Man pages for Pasquali-lab/UMI4Cats
UMI4Cats: Processing, analysis and visualization of UMI-4C chromatin contact data
| addGrouping | Add grouping of UMI-4C samples |
| addStepping | Add stepping for plotting genes |
| alignmentUMI4C | UMI4C alignment |
| calculateAdaptativeTrend | Adaptative smoothing of normalized trend |
| calculateDomainogram | Create Domainogram |
| callInteractions | Call significant interactions |
| combineUMI4C | Combine UMI4C fragments |
| contactsUMI4C | UMI4C Contacts Processing |
| counterUMI4C | UMI counting |
| createGeneAnnotation | Create gene annotation object |
| createStatsTable | Create stats table |
| darken | Darken colors |
| dds2UMI4C | DDS object to UMI4Cats object. |
| demultiplexFastq | Demultiplex FASTQ files using fastq-multx |
| differentialNbinomWaldTestUMI4C | Differential UMI4C contacts using DESeq2 Wald Test |
| digestGenome | Digest reference genome |
| dot-getCache | Get BiocFileCache object |
| dot-getSummaryBam | Summarize BAM file |
| dot-singleAlignmentUMI4C | Align split fastq file |
| dot-singleCounterUMI4C | Count UMIs for a given bam file. |
| dot-singlePrepUMI4C | Prepar fastq files at a given barcode. |
| dot-singleSplitUMI4C | Split fastq files at a given restriction site. |
| dot-smoothMonotone | Monotone smoothing of the VST counts |
| downloadUMI4CexampleData | Download UMI4Cats example datasets |
| ex_ciita_umi4c | Contacs with CIITA promoter |
| fisherUMI4C | Differential UMI4C contacts using Fisher's Exact test |
| formatPlotsUMI4C | Format plots for UMI4C |
| geoMeanCoordinates | Get geometric mean of given coordinates |
| getColors | Get default colors |
| getFactors | Get factors fro plotting |
| getNormalizationMatrix | Get normalization matrix |
| getSignInteractions | Get significant interactions from a GRangesList |
| getViewpointCoordinates | Get viewpoint coordinates |
| groupSamplesUMI4C | Group UMI4C samples |
| makeWindowFragments | Make windows merging restriction fragments |
| nbinomWaldTestUMI4C | Differential UMI4C contacts using DESeq2 Wald Test |
| pipe | Pipe operator |
| plotDifferential | Plot differential contacts |
| plotDomainogram | Plot domainogram |
| plotGenes | Plot genes |
| plotInteractions | Plot interactions |
| plotInteractionsUMI4C | Plot Interactions UMI4C |
| plotTrend | Plot adaptative smoothen trend |
| plotUMI4C | Plot UMI4C data |
| prepUMI4C | Prepare UMI4C data |
| smoothMonotoneUMI4C | Monotone smoothing of the DDS object VST counts |
| splitUMI4C | Split UMI4C reads |
| statsUMI4C | Statistics UMI4C |
| theme | Theme |
| themeXblank | Theme X blank |
| themeXYblank | Theme Y blank |
| themeYblank | Theme Y blank |
| UMI4C | UMI4C-class |
| UMI4C2dds | UMI4Cats object to DDS object. |
| UMI4Cats | UMI4Cats: A package for analyzing UMI-4C chromatin contact... |
| UMI4C-methods | UMI4C class methods |
| vstUMI4C | Variance stabilizing transformation |
| waldUMI4C | DESeq2 Wald test for differential contacts |
| zscoreUMI4C | Z-score calculation using residuals of trend and fit UMI4C... |
