Man pages for Basic4Cseq
Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data
| checkRestrictionEnzymeSequence | Remove invalid 4C-seq reads from a SAM file |
| chooseNearCisFragments | Choose fragments in a provided region around the viewpoint |
| createVirtualFragmentLibrary | Create a virtual fragment library from a provided genome and... |
| Data4Cseq | Creating a Data4Cseq object |
| Data4Cseq-class | Class '"Data4Cseq"' |
| drawDigestionFragmentHistogram | Visualize digestion fragments with a histogram |
| drawHeatmap | Draw a heatmap-like multi-scale contact profile |
| exportVisualizationFragmentData | Export near-cis fragment data of a 'Data4Cseq' object |
| getReadDistribution | Calculate the read distribution for a 4C-seq experiment |
| giveEnzymeSequence | Provide the corresponding enzyme sequence for an enzyme name |
| importVisualizationFragmentData | Import visualization data from a file |
| liverData | Example 4C-seq data set of fetal liver data |
| liverDataRaw | Example 4C-seq data set of fetal liver data |
| normalizeFragmentData | Normalize near-cis fragment data read count |
| plotTransInteractions | Visualize trans interaction intervals |
| prepare4CseqData | Alignment and filtering of raw 4C-seq data |
| printBEDFragmentLibrary | Print a BED-file fragment library |
| printWigFile | Print a wig file from 4C-seq read data |
| readPointsOfInterestFile | Read a file with coordinates of marker points |
| readsToFragments | Determine fragment coverage of a 4C-seq fragment library |
| simulateDigestion | Simulate the digestion of a genome |
| visualizeViewpoint | Draw a near-cis coverage plot for 4C-seq data |
