Introduction | Prerequisite | Aligning | LASTZ aligner | last aligner | YASS aligner | Chaining: | Netting: | axtNet | Session info
Package: CNEr 1.49.0
Boris Lenhard
CNEr: CNE Detection and Visualization
Large-scale identification and advanced visualization of sets of conserved noncoding elements.
Authors:
CNEr_1.49.0.tar.gz
CNEr_1.49.0.zip(r-4.7)CNEr_1.49.0.zip(r-4.6)CNEr_1.49.0.zip(r-4.5)
CNEr_1.49.0.tgz(r-4.6-x86_64)CNEr_1.49.0.tgz(r-4.6-arm64)CNEr_1.49.0.tgz(r-4.5-x86_64)CNEr_1.49.0.tgz(r-4.5-arm64)
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CNEr_1.49.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
CNEr/json (API)
| # Install 'CNEr' in R: |
| install.packages('CNEr', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/ge11232002/cner/issues
Datasets:
- axisTrack - Example data for plotting annotation.
- CNEDanRer10Hg38 - CNEHg38DanRer10 and CNEDanRer10Hg38 dataset
- cneFinalListDanRer10Hg38 - CneFinalListDanRer10Hg38 dataset
- CNEHg38DanRer10 - CNEHg38DanRer10 and CNEDanRer10Hg38 dataset
- cpgIslands - Example data for plotting annotation.
- grangesPairsForDotplot - GrangesPairsForDotplot
- refGenes - Example data for plotting annotation.
On BioConductor:CNEr-1.49.0(bioc 3.24)CNEr-1.48.0(bioc 3.23)
generegulationvisualizationdataimport
Last updated from:00483733b6. Checks:3 ERROR, 9 WARNING, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 417 | ||
| linux-devel-arm64 | WARNING | 627 | ||
| linux-devel-x86_64 | WARNING | 869 | ||
| source / vignettes | OK | 558 | ||
| linux-release-arm64 | WARNING | 663 | ||
| linux-release-x86_64 | WARNING | 787 | ||
| macos-release-arm64 | ERROR | 609 | ||
| macos-release-x86_64 | WARNING | 918 | ||
| macos-oldrel-arm64 | ERROR | 631 | ||
| macos-oldrel-x86_64 | WARNING | 1186 | ||
| windows-devel | WARNING | 646 | ||
| windows-release | WARNING | 607 | ||
| windows-oldrel | WARNING | 774 | ||
| wasm-release | OK | 423 |
Exports:AxtaxtChainaxtInfobinFromCoordRangebinRangesFromCoordRangebinRestrictionStringblatCNEceScanchainMergeSortchainNetSyntenicchainPreNetCNECNE12CNE21CNEDensityCNEFinalcneMergeCNEMergedfetchChromSizesfirstfixCoordinatesGRangePairsgrglistlastlastallastzlavToPslmakeAncoraFilesmakeAxtTracksmakeCNEDensitymakeGRBsmatchDistributionN50N90netToAxtplotCNEDistributionplotCNEWidthpsubAxtqueryRangesquerySeqsread.rmMask.GRangesread.rmskFastareadAncorareadAncoraIntoSQLitereadAxtreadBedreadCNERangesFromSQLitereverseCigarsaveCNEToSQLitescorescoringMatrixsecondseqinfoseqnamesstrandsubAxtsummaryswapsymCountsyntenicDotplottargetRangestargetSeqsthresholdsuniquewriteAxt
Dependencies:abindannotateAnnotationDbiaskpassBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobcachemcigarilloclicliprcodetoolscpp11crayoncurlDBIDelayedArrayfarverfastmapformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicRangesggplot2glueGO.dbgtablehmshttrIRangesisobandjsonliteKEGGRESTlabelinglambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigplyrpngpoweRlawpracmaprettyunitsprogresspwalignR.methodsS3R.ooR.utilsR6RColorBrewerRcppRCurlreadrreshape2restfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsS7scalesSeqinfosnowSparseArraystringistringrSummarizedExperimentsystibbletidyselecttzdbUCSC.utilsutf8vctrsviridisLitevroomwithrXMLxtableXVectoryaml
Pairwise whole genome alignment
Last update: 2016-10-06
Started: 2016-02-03
CNE identification and visualisation
Introduction | Workflow of the package | CNE identification | CNE visualisation | Input | axt alignment file | Filtering information | Creating a CNE class | Scan axt alignments | Merge CNEs | Realignment of CNEs | CNE storage and query | CNE length distribution | Genomic distribution of CNEs along the chromosome | Output of bed and bedGraph files | CNEs visualisation | Gene annotation visualisation | CNEs horizon plot | Conclusions | References
Last update: 2016-08-22
Started: 2015-10-08
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Add ancestor GO IDs | addAncestorGO |
| Example data for plotting annotation. | axisTrack cpgIslands refGenes |
| Class '"Axt"' | Axt Axt-class c,Axt-method length,Axt-method queryRanges queryRanges,Axt-method querySeqs querySeqs,Axt-method score,Axt-method symCount symCount,Axt-method targetRanges targetRanges,Axt-method targetSeqs targetSeqs,Axt-method [,Axt,ANY,ANY-method |
| axtChain | axtChain |
| axtInfo function | axtInfo |
| UCSC bin indexing system utility functions | binFromCoordRange binRangesFromCoordRange binRestrictionString |
| Wrapper function of blat for 'CNE' object | blatCNE |
| ceScan function | ceScan ceScan,Axt-method ceScan,CNE-method |
| chainMergeSort | chainMergeSort |
| chainNetSyntenic | chainNetSyntenic |
| chainPreNet | chainPreNet |
| Class '"CNE"' | CNE CNE-class CNE12 CNE12,CNE-method CNE21 CNE21,CNE-method CNEFinal CNEFinal,CNE-method CNEMerged CNEMerged,CNE-method thresholds thresholds,CNE-method |
| CNEHg38DanRer10 and CNEDanRer10Hg38 dataset | CNEDanRer10Hg38 CNEHg38DanRer10 |
| CNEDensity function | CNEDensity CNEDensity,ANY,character,character,missing,missing-method CNEDensity,ANY,missing,character,character,character-method CNEDensity-methods |
| cneFinalListDanRer10Hg38 dataset | cneFinalListDanRer10Hg38 |
| CNE merge function | cneMerge cneMerge,CNE,missing-method cneMerge,GRangePairs,GRangePairs-method |
| fetchChromSizes function. | fetchChromSizes |
| Fix the coordinates in 'Axt' object | fixCoordinates fixCoordinates,Axt-method |
| GRangePairs objects | c,GRangePairs-method class:GRangePairs coerce,GRangePairs,GRanges-method coerce,GRangePairs,GRangesList-method first,GRangePairs-method GRangePairs GRangePairs-class grglist,GRangePairs-method last last,GRangePairs-method second,GRangePairs-method seqinfo,GRangePairs-method seqnames,GRangePairs-method strand,GRangePairs-method swap swap,GRangePairs-method unique,GRangePairs-method unlist,GRangePairs-method |
| grangesPairsForDotplot | grangesPairsForDotplot |
| lastal wrapper | lastal |
| lastz wrapper | lastz |
| lavToPsl | lavToPsl |
| makeAncoraFiles | makeAncoraFiles |
| makeAxtTracks | makeAxtTracks |
| Make 'Bed', 'bedGraph' and 'BigWig' files | makeCNEDensity |
| makeGRBs | makeGRBs |
| Plot the distribution of matched alignments. | matchDistribution matchDistribution,Axt-method |
| Assembly statistics. | N50 N90 |
| netToAxt | netToAxt |
| Fetch mapping from KEGG IDs to Entrez IDs | orgKEGGIds2EntrezIDs |
| Plot sequential CNE number against CNE genomic location | plotCNEDistribution |
| Plot the CNE widths distribution | plotCNEWidth |
| Parallel subset of Axt alignment | psubAxt |
| Query the CNEData package to fetch the CNEs | queryCNEData |
| Read a RepeatMasker .out file | read.rmMask.GRanges |
| Read a soft repeat masked fasta | read.rmskFasta |
| Read the cne file from Ancora format. | readAncora |
| Read Ancora legacy CNE format | readAncoraIntoSQLite |
| Read 'Axt' file | readAxt |
| Read bed file | readBed |
| readCNERangesFromSQLite function | readCNERangesFromSQLite |
| reverseCigar function | reverseCigar |
| Save CNE to SQLite | saveCNEToSQLite |
| scoringMatrix | scoringMatrix |
| Subset an 'Axt' object | subAxt subAxt,Axt,character,integer,integer-method subAxt,Axt,character,missing,missing-method subAxt,Axt,character,numeric,numeric-method subAxt,Axt,GRanges,missing,missing-method subAxt-methods |
| Utility functions related to Axt alignment | summary summary,Axt-method |
| Syntenic dotplot | syntenicDotplot syntenicDotplot,Axt-method syntenicDotplot,GRangePairs-method |
| 'writeAxt' function | writeAxt |
