Man pages for KnowSeq
A R package to extract knowledge by using RNA-seq raw files

batchEffectRemovalCorrects the batch effect of the data by using the selected...
calculateGeneExpressionValuesCalculates the gene expression values by using a matrix of...
countsToMatrixcountsToMatrix merges in a matrix the information in the...
dataPlotPlot different graphs depending on the current step of...
DEGsPathwayVisualizationThe function uses the DEGs to show graphically the expression...
DEGsToDiseasesDEGsToDiseases obtains the information about what diseases...
downloadPublicSeriesDownload automatically samples from NCBI/GEO and ArrayExpress...
featureSelectionfeatureSelection function calculates the optimal order of...
fileMoveThis function is used to move files to other locations.
gdcClientDownloadThis function downloads a list of controlled files from GDC...
geneOntologyEnrichmentgeneOntologyEnrichment obtains the information about what...
getAnnotationFromEnsemblgetAnnotationFromEnsembl returns the required information...
hisatAlignmenthisatAlignment allows downloading and processing the fastq...
kallistoAlignmentkallistoAlignment allows downloading and processing the fastq...
knn_CVknn_CV allows assessing the final DEGs through a machine...
knn_testknn_test allows assessing the final DEGs through a machine...
limmaDEGsExtractionlimmaDEGsExtraction performs the analysis to extract the...
plotConfMatrixplotConfMatrix plots a confusion matrix with some statistics.
rawAlignmentrawAlignment allows downloading and processing the fastq...
rf_CVrf_CV allows assessing the final DEGs through a machine...
rf_testrf_test allows assessing the final DEGs through a machine...
RNAseqQARNAseqQA performs the quality analysis of an expression...
salmonAlignmentsalmonAlignment allows downloading and processing the fastq...
sraToFastqsraToFastq downloads and converts the sra files to fastq...
svm_CVsvm_CV allows assessing the final DEGs through a machine...
svm_testsvm_test allows assessing the final DEGs through a machine...
tophatAlignmenttophatAlignment allows downloading and processing the fastq...
KnowSeq documentation built on Oct. 31, 2019, 6:05 a.m.