# KnowSeq R/Bioc package: Beyond the traditional Transcriptomic pipeline

## Documentation for package ‘KnowSeq’ version 1.1.27

- 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.
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.
kallistoAlignment | kallistoAlignment allows downloading and processing the fastq samples in a CSV file by using kallisto 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.
salmonAlignment | salmonAlignment allows downloading and processing the fastq samples in a CSV file by using salmon aligner.
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.