Man pages for bioinfo16/RIPAT
Retroviral Integration Pattern Analysis Tool (RIPAT)

annoByCGCAnnotate integration sites by cancer-related genes.
annoByCpGAnnotate integration sites by CpG sites.
annoByGeneAnnotate integration sites by genes and TSSs.
annoByRepeatAnnotate integration sites by repeats and microsatellites.
annoByVarAnnotate integration sites by clinical variants.
blast_geneIntegration site annotation by gene data
blast_objRetroviral vector integration site object
compareCasesAnnotate integration sites by genes and TSSs.
cpg_exam_dbData file for annoByCpG vignette
drawingKaryoDraw the karyogram plot.
gene_exam_dbData file for annoByGene vignette
integPatternByChrRetroviral integration pattern on chromosomes
makeDataMake data files for RIPAT.
makeDocumentMake the result object and document.
makeExpSetMake the retroviral vector integration site object.
makeExpSet2Make the retroviral vector integration site object.
makeInputObjMake the retroviral vector integration site object.
makeInputObj2Make the retroviral vector integration site object.
makeRanSetRandom data of viral vector integration site
micro_exam_dbData file for annoByRepeat vignette
ranSetGeneratorRandom data of viral vector integration site
repeat_exam_dbData file for annoByRepeat vignette
tss_exam_dbData file for annoByGene vignette
var_exam_dbData file for annoByVar vignette
bioinfo16/RIPAT documentation built on Oct. 16, 2020, 1:39 p.m.