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<div class="title">UTILS documentation </div> </div>
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<div class="textblock"><p>Besides TOPP, OpenMS offers a range of other tools. They are not included in TOPP as they are not part of typical analysis pipelines, but they still might be very helpful to you.</p>
<p>Just as the TOPP tools, they can be found to the OpenMS/bin folder.</p>
<p>The UTILS tools are divided into several subgroups:</p>
<p><b>Maintenance</b></p>
<ul>
<li><a class="el" href="UTILS_INIUpdater.html">INIUpdater</a> - Update INI and TOPPAS files from previous versions of OpenMS as parameters and storage method might have changed</li>
</ul>
<p><b>Signal Processing and Preprocessing</b></p>
<ul>
<li><a class="el" href="UTILS_RNPxlXICFilter.html">RNPxlXICFilter</a> - Remove MS2 spectra from treatment based on the fold change between control and treatment for RNP cross linking experiments.</li>
</ul>
<p><b>File handling</b></p>
<ul>
<li><a class="el" href="UTILS_FuzzyDiff.html">FuzzyDiff</a> - Compares two files, tolerating numeric differences.</li>
<li><a class="el" href="UTILS_XMLValidator.html">XMLValidator</a> - Validates XML files against an XSD schema.</li>
<li><a class="el" href="UTILS_SemanticValidator.html">SemanticValidator</a> - SemanticValidator for analysisXML and mzML files.</li>
<li><a class="el" href="UTILS_CVInspector.html">CVInspector</a> - A tool for visualization and validation of PSI mapping and CV files.</li>
<li><a class="el" href="UTILS_IDSplitter.html">IDSplitter</a> - Splits protein/peptide identifications off of annotated data files.</li>
<li><a class="el" href="UTILS_ConvertTSVToTraML.html">ConvertTSVToTraML</a> - Converts a tsv file (tab separated) to TraML.</li>
<li><a class="el" href="UTILS_ConvertTraMLToTSV.html">ConvertTraMLToTSV</a> - Converts a TraML file to TSV.</li>
<li><a class="el" href="UTILS_OpenSwathMzMLFileCacher.html">OpenSwathMzMLFileCacher</a> - Caching of large mzML files</li>
</ul>
<p><b>Algorithm evaluation</b></p>
<ul>
<li><a class="el" href="UTILS_FFEval.html">FFEval</a> - Evaluation tool for feature detection algorithms.</li>
<li><a class="el" href="UTILS_IDEvaluator.html">IDEvaluator</a> - Evaluation tool, comparing peptide recovery at different q-value thresholds for multiple search engines (e.g., after ConsensusID). For interactive version use the <a class="el" href="UTILS_IDEvaluatorGUI.html">IDEvaluatorGUI</a> tool.</li>
<li><a class="el" href="UTILS_LabeledEval.html">LabeledEval</a> - Evaluation tool for isotope-labeled quantitation experiments.</li>
<li><a class="el" href="UTILS_MapAlignmentEvaluation.html">MapAlignmentEvaluation</a> - Evaluates alignment results against a ground truth.</li>
<li><a class="el" href="UTILS_RTEvaluation.html">RTEvaluation</a> - Application that evaluates TPs (true positives), TNs, FPs, and FNs for an idXML file with predicted RTs.</li>
<li><a class="el" href="UTILS_TransformationEvaluation.html">TransformationEvaluation</a> - Simple evaluation of transformations (e.g. RT transformations produced by a MapAligner tool).</li>
</ul>
<p><b>Peptide identification</b></p>
<ul>
<li><a class="el" href="UTILS_Digestor.html">Digestor</a> - Digests a protein database in-silico.</li>
<li><a class="el" href="UTILS_DigestorMotif.html">DigestorMotif</a> - Digests a protein database in-silico (optionally allowing only peptides with a specific motif) and produces statistical data for all peptides.</li>
<li><a class="el" href="UTILS_DecoyDatabase.html">DecoyDatabase</a> - Create decoy peptide databases from normal ones.</li>
<li><a class="el" href="UTILS_SequenceCoverageCalculator.html">SequenceCoverageCalculator</a> - Prints information about idXML files.</li>
<li><a class="el" href="UTILS_IDExtractor.html">IDExtractor</a> - Extracts n peptides randomly or best n from idXML files.</li>
<li><a class="el" href="UTILS_IDMassAccuracy.html">IDMassAccuracy</a> - Calculates a distribution of the mass error from given mass spectra and IDs.</li>
<li><a class="el" href="UTILS_SpecLibCreator.html">SpecLibCreator</a> - Creates an MSP formated spectral library.</li>
<li><a class="el" href="UTILS_RNPxl.html">RNPxl</a> - Tool for RNP cross linking experiment analysis.</li>
</ul>
<p><b>Quantitation</b></p>
<ul>
<li><a class="el" href="UTILS_ERPairFinder.html">ERPairFinder</a> - Evaluate pair ratios on enhanced resolution (zoom) scans.</li>
<li><a class="el" href="UTILS_MRMPairFinder.html">MRMPairFinder</a> - Evaluate labeled pair ratios on MRM features.</li>
<li><a class="el" href="UTILS_FeatureFinderSuperHirn.html">FeatureFinderSuperHirn</a> - Find Features using the SuperHirn Algorithm (it can handle centroided or profile data, see .ini file)</li>
</ul>
<p><b>Misc</b></p>
<ul>
<li><a class="el" href="UTILS_ImageCreator.html">ImageCreator</a> - Creates images from MS1 data (with MS2 data points indicated as dots).</li>
<li><a class="el" href="UTILS_MassCalculator.html">MassCalculator</a> - Calculates masses and mass-to-charge ratios of peptide sequences.</li>
<li><a class="el" href="UTILS_MSSimulator.html">MSSimulator</a> - A highly configurable simulator for mass spectrometry experiments.</li>
<li><a class="el" href="UTILS_SvmTheoreticalSpectrumGeneratorTrainer.html">SvmTheoreticalSpectrumGeneratorTrainer</a> - A trainer for svm models as input for SvmTheoreticalSpectrumGenerator.</li>
<li><a class="el" href="UTILS_DeMeanderize.html">DeMeanderize</a> - Orders the spectra of MALDI spotting plates correctly.</li>
<li><a class="el" href="UTILS_OpenSwathDIAPreScoring.html">OpenSwathDIAPreScoring</a> - SWATH (data independent acquisition) pre-scoring</li>
<li><a class="el" href="UTILS_OpenSwathRewriteToFeatureXML.html">OpenSwathRewriteToFeatureXML</a> - rewrite results from mProphet back into featureXML</li>
</ul>
<p><b>Metabolite identification</b></p>
<ul>
<li><a class="el" href="UTILS_AccurateMassSearch.html">AccurateMassSearch</a> - Find potential HMDB ids within the given mass error window.</li>
</ul>
<p><b>Quality control</b></p>
<ul>
<li><a class="el" href="UTILS_QCCalculator.html">QCCalculator</a> -</li>
<li><a class="el" href="UTILS_QCImporter.html">QCImporter</a> -</li>
<li><a class="el" href="UTILS_QCEmbedder.html">QCEmbedder</a> -</li>
<li><a class="el" href="UTILS_QCExporter.html">QCExporter</a> -</li>
<li><a class="el" href="UTILS_QCExtractor.html">QCExtractor</a> -</li>
<li><a class="el" href="UTILS_QCMerger.html">QCMerger</a> -</li>
<li><a class="el" href="UTILS_QCShrinker.html">QCShrinker</a> -</li>
</ul>
<p><b>Deprecated</b></p>
<ul>
<li><a class="el" href="UTILS_IDDecoyProbability.html">IDDecoyProbability</a> - Estimates peptide probabilities using a decoy search strategy. <br/>
WARNING: This util is deprecated. </li>
</ul>
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<TD><font color="#c0c0c0">OpenMS / TOPP release 1.11.1</font></TD>
<TD align="right"><font color="#c0c0c0">Documentation generated on Thu Nov 14 2013 11:19:25 using doxygen 1.8.5</font></TD>
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