Man pages for CasedUgr/KnowSeq
KnowSeq R/Bioc package: The Smart Transcriptomic Pipeline
| batchEffectRemoval | Corrects the batch effect of the data by using the selected... |
| calculateGeneExpressionValues | Calculates the gene expression values by using a matrix of... |
| countsToMatrix | countsToMatrix merges in a matrix the information in the... |
| dataPlot | Plot different graphs depending on the current step of... |
| DEGsEvidences | DEGsEvidences function returns for each DEG a list of... |
| DEGsExtraction | DEGsExtraction performs the analysis to extract the... |
| DEGsToDiseases | DEGsToDiseases obtains the information about what diseases... |
| DEGsToPathways | The function uses the DEGs to retrieves the different... |
| downloadPublicSeries | Download automatically samples from NCBI/GEO and ArrayExpress... |
| featureSelection | featureSelection function calculates the optimal order of... |
| fileMove | This function is used to move files to other locations. |
| gdcClientDownload | This function downloads a list of controlled files from GDC... |
| geneOntologyEnrichment | geneOntologyEnrichment obtains the information about what... |
| getGenesAnnotation | getGenesAnnotation returns the required information about a... |
| hisatAlignment | hisatAlignment allows downloading and processing the fastq... |
| knn_test | knn_test allows assessing the final DEGs through a machine... |
| knn_trn | knn_trn allows assessing the final DEGs through a machine... |
| knowseqReport | knowseqReport creates a report for a given set of genes which... |
| plotConfMatrix | plotConfMatrix plots a confusion matrix with some statistics. |
| rawAlignment | rawAlignment allows downloading and processing the fastq... |
| rf_test | rf_test allows assessing the final DEGs through a machine... |
| rf_trn | rf_trn allows assessing the final DEGs through a machine... |
| RNAseqQA | RNAseqQA performs the quality analysis of an expression... |
| sraToFastq | sraToFastq downloads and converts the sra files to fastq... |
| svm_test | svm_test allows assessing the final DEGs through a machine... |
| svm_trn | svm_trn allows assessing the final DEGs through a machine... |
