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