# KnowSeq R/Bioc package: The Smart Transcriptomic Pipeline

## Documentation for package ‘KnowSeq’ version 1.16.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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.
DEGsToDiseases | DEGsToDiseases obtains the information about what diseases are related to the DEGs indicated by parameter.
DEGsToPathways | The function uses the DEGs to retrieves the different pathways in which those DEGs involve any interaction.
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. Furthermore, the ranking is returned and can be used as input of the parameter vars_selected in the machine learning functions.
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_test | knn_test allows assessing the final DEGs through a machine learning step by using k-NN with a test dataset.
knn_trn | knn_trn allows assessing the final DEGs through a machine learning step by using k-NN in a cross validation process.
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_test | rf_test allows assessing the final DEGs through a machine learning step by using Random Forest with a test dataset.
rf_trn | rf_trn allows assessing the final DEGs through a machine learning step by using Random Forest in a cross validation process.
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_test | svm_test allows assessing the final DEGs through a machine learning step by using SVM with a test dataset.
svm_trn | svm_trn allows assessing the final DEGs through a machine learning step by using svm in a cross validation process.