Man pages for frankRuehle/systemsbio
Streamlined Analysis and Integration of Systems Biology Data

attach_packageOrganise temporarily needed packages
basicAnnoBasic gene annotation
basic_SNP_annotationSNP annotation using biomaRt and/or manufacturer data
clusterprofWrapper for gene enrichment analysis using clusterProfiler
comparefuncFunctional analysis of of gene sets
DavidEnrichGene enrichment analysis using the DAVID Database
determineNonOverlapGenelayersNon-overlapping gene layers for plotting
diffLimmaDifferential expression analysis with limma
diffMinfiFinding differentially methylated CpG positions or regions
filterGeneListsFilter gene lists
genoAssocAssociation analysis with GenABEL
genoQCQuality Control for genotype data
gexexpression data
makeDomainsFromExonsCalculate genomic coordinates for amino acid positions of...
matrixQTLQTL Analysis for expression and/or methylation data.
norm_exprsProcessing of expression data
plot.regionPlot p-values in regional genomic context
prep_anno_methPreprocessing and annotation of methylation array data
processLNCipediaProcess LNCipedia bed-file
QC_expressionsetQuality Control procedures for expression data
QC_methylationQuality control of methylation array data
readData2esetCreate ExpressionSet object from expression data
readGenoRead Genotype Data Using GenABEL.
read_Illu_expr_arrayReading expression data from Illumina arrays
read_Illu_meth450kReading methylation data from Illumina array...
regionalplot.genelabelsPlot genes as arrows
subsetByOverlaps.keepAllMetaHelp functions for handling gene ranges
TFsearchTranscription factor binding site enrichment
wrapPCAgopromPrincipal component analysis for gene expression data
wrapWGCNAWrapper for weighted gene co-expression network analysis.
frankRuehle/systemsbio documentation built on Feb. 5, 2018, 5:41 p.m.