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:Robert G Young [aut, cre, cph]

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-4.5-any)DBTC_0.1.0.tgz(r-4.4-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

On CRAN:

3.78 score 1 packages 507 downloads 8 exports 98 dependencies

Last updated 11 months agofrom:3ae1edee16. Checks:7 OK. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Feb 25 2025
R-4.5-win	OK	Feb 25 2025
R-4.5-mac	OK	Feb 25 2025
R-4.5-linux	OK	Feb 25 2025
R-4.4-win	OK	Feb 25 2025
R-4.4-mac	OK	Feb 25 2025
R-4.3-win	OK	Feb 25 2025

Exports:combine_assign_output combine_dada_output combine_reduced_output dada_implement make_BLAST_DB reduce_taxa seq_BLAST taxon_assign

Dependencies:abind askpass BH Biobase BiocGenerics BiocParallel Biostrings bit bit64 bitops blob cachem cli codetools colorspace cpp11 crayon curl dada2 data.table DBI DelayedArray deldir fansi farver fastmap formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicRanges ggplot2 glue gtable httr hwriter interp IRanges isoband jpeg jsonlite labeling lambda.r lattice latticeExtra lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme openssl pbapply pillar pkgconfig plogr plyr png pwalign R.methodsS3 R.oo R.utils R6 RColorBrewer Rcpp RcppEigen RcppParallel reshape2 Rhtslib rlang Rsamtools RSQLite S4Arrays S4Vectors scales ShortRead snow SparseArray stringi stringr SummarizedExperiment sys taxonomizr tibble UCSC.utils utf8 vctrs viridisLite withr XVector

Citation

Development and contributors

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