Package: DBTC 0.1.0
DBTC: Dada-BLAST-Taxon Assign-Condense Metabarcode Analysis
First using 'dada2' R tools to analyse metabarcode data, the 'DBTC' package then uses the BLAST algorithm to search unknown sequences against local databases, and then takes reduced matched results and provides best taxonomic assignments.
Authors:
DBTC_0.1.0.tar.gz
DBTC_0.1.0.zip(r-4.5)DBTC_0.1.0.zip(r-4.4)DBTC_0.1.0.zip(r-4.3)
DBTC_0.1.0.tgz(r-4.4-any)DBTC_0.1.0.tgz(r-4.3-any)
DBTC_0.1.0.tar.gz(r-4.5-noble)DBTC_0.1.0.tar.gz(r-4.4-noble)
DBTC_0.1.0.tgz(r-4.4-emscripten)DBTC_0.1.0.tgz(r-4.3-emscripten)
DBTC.pdf |DBTC.html✨
DBTC/json (API)
| # Install 'DBTC' in R: |
| install.packages('DBTC', repos = c('https://rgyoung6.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/rgyoung6/dbtc/issues
Last updated 6 months agofrom:3ae1edee16. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 26 2024 |
| R-4.5-win | OK | Oct 26 2024 |
| R-4.5-linux | OK | Oct 26 2024 |
| R-4.4-win | OK | Oct 26 2024 |
| R-4.4-mac | OK | Oct 26 2024 |
| R-4.3-win | OK | Oct 26 2024 |
| R-4.3-mac | OK | Oct 26 2024 |
Exports:combine_assign_outputcombine_dada_outputcombine_reduced_outputdada_implementmake_BLAST_DBreduce_taxaseq_BLASTtaxon_assign
Dependencies:abindaskpassBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64bitopsblobcachemclicodetoolscolorspacecpp11crayoncurldada2data.tableDBIDelayedArraydeldirfansifarverfastmapformatRfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggplot2gluegtablehttrhwriterinterpIRangesisobandjpegjsonlitelabelinglambda.rlatticelatticeExtralifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpbapplypillarpkgconfigplogrplyrpngpwalignR.methodsS3R.ooR.utilsR6RColorBrewerRcppRcppEigenRcppParallelreshape2RhtslibrlangRsamtoolsRSQLiteS4ArraysS4VectorsscalesShortReadsnowSparseArraystringistringrSummarizedExperimentsystaxonomizrtibbleUCSC.utilsutf8vctrsviridisLitewithrXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Combine Taxa Assignment for Same ASV Using Different Databases | combine_assign_output |
| Combine Dada Output | combine_dada_output |
| Combine Reduce Taxa Files for the Same Biological Samples using Different Markers | combine_reduced_output |
| Dada Implement | dada_implement |
| Make a BLAST Database | make_BLAST_DB |
| Reduce Taxa Assignment | reduce_taxa |
| BLAST Query File Against Local Database | seq_BLAST |
| Assign Taxa using BLAST Results | taxon_assign |
