KnowSeq R/Bioc package: The Smart Transcriptomic Pipeline

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Documentation for package ‘KnowSeq’ version 1.4.5

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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.