Man pages for ge11232002/CNEr
CNE Detection and Visualization
| addAncestorGO | Add ancestor GO IDs |
| AssemblyStats | Assembly statistics. |
| axisTrack | Example data for plotting annotation. |
| axtChain | axtChain |
| Axt-class | Class '"Axt"' |
| axtInfo | axtInfo function |
| Axt-util | Utility functions related to Axt alignment |
| binner | UCSC bin indexing system utility functions |
| blatCNE | Wrapper function of blat for 'CNE' object |
| ceScan-methods | ceScan function |
| chainMergeSort | chainMergeSort |
| chainNetSyntenic | chainNetSyntenic |
| chainPreNet | chainPreNet |
| CNE-class | Class '"CNE"' |
| CNEDanRer10Hg38 | CNEHg38DanRer10 and CNEDanRer10Hg38 dataset |
| CNEDensity | CNEDensity function |
| cneFinalListDanRer10Hg38 | cneFinalListDanRer10Hg38 dataset |
| cneMerge | CNE merge function |
| fetchChromSizes | fetchChromSizes function. |
| fixCoordinates | Fix the coordinates in 'Axt' object |
| GRangePairs-class | GRangePairs objects |
| grangesPairsForDotplot | grangesPairsForDotplot |
| last | lastal wrapper |
| lastz | lastz wrapper |
| lavToPsl | lavToPsl |
| makeAncoraFiles | makeAncoraFiles |
| makeAxtTracks | makeAxtTracks |
| makeCNEDensity | Make 'Bed', 'bedGraph' and 'BigWig' files |
| makeGRBs | makeGRBs |
| matchDistribution | Plot the distribution of matched alignments. |
| netToAxt | netToAxt |
| orgKEGGIds2EntrezIDs | Fetch mapping from KEGG IDs to Entrez IDs |
| plotCNEDistribution | Plot sequential CNE number against CNE genomic location |
| plotCNEWidth | Plot the CNE widths distribution |
| psubAxt | Parallel subset of Axt alignment |
| queryCNEData | Query the CNEData package to fetch the CNEs |
| readAncora | Read the cne file from Ancora format. |
| readAncoraIntoSQLite | Read Ancora legacy CNE format |
| readAxt | Read 'Axt' file |
| readBed | Read bed file |
| readCNERangesFromSQLite | readCNERangesFromSQLite function |
| read.rmMask.GRanges | Read a RepeatMasker .out file |
| read.rmskFasta | Read a soft repeat masked fasta |
| reverseCigar | reverseCigar function |
| saveCNEToSQLite | Save CNE to SQLite |
| scoringMatrix | scoringMatrix |
| subAxt-methods | Subset an 'Axt' object |
| syntenicDotplot | Syntenic dotplot |
| writeAxt | 'writeAxt' function |
