| batchEffectRemoval | Corrects the batch effect of the data by using the selected method. |
| calculateGeneExpressionValues | Calculates the gene expression values by using a matrix of counts from RNA-seq. |
| countsToMatrix | countsToMatrix merges in a matrix the information in the count files. |
| dataPlot | Plot different graphs depending on the current step of KnowSeq pipeline. |
| DEGsEvidences | DEGsEvidences function returns for each DEG a list of evidences that correlate it with the studied disease. |
| DEGsExtraction | DEGsExtraction performs the analysis to extract the Differentially Expressed Genes (DEGs) among the classes to compare. |
| DEGsPathwayVisualization | The function uses the DEGs to show graphically the expression of the samples in the pathways in which those genes appear. |
| DEGsToDiseases | DEGsToDiseases obtains the information about what diseases are related to the DEGs indicated by parameter. |
| downloadPublicSeries | Download automatically samples from NCBI/GEO and ArrayExpress public databases. |
| featureSelection | featureSelection function calculates the optimal order of DEGs to achieve the best result in the posterior machine learning process by using mRMR algorithm or Random Forest. |
| fileMove | This function is used to move files to other locations. |
| gdcClientDownload | This function downloads a list of controlled files from GDC Portal with the user token and the manifest with the information about the desired controlled files. |
| geneOntologyEnrichment | geneOntologyEnrichment obtains the information about what Gene Ontology terms are related to the DEGs. |
| getGenesAnnotation | getGenesAnnotation returns the required information about a list of genes from Ensembl biomart. |
| hisatAlignment | hisatAlignment allows downloading and processing the fastq samples in a CSV file by using hisat2 aligner. |
| knn_CV | knn_CV allows assessing the final DEGs through a machine learning step by using k-NN in a cross validation process. |
| knn_test | knn_test allows assessing the final DEGs through a machine learning step by using k-NN with a test dataset. |
| knowseqReport | knowseqReport creates a report for a given set of genes which their label. |
| plotConfMatrix | plotConfMatrix plots a confusion matrix with some statistics. |
| rawAlignment | rawAlignment allows downloading and processing the fastq samples in a CSV file. |
| rf_CV | rf_CV allows assessing the final DEGs through a machine learning step by using Random Forest in a cross validation process. |
| rf_test | rf_test allows assessing the final DEGs through a machine learning step by using Random Forest with a test dataset. |
| RNAseqQA | RNAseqQA performs the quality analysis of an expression matrix. |
| sraToFastq | sraToFastq downloads and converts the sra files to fastq files. The function admits both gz and sra formats. |
| svm_CV | svm_CV allows assessing the final DEGs through a machine learning step by using svm in a cross validation process. |
| svm_test | svm_test allows assessing the final DEGs through a machine learning step by using SVM with a test dataset. |