R packages by rgyoung6

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.

Last updated 11 months ago

3.78 score 1 dependents 507 downloads

DBTCShiny - Dada-BLAST-Taxon Assign-Condense Metabarcode Analysis 'shiny' Application

Metabarcoding analysis using the 'DBTC' package is implemented here using 'shiny' in an interactive graphical user interface to conduct Metabarcode analyses and visualize and filter results.

Last updated 9 months ago

3.74 score 1 scripts 495 downloads

MACER - Molecular Acquisition, Cleaning, and Evaluation in R 'MACER'

To assist biological researchers in assembling taxonomically and marker focused molecular sequence data sets. 'MACER' accepts a list of genera as a user input and uses NCBI-GenBank and BOLD as resources to download and assemble molecular sequence datasets. These datasets are then assembled by marker, aligned, trimmed, and cleaned. The use of this package allows the publication of specific parameters to ensure reproducibility. The 'MACER' package has four core functions and an example run through using all of these functions can be found in the associated repository <https://github.com/rgyoung6/MACER_example>.

Last updated 1 years ago

3.00 score 2 stars 3 scripts 804 downloads