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. |
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. |
getAnnotationFromEnsembl |
getAnnotationFromEnsembl 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. |
limmaDEGsExtraction |
limmaDEGsExtraction performs the analysis to extract the Differentially Expressed Genes (DEGs) among the classes to compare. |
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. |
tophatAlignment |
tophatAlignment allows downloading and processing the fastq samples in a CSV file by using tophat2 aligner. |