attach_package | Organise temporarily needed packages |
basicAnno | Basic gene annotation |
basic_SNP_annotation | SNP annotation using biomaRt and/or manufacturer data |
determineNonOverlapGenelayers | Non-overlapping gene layers for plotting |
filterGeneLists | Filter gene lists |
genoAssoc | Association analysis with GenABEL |
genoQC | Quality Control for genotype data |
gex | expression data |
makeDomainsFromExons | Calculate genomic coordinates for amino acid positions of... |
plot_region | Plot p-values in regional genomic context |
plot_volcano | Generating Volcano plot for differential gene expression... |
process_dds | Processing and data transformation of DESeqDataSet |
process_eset | Processing of expression data |
processLNCipedia | Process LNCipedia bed-file |
process_meth | Preprocessing and annotation of methylation array data |
QC_expressionset | Quality Control procedures for expression data |
QC_methylation | Quality control of methylation array data |
readData2eset | Create ExpressionSet object from expression data |
readGeno | Read Genotype Data Using GenABEL. |
read_Illu_expr_array | Reading expression data from Illumina arrays |
read_Illu_meth450k | Reading methylation data from Illumina array... |
regionalplot.genelabels | Plot genes as arrows |
subsetByOverlaps.keepAllMeta | Help functions for handling gene ranges |
wrapClusterProfiler | Wrapper for gene enrichment analysis using clusterProfiler |
wrapDESeq2 | Differential expression analysis with DESeq2 |
wrapLimma | Differential expression analysis with limma |
wrapMatrixEQTL | QTL Analysis for expression and methylation data. |
wrapMinfi | Finding differentially methylated CpG positions or regions |
wrapPCAgoprom | Principal component analysis for gene expression data |
wrapPWMEnrich | Transcription factor binding site enrichment |
wrapRDAVID | Gene enrichment analysis using the DAVID Database |
wrapWGCNA | Wrapper for weighted gene co-expression network analysis. |
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