Package: MACER 0.2.2
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>.
Authors:
MACER_0.2.2.tar.gz
MACER_0.2.2.zip(r-4.5)MACER_0.2.2.zip(r-4.4)MACER_0.2.2.zip(r-4.3)
MACER_0.2.2.tgz(r-4.4-any)MACER_0.2.2.tgz(r-4.3-any)
MACER_0.2.2.tar.gz(r-4.5-noble)MACER_0.2.2.tar.gz(r-4.4-noble)
MACER_0.2.2.tgz(r-4.4-emscripten)MACER_0.2.2.tgz(r-4.3-emscripten)
MACER.pdf |MACER.html✨
MACER/json (API)
# Install 'MACER' in R: |
install.packages('MACER', repos = c('https://rgyoung6.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/rgyoung6/macer/issues
Last updated 1 years agofrom:225963fc13. Checks:OK: 7. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Nov 10 2024 |
R-4.5-win | OK | Nov 10 2024 |
R-4.5-linux | OK | Nov 10 2024 |
R-4.4-win | OK | Nov 10 2024 |
R-4.4-mac | OK | Nov 10 2024 |
R-4.3-win | OK | Nov 10 2024 |
R-4.3-mac | OK | Nov 10 2024 |
Exports:align_to_refauto_seq_downloadbarcode_cleancreate_fastas
Dependencies:apeaskpassclicolorspacecurldigestfansifarverggplot2gluegtablehttrisobandjsonlitelabelinglatticelifecyclemagrittrMASSMatrixmgcvmimemunsellnlmeopensslpbapplypillarpkgconfigpngR6RColorBrewerRcpprentrezrlangscalessystibbleutf8vctrsviridisLitewithrXML
Readme and manuals
Help Manual
Help page | Topics |
---|---|
Align and Trim MSA Against a Reference | align_to_ref |
Automatic Sequence Download | auto_seq_download |
DNA Barcode Clean | barcode_clean |
Table To FASTA | create_fastas |