This package is hidden from search results because it is not hosted in the universe of the upstream ownerscunnac. To fix this you can add URL: https://ropensci-staging.r-universe.dev/tantale to the package DESCRIPTION file. See also theR-universe documentation.

Package: tantale 0.99.0.9000

Sebastien Cunnac

tantale: Mining and Analysis of Transcription Activator-Like Effectors

A toolkit for the study of transcription activator-like effectors (TALEs) of Xanthomonas. tell_tales() finds TALE genes in genome assemblies and can correct the frameshifts that make them hard to annotate in error-prone long-read assemblies. TALEs are held in S3 classes that record each one as a series of parts (N-terminus, repeats with their repeat-variable diresidues (RVDs), C-terminus), with methods to validate, subset, combine and plot them. TALEs are aligned repeat by repeat, compared with R implementations of the 'DisTAL' and 'FuncTAL' distances <doi:10.3389/fpls.2015.00545>, and grouped into families by hierarchical clustering or k-medoids. Wrappers for 'AnnoTALE' <doi:10.1038/srep21077>, 'TALEcorrection' <doi:10.1186/s12864-023-09228-1>, 'TALVEZ' <doi:10.1371/journal.pone.0068464> and 'PrediTALE' <doi:10.1371/journal.pcbi.1007206> read their results into the same objects; the last two predict target sites in host genomes.

Authors:Bao Tram Vi [aut], Sebastien Cunnac [aut, cre], Alvaro L. Pérez-Quintero [cph], Molly Megraw [cph], Artemis G. Hatzigeorgiou [cph]

tantale_0.99.0.9000.tar.gz
tantale_0.99.0.9000.tgz(r-4.6-any)tantale_0.99.0.9000.tgz(r-4.5-any)
tantale_0.99.0.9000.tar.gz(r-4.7-any)tantale_0.99.0.9000.tar.gz(r-4.6-any)
tantale_0.99.0.9000.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
tantale/json (API)

# Install 'tantale' in R:

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

Reviews:rOpenSci Software Review #()

Bug tracker:https://github.com/scunnac/tantale/issues

Pkgdown/docs site:https://scunnac.github.io

Datasets:

rvd_dna_specificity - RVD-to-DNA-binding-specificity weights
tale_annotations - Curated TALE annotations for ten published _Xanthomonas oryzae_ genomes

On CRAN:

software quarto

3.61 score 27 scripts 54 exports 151 dependencies

Last updated from:398c06635a. Checks:5 ERROR, 5 OK. Indexed: no.

Target	Result	Time
linux-devel	ERROR	347
pkgdown docs	ERROR	421
source / vignettes	OK	340
linux-release	ERROR	565
macos-release	ERROR	407
macos-oldrel	ERROR	358
windows-devel	OK	223
windows-release	OK	209
windows-oldrel	OK	161
wasm-release	OK	199

Exports:as_tales correct_tales distances_assert_square distances_restrict domain_distances is_pairwise_distances is_tales is_tales_msa pairwise_distances plot_target_preds preditale run_annotale_assign run_annotale_build run_annotale_load_classes run_annotale_predict tale_distances tales tales_align tales_anchor_codes tales_anomalies tales_assert_complete tales_assign_domain_codes tales_bind tales_coded_strings tales_compare_distal tales_compare_functal tales_consensus tales_consensus_match tales_domain_codes tales_domain_distances tales_from_annotale tales_from_telltales tales_get_dna_seq tales_get_protein_seq tales_group_hclust tales_group_kmedoids tales_msa tales_msa_params tales_msa_width tales_names tales_namespace tales_predict_targets tales_requirements tales_rvd_strings tales_tale_distances tales_to_universalmotif talomes_heatmap talvez tantale_genome tantale_setup tell_tales validate_pairwise_distances validate_tales validate_tales_msa

Dependencies:abind ape aplot askpass base64enc BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops BSgenome bslib cachem caTools cigarillo cli clipr cluster codetools cpp11 crayon curl DBI DECIPHER DelayedArray deldir digest dplyr evaluate farver fastmap fontawesome fontBitstreamVera fontLiberation fontquiver formatR fs futile.logger futile.options gdtools generics GenomeInfoDb GenomicAlignments GenomicRanges ggfun ggiraph ggnewscale ggplot2 ggplotify ggtree glue gplots gridGraphics gtable gtools here highr hms htmltools htmlwidgets httr hwriter interp IRanges isoband jpeg jquerylib jsonlite KernSmooth knitr labeling lambda.r lattice latticeExtra lazyeval lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mime nlme openssl patchwork pillar pkgconfig plyranges png prettyunits progress purrr pwalign R6 rappdirs RColorBrewer Rcpp RcppEigen RcppThread RcppTOML RCurl readr restfulr reticulate Rhtslib rjson rlang rmarkdown rprojroot Rsamtools rtracklayer S4Arrays S4Vectors S7 sass scales Seqinfo ShortRead snow SparseArray stringi stringr SummarizedExperiment sys systemfonts systemPipeR tibble tidyr tidyselect tidytree tinytex treeio tzdb UCSC.utils universalmotif utf8 vctrs viridisLite vroom withr xfun XML XVector yaml yulab.utils

Getting started with tantale

A tales object | Checking for trouble | Looking at the arrays | Where to next | These four articles form one analysis

Rendered fromtantale.qmdusingquarto::html

Last update: 2026-10-08
Started: 2026-10-01

Help page	Topics
tantale: Transcription Activator-Like Effectors (TALEs) tools	tantale-package tantale
Subset a pairwise_distances object	[.pairwise_distances
Subset a tales object	[.tales
Coerce sequences of TALE parts to a tales object	as_tales as_tales.data.frame as_tales.default
Render a distance table as a square matrix	as.matrix.pairwise_distances
Render a TALE alignment as a matrix	as.matrix.tales_msa
Correct TALE ORFs in error-prone sequences	correct_tales
Assert that a distance table is complete and square	distances_assert_square
Restrict a distance table to a set of entities	distances_restrict
Render a tales object as lines of text	format.tales
Render a tales_msa object as lines of text	format.tales_msa
Is this a pairwise distance table?	is_pairwise_distances
Is this a tales object?	is_tales
Is this a tales_msa object?	is_tales_msa
Create a pairwise distance table	domain_distances pairwise_distances tale_distances
Plot TALE RVD sequences along a potential DNA target region	plot_target_preds
Plot the domain composition of a set of TALE arrays	plot.tales
Plot a multiple alignment of TALEs	plot.tales_msa
Run TALE target predictions on DNA sequence(s) using PrediTale	preditale
Print a tales object	print.tales
Print a tales_msa object	print.tales_msa
Assign TALEs to AnnoTALE's published classes	run_annotale_assign
Run the "build" stage of AnnoTALE	run_annotale_build
Download AnnoTALE's catalogue of TALE classes	run_annotale_load_classes
Runs the "predict" and "analyze" steps of AnnoTALE on a fasta file	run_annotale_predict
RVD-to-DNA-binding-specificity weights	rvd_dna_specificity
Summarise a tales object	print.summary.tales summary.tales
Summarise a tales_msa object	print.summary.tales_msa summary.tales_msa
Curated TALE annotations for ten published _Xanthomonas oryzae_ genomes	tale_annotations
Create a tales object	tales
Align the repeat arrays of a tales object	tales_align
Codes marking a TALE array terminus	tales_anchor_codes
Report the biological anomalies in a tales object	tales_anomalies
Assert that a tales object holds complete arrays	tales_assert_complete
Assign a domain code to every distinct part sequence	tales_assign_domain_codes
Combine tales objects	tales_bind
Domain-coded strings, one per TALE array	tales_coded_strings
Compute TALE and domain relatedness by domain-sequence alignment (DisTAL)	tales_compare_distal
Compare TALEs by predicted DNA-binding specificity (FuncTAL)	tales_compare_functal
Compute a consensus from a TALE msa	tales_consensus
Do elements in a TALE msa match the consensus?	tales_consensus_match
The domain code lookup table	tales_domain_codes
Pairwise distances between distinct TALE domains	tales_domain_distances
Build a tales object from AnnoTALE's own TALE predictions	tales_from_annotale
Build a tales object from a tell_tales run directory	tales_from_telltales
Whole-array DNA sequence, one per TALE array	tales_get_dna_seq
Whole-array protein sequence, one per TALE array	tales_get_protein_seq
Group TALEs by hierarchical clustering of their pairwise distance	tales_group_hclust
Group TALEs by k-medoids clustering of their pairwise distance	tales_group_kmedoids
Create a tales_msa object	tales_msa
Settings a TALE alignment was made with	tales_msa_params
Width of a TALE alignment	tales_msa_width
The names of the TALEs in a tales object	tales_names
The dom_code namespace of a tales object	tales_namespace
Predict TALE target boxes	tales_predict_targets
Column requirements of the tales consumers	tales_requirements
RVD strings, one per TALE array	tales_rvd_strings
Pairwise distances between TALE arrays	tales_tale_distances
Convert a tales object to a list of predicted DNA-binding-specificity PWMs	tales_to_universalmotif
Heatmap of RVD sequence variants across strains and TALE groups	talomes_heatmap
Run TALE target predictions on DNA sequence(s) using Talvez	talvez
Path to one of the example genomes	tantale_genome
Check, and optionally build, tantale's external dependencies	tantale_setup
Search and report on the features of TALE protein domains potentially encoded in subject DNA sequences	tell_tales
Validate a pairwise distance table	validate_pairwise_distances
Validate a tales object	validate_tales
Validate a tales_msa object	validate_tales_msa

Package: tantale 0.99.0.9000

tantale: Mining and Analysis of Transcription Activator-Like Effectors

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)