Man pages for markrobinsonuzh/Repitools
Epigenomic tools
| abcdDNA | A wrapper for fitting the offset-adjusted ABCD-DNA GLM |
| absoluteCN | Calculate and Segment Absolute Copy Number from Sequencing... |
| AdjustedCopyEstimate-class | Container for results of GC adjusted copy number estimation. |
| AffymetrixCdfFile-class | Placeholder For AffymetrixCdfFile Documentation |
| AffymetrixCelSet-class | Placeholder For AffymetrixCelSet Documentation |
| annoDF2GR | Convert a 'data.frame' to a 'GRanges'. |
| annoGR2DF | Convert an annotated 'GRanges' to a 'data.frame'. |
| annotationBlocksCounts | Counts the number of sequencing reads within supplied genomic... |
| annotationBlocksLookup | Forms a mapping between probe locations and chromosomal... |
| annotationCounts | Counts the number of sequencing reads surrounding supplied... |
| annotationLookup | Forms a mapping between probes on a tiling array and windows... |
| BAM2GRanges | Read in a (list of) BAM file(s) into a GRanges(List) object. |
| BayMethList-class | Class '"BayMethList"' |
| binPlots | Create line plots of averaged signal across a promoter |
| blocksStats | Calculate statistics for regions in the genome |
| checkProbes | Check Probe Specificity for Some Regions |
| chr21genes | Positions of Genes on Human Chromosome 21 |
| ChromaBlocks | A function to find areas of enrichment in sequencing data |
| ChromaResults-class | ChromaResults class |
| chromosomeCNplots | Plot copy number by chromosome |
| ClusteredScoresList-class | Container for coverage matrices with clustering results. |
| clusterPlots | Visualisation of tables of feature coverages. |
| CopyEstimate-class | Container for results of fold change copy number estimation. |
| cpgBoxPlots | Boxplots of intensity, binned by Cpg Density |
| cpgDensityCalc | Calculate CpG Density in a Window |
| cpgDensityPlot | Plot the distribution of sequencing reads CpG densities. |
| determineOffset | Function to determine the normalising offset f that accounts... |
| empBayes | Function to calculate prior parameters using empirical Bayes. |
| enrichmentCalc | Calculate sequencing enrichment |
| enrichmentPlot | Plot the distribution of sequencing enrichment. |
| expr | Vector of expression differences |
| FastQC-class | FastQC and associated classes |
| featureBlocks | Make windows for distances around a reference point. |
| featureScores | Get scores at regular sample points around genomic features. |
| findClusters | Find Clusters Epigenetically Modified Genes |
| GCadjustCopy | Calculate Absolute Copy Number from Sequencing Counts |
| GCAdjustParams-class | Container for parameters for mappability and GC content... |
| GCbiasPlots | Plot GC content vs. Read Counts Before Normalising, and GC... |
| gcContentCalc | Calculate The gcContent of a Region |
| genomeBlocks | Creates bins across a genome. |
| genQC | Plot Quality Checking Information for Sequencing Data |
| getProbePositionsDf | Translate Affymetrix probe information in a table. |
| getSampleOffsets | Calculates the sample-specific offsets, using the neutral... |
| hcRegions | Masking files for hg19 |
| hyper | Gaussian hypergeometric function for vectorial arguments |
| loadPairFile | A routine to read Nimblegen tiling array intensities |
| loadSampleDirectory | A routine to read Nimblegen tiling array intensities |
| makeWindowLookupTable | Using the output of 'annotationLookup', create a tabular... |
| mappabilityCalc | Calculate The Mappability of a Region |
| MappabilitySource-class | Superclass for datatypes that can refer to genome mappability... |
| maskOut | Function to mask suspicious regions. |
| mergeReplicates | Merge GRanges that are of replicate experiments. |
| methylEst | Function to derive regional methylation estimates. |
| multiHeatmap | Superfigure plots |
| plotClusters | Plot Scores of Cluster Regions |
| plotQdnaByCN | Plotting the response of qDNA-seq data by CNV |
| processNDF | Reads in a Nimblegen microarray design file (NDF) |
| profilePlots | Create line plots of averaged signal across a promoter for... |
| QdnaData | A container for quantitative DNA sequencing data for ABCD-DNA... |
| regionStats | Find Regions of significance in microarray data |
| relativeCN | Calculate and Segment Relative Copy Number From Sequencing... |
| samplesList | Short Reads from Cancer and Normal |
| ScoresList-class | Container for 'featureScores()' output. |
| sequenceCalc | Find occurences of a DNA pattern |
| setCNVOffsets | Set the CNVOffsets of a 'QdnaData' object |
| summarizeScores | Subtract scores of different samples. |
| writeWig | Writes sequencing data out into wiggle files |
