Package: primerTree 1.0.7

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]

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primerTree.pdf |primerTree.html✨
primerTree/json (API)

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

Peer review:

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

Datasets:

On CRAN:

5.54 score 51 stars 15 scripts 201 downloads 3 mentions 14 exports 53 dependencies

Last updated 1 years agofrom:6b257ba8f6. Checks:OK: 7 NOTE: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 06 2024
R-4.5-win-x86_64NOTENov 06 2024
R-4.5-linux-x86_64NOTENov 06 2024
R-4.4-win-x86_64OKNov 06 2024
R-4.4-mac-x86_64OKNov 06 2024
R-4.4-mac-aarch64OKNov 06 2024
R-4.3-win-x86_64OKNov 06 2024
R-4.3-mac-x86_64OKNov 06 2024
R-4.3-mac-aarch64OKNov 06 2024

Exports:accession2taxidcalc_rank_dist_aveclustalofilter_seqsget_sequenceget_sequencesget_taxonomyparse_primer_hitsplot_treeplot_tree_ranksprimer_searchsearch_primer_pairseq_lengthstree_from_alignment

Dependencies:apeaskpassclicodetoolscolorspacecpp11curldigestdirectlabelsfansifarverforeachgenericsggplot2gluegridExtragtablehttrisobanditeratorsjsonlitelabelinglatticelifecyclelubridatemagrittrMASSMatrixmgcvmimemunsellnlmeopensslpillarpkgconfigplyrquadprogR6RColorBrewerRcppreshape2rlangscalesstringistringrsystibbletimechangeutf8vctrsviridisLitewithrXML

Readme and manuals

Help Manual

Help pageTopics
Maps a nucleotide database accession to a taxonomy database taxIdaccession2taxid
PrimerTree results for the bryophyte trnL primersbryophytes_trnL
Summarize pairwise differences.calc_rank_dist_ave
Multiple sequence alignment with clustal omegaclustalo
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 ranksidentify.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 primersmammals_16S
Parse the primer hitsparse_primer_hits
plots a tree, optionally with colored and labeled points by taxonomic rankplot_tree
plots a tree along with a series of taxonomic ranksplot_tree_ranks
plot function for a primerTree object, calls plot_tree_ranksplot.primerTree
Query a pair of primers using ncbi's Primer-BLAST, if primers contain iupacprimer_search
'primerTree' Visually Assessing the Specificity and Informativeness of Primer PairsprimerTree-package primerTree
Automatic primer searching Search a given primer pair, retrieving the alignment results, their product sequences, the taxonomic information for the sequences, a multiple alignment of the productssearch_primer_pair
Get a summary of sequence lengths from a primerTree objectseq_lengths
Method for primerTree objectsseq_lengths.primerTree
Summarize a primerTree result, printing quantiles of sequence length and pairwise differences.summary.primerTree
Construct a neighbor joining tree from a dna alignmenttree_from_alignment