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
DavidEnrichGene enrichment analysis using the DAVID Database
determineNonOverlapGenelayersNon-overlapping gene layers for plotting
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 methylation data.
plot.regionPlot p-values in regional genomic context
process_ddsProcessing and data transformation of DESeqDataSet
process_esetProcessing of expression data
processLNCipediaProcess LNCipedia bed-file
process_methPreprocessing and annotation of methylation array data
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
wrapDESeqDifferential expression analysis with DESeq2
wrapLimmaDifferential expression analysis with limma
wrapMinfiFinding differentially methylated CpG positions or regions
wrapPCAgopromPrincipal component analysis for gene expression data
wrapWGCNAWrapper for weighted gene co-expression network analysis.
frankRuehle/systemsbio documentation built on June 6, 2018, 2:13 a.m.