Introduction | Installation | Input data | Getting to know the example data sets | Data preparation | Classifying duplicated gene pairs and genes | The binary scheme (SD vs SSD) | The standard scheme (SSD → TD, PD, DD) | The extended scheme (SSD → TD, PD, TRD, DD) | The full scheme (SSD → TD, PD, rTRD, dTRD, DD) | Classifying genes into unique modes of duplication | Calculating substitution rates for duplicated gene pairs | Identifying and visualizing $K_s$ peaks | Classifying genes by age groups | Data visualization | Visualizing the frequency of duplicates per mode | Visualizing $K_s$ distributions | Visualizing substitution rates by species | Session information | References
Package: doubletrouble 1.13.0
Fabrício Almeida-Silva
doubletrouble: Identification and classification of duplicated genes
doubletrouble aims to identify duplicated genes from whole-genome protein sequences and classify them based on their modes of duplication. The duplication modes are i. segmental duplication (SD); ii. tandem duplication (TD); iii. proximal duplication (PD); iv. transposed duplication (TRD) and; v. dispersed duplication (DD). Transposon-derived duplicates (TRD) can be further subdivided into rTRD (retrotransposon-derived duplication) and dTRD (DNA transposon-derived duplication). If users want a simpler classification scheme, duplicates can also be classified into SD- and SSD-derived (small-scale duplication) gene pairs. Besides classifying gene pairs, users can also classify genes, so that each gene is assigned a unique mode of duplication. Users can also calculate substitution rates per substitution site (i.e., Ka and Ks) from duplicate pairs, find peaks in Ks distributions with Gaussian Mixture Models (GMMs), and classify gene pairs into age groups based on Ks peaks.
Authors:
doubletrouble_1.13.0.tar.gz
doubletrouble_1.13.0.zip(r-4.7)doubletrouble_1.13.0.zip(r-4.6)doubletrouble_1.13.0.zip(r-4.5)
doubletrouble_1.13.0.tgz(r-4.6-any)doubletrouble_1.13.0.tgz(r-4.5-any)
doubletrouble_1.13.0.tar.gz(r-4.7-any)doubletrouble_1.13.0.tar.gz(r-4.6-any)
doubletrouble_1.13.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
doubletrouble/json (API)
| # Install 'doubletrouble' in R: |
| install.packages('doubletrouble', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/almeidasilvaf/doubletrouble/issues
Datasets:
- cds_scerevisiae - Coding sequences (CDS) of S. cerevisiae
- diamond_inter - Interspecies DIAMOND output for yeast species
- diamond_intra - Intraspecies DIAMOND output for S. cerevisiae
- fungi_kaks - Duplicate pairs and Ka, Ks, and Ka/Ks values for fungi species
- gmax_ks - Duplicate pairs and Ks values for Glycine max
- yeast_annot - Genome annotation of the yeast species S. cerevisiae and C. glabrata
- yeast_seq - Protein sequences of the yeast species S. cerevisiae and C. glabrata
On BioConductor:doubletrouble-1.13.0(bioc 3.24)doubletrouble-1.12.0(bioc 3.23)
softwarewholegenomecomparativegenomicsfunctionalgenomicsphylogeneticsnetworkclassificationbioinformaticscomparative-genomicsgene-duplicationmolecular-evolutionwhole-genome-duplication
Last updated from:4f93b41cf4. Checks:1 NOTE, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 267 | ||
| linux-devel-x86_64 | OK | 460 | ||
| source / vignettes | OK | 443 | ||
| linux-release-x86_64 | OK | 433 | ||
| macos-release-arm64 | OK | 252 | ||
| macos-oldrel-arm64 | OK | 339 | ||
| windows-devel | OK | 374 | ||
| windows-release | OK | 341 | ||
| windows-oldrel | OK | 336 | ||
| wasm-release | OK | 176 |
Exports:classify_gene_pairsclassify_genesduplicates2countsfind_ks_peaksget_anchors_listget_intron_countsget_segmentalget_tandem_proximalget_transposedget_transposed_classespairs2kaksplot_duplicate_freqsplot_ks_distroplot_ks_peaksplot_rates_by_speciessplit_pairs_by_peak
Dependencies:abindade4AnnotationDbiapeaskpassBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobbriocachemcallrcigarilloclicodacodetoolscpp11crayoncurlDBIDelayedArraydescdiffobjdigestdoParalleldplyrevaluatefarverfastmapforeachformatRfsfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicFeaturesGenomicRangesggnetworkggplot2ggrepelgluegtablehttrigraphintergraphIRangesisobanditeratorsjsonliteKEGGRESTlabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmclustmemoisemimeMSA2distMultipleAlignmentnetworknlmeopensslotelpheatmappillarpixmappkgbuildpkgconfigpkgloadpngpraiseprocessxpspurrrpwalignR6RColorBrewerRcppRcppArmadilloRcppThreadRCurlrestfulrRhtslibrjsonrlangrprojrootRsamtoolsRSQLitertracklayerS4ArraysS4VectorsS7scalessegmentedSeqinfoseqinrsnasnowspSparseArraystatnet.commonstringistringrSummarizedExperimentsyntenetsystestthattibbletidyrtidyselectutf8vctrsviridisLitewaldowithrXMLXVectoryaml
