resetProteinFiltering|reset protein/protein group filter]] | ||
- | * **Changed** :!: [[compareMultiContexts|compare several contexts]] | + | * [[compareMultiContexts|compare several contexts]] |
* [[compareContextWithExtAccession|compare a context with an external accession list]] | * [[compareContextWithExtAccession|compare a context with an external accession list]] | ||
- | * **Changed** :!: [[accessspectralcountdata|run and/or view spectral count data]] | + | * [[accessspectralcountdata|run and/or view spectral count data]] |
* [[idfFilters|check that all identifications have been filtered with the same parameters]] | * [[idfFilters|check that all identifications have been filtered with the same parameters]] | ||
* [[writeSqlQueries|write SQL Queries to explore database]] | * [[writeSqlQueries|write SQL Queries to explore database]] | ||
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* [[alignRetentionTime|[AMT] align retention time]] | * [[alignRetentionTime|[AMT] align retention time]] | ||
* [[recomputeRetentionTime|[AMT] recompute retention time]] | * [[recomputeRetentionTime|[AMT] recompute retention time]] | ||
- | * **New** :!: [[batchProcessing| make batch processing]] | + | * [[batchProcessing| make batch processing]] |
- | * **New** :!: [[computeFalsePositiveRate|Compute False Positive Rate]] | + | * [[computeFalsePositiveRate|Compute False Positive Rate]] |