Package: primerTree 1.1.0

primerTree: Visually Assessing the Specificity and Informativeness of Primer Pairs

Identifies potential target sequences for a given set of primers and generates phylogenetic trees annotated with the taxonomies of the predicted amplification products.

Authors:Jim Hester [aut], Matt Cannon [aut, cre]

primerTree_1.1.0.tar.gz
primerTree_1.1.0.zip(r-4.7-x86_64)primerTree_1.1.0.zip(r-4.7-arm64)primerTree_1.1.0.zip(r-4.6-x86_64)primerTree_1.1.0.zip(r-4.6-arm64)primerTree_1.1.0.zip(r-4.5-x86_64)
primerTree_1.1.0.tgz(r-4.6-x86_64)primerTree_1.1.0.tgz(r-4.6-arm64)primerTree_1.1.0.tgz(r-4.5-x86_64)primerTree_1.1.0.tgz(r-4.5-arm64)
primerTree_1.1.0.tar.gz(r-4.7-arm64)primerTree_1.1.0.tar.gz(r-4.7-x86_64)primerTree_1.1.0.tar.gz(r-4.6-arm64)primerTree_1.1.0.tar.gz(r-4.6-x86_64)
primerTree_1.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
primerTree/json (API)

# Install 'primerTree' in R:

install.packages('primerTree', repos = c('https://mvesuviusc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/mvesuviusc/primertree/issues

Datasets:

bryophytes_trnL - PrimerTree results for the bryophyte trnL primers
mammals_16S - PrimerTree results for the mammalian 16S primers

On CRAN:

5.63 score 53 stars 18 scripts 368 downloads 3 mentions 14 exports 45 dependencies

Last updated from:3df2a16c1d. Checks:15 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	OK	140
linux-devel-x86_64	OK	143
source / vignettes	OK	199
linux-release-arm64	OK	104
linux-release-x86_64	OK	132
macos-release-arm64	OK	192
macos-release-x86_64	OK	353
macos-oldrel-arm64	OK	178
macos-oldrel-x86_64	OK	391
windows-devel-arm64	OK	335
windows-devel-x86_64	OK	134
windows-release-arm64	OK	344
windows-release-x86_64	OK	94
windows-oldrel-x86_64	OK	106
wasm-release	OK	109

Exports:accession2taxid calc_rank_dist_ave clustalo filter_seqs get_sequence get_sequences get_taxonomy parse_primer_hits plot_tree plot_tree_ranks primer_search search_primer_pair seq_lengths tree_from_alignment

Dependencies:ape askpass cli codetools cpp11 curl data.table digest directlabels farver foreach generics ggplot2 glue gridExtra gtable httr httr2 isoband iterators jsonlite labeling lattice lifecycle lubridate magrittr mime nlme openssl plyr R6 RColorBrewer Rcpp reshape2 rlang S7 scales stringi stringr sys timechange vctrs viridisLite withr XML

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Maps a nucleotide database accession to a taxonomy database taxId	accession2taxid
PrimerTree results for the bryophyte trnL primers	bryophytes_trnL
Summarize pairwise differences.	calc_rank_dist_ave
Multiple sequence alignment with clustal omega	clustalo
Filter out sequences retrieved by search_primer_pair() that are either too short or too long. The alignment and tree will be recalculated after removing unwanted reads.	filter_seqs filter_seqs.primerTree
Retrieves a fasta sequence from NCBI nucleotide database.	get_sequence
Retrieves fasta sequences from NCBI nucleotide database.	get_sequences
Retrieve the taxonomy information from NCBI for a set of nucleotide gis.	get_taxonomy
identify the point closest to the mouse click only works on single ranks	identify.primerTree_plot
layout a tree using ape, return an object to be plotted by 'plot_tree'	layout_tree_ape
PrimerTree results for the mammalian 16S primers	mammals_16S
Parse the primer hits	parse_primer_hits
plots a tree, optionally with colored and labeled points by taxonomic rank	plot_tree
plots a tree along with a series of taxonomic ranks	plot_tree_ranks
plot function for a primerTree object, calls plot_tree_ranks	plot.primerTree
Query a pair of primers using ncbi's Primer-BLAST, if primers contain iupac	primer_search
'primerTree' Visually Assessing the Specificity and Informativeness of Primer Pairs	primerTree-package primerTree
Automatic primer search Search a given primer pair, retrieving the alignment results, their product sequences, taxonomic information for the sequences, a multiple alignment of the products	search_primer_pair
Get a summary of sequence lengths from a primerTree object	seq_lengths
Method for primerTree objects	seq_lengths.primerTree
Summarize a primerTree result, printing quantiles of sequence length and pairwise differences.	summary.primerTree
Construct a neighbor joining tree from a dna alignment	tree_from_alignment