Man pages for chernolab/ASpli
Analysis of Alternative Splicing Using RNA-Seq
| acc_AS | Accessors for ASpliAS object |
| acc_counts | Accessors for ASpliCounts object |
| acc_DU | Accessors for ASpliDU object |
| acc_features | Accessors for ASpliFeatures object |
| acc_is | Accessors for ASpliIntegratedSignals object |
| acc_JDU | Accessors for ASpliJDU object |
| acc_MergedReport | Accessors for ASpliSplicingReport object |
| ASpliAS-class | Class '"ASpliAS"' |
| ASpliCounts | Class '"ASpliCounts"' |
| ASpliCounts-class | Class '"ASpliCounts"' |
| ASpli-deprecated | Deprecated functions in package 'ASpli' |
| ASpliDU-class | Class '"ASpliDU"' |
| ASpliFeatures-class | Class '"ASpliFeatures"' |
| ASpliIntegratedSignals-class | Class '"ASpliIntegratedSignals"' |
| ASpliJDU-class | Class '"ASpliJDU"' |
| ASpli-package | Analysis of Alternative Splicing Using RNAseq |
| ASpliSplicingReport-class | Class '"ASpliSplicingReport"' |
| binGenome | Feature coordinates extraction |
| binGenome-methods | Feature coordinates extraction |
| containsJunctions-function | Examine ASpliDU objects |
| DUreport | Differential gene expression and differential bin usage... |
| DUreportBinSplice-method | Differential gene expression and differential bin usage... |
| DUreport.norm | Differential gene expression and differential bin usage... |
| DUreport.offset | Differential gene expression and differential bin usage... |
| example_data | Example Aspli objects |
| exportIntegratedSignals | Export integrated signals. |
| exportSplicingReports | Export splicing reports |
| filterDU-method | Filtering ASpliDU objects |
| filterSignals | Filter signals |
| gbCounts | Summarize read overlaps |
| gbDUreport-method | Differential gene expression and differential bin usage... |
| getConditions-function | Retrieve condition names from a targets data frame. |
| integrateSignals | Integrate signals |
| jCounts-methods | Report PSI, PJU and PIR using experimental junctions |
| jDUreport | Differential junction usage estimation |
| junctionDUreport | Differential junction usage estimation |
| loadBAM | Load BAM files |
| mergeBinDUAS-method | Differential usage of bins and PSI/PIR. |
| plotBins | Draw plots of gene counts, bin counts, PSI/PIR value,... |
| plotGenomicRegions | Create genomic regions coverage plots |
| rds | Read density of gene and bins |
| show-methods | Display a summary of data contained in ASpliObjects |
| splicingReport | Splicing report |
| subset-methods | Subset ASpli objects |
| write | Write results |
| write-methods | Write results |
