Package index • tantale

Overview

Which object each exported function takes and returns. Boxes are object classes, dots are functions. Hover over a node to see what it takes and returns, click it to highlight its neighbours, and scroll to zoom. Open the map in a full window.

TALE discovery

Find TALE genes in genomic sequence and parse them into arrays of parts.

correct_tales(): Correct TALE ORFs in error-prone sequences
tale_annotations: Curated TALE annotations for ten published Xanthomonas oryzae genomes
tales_from_annotale(): Build a tales object from AnnoTALE's own TALE predictions
tales_from_telltales(): Build a tales object from a tell_tales run directory
tell_tales(): Search and report on the features of TALE protein domains potentially encoded in subject DNA sequences

tales objects

The central long table of TALE array parts, its constructor and validators.

as_tales(): Coerce sequences of TALE parts to a tales object
format(<tales>): Render a tales object as lines of text
format(<tales_msa>): Render a tales_msa object as lines of text
is_tales(): Is this a tales object?
print(<tales>): Print a tales object
print(<tales_msa>): Print a tales_msa object
`[`(<tales>): Subset a tales object
summary(<tales>) print(<summary.tales>): Summarise a tales object
summary(<tales_msa>) print(<summary.tales_msa>): Summarise a tales_msa object
tales(): Create a tales object
tales_anchor_codes(): Codes marking a TALE array terminus
tales_anomalies(): Report the biological anomalies in a tales object
tales_assert_complete(): Assert that a tales object holds complete arrays
tales_bind(): Combine tales objects
tales_names(): The names of the TALEs in a tales object
tales_namespace(): The dom_code namespace of a tales object
tales_requirements(): Column requirements of the tales consumers
validate_tales(): Validate a tales object

Pairwise distances

Comparing TALEs and their domains, and the typed tables that result.

as.matrix(<pairwise_distances>): Render a distance table as a square matrix
distances_assert_square(): Assert that a distance table is complete and square
distances_restrict(): Restrict a distance table to a set of entities
is_pairwise_distances(): Is this a pairwise distance table?
pairwise_distances() tale_distances() domain_distances(): Create a pairwise distance table
rvd_dna_specificity: RVD-to-DNA-binding-specificity weights
`[`(<pairwise_distances>): Subset a pairwise_distances object
tales_assign_domain_codes(): Assign a domain code to every distinct part sequence
tales_compare_distal(): Compute TALE and domain relatedness by domain-sequence alignment (DisTAL)
tales_compare_functal(): Compare TALEs by predicted DNA-binding specificity (FuncTAL)
tales_domain_distances(): Pairwise distances between distinct TALE domains
tales_group_hclust(): Group TALEs by hierarchical clustering of their pairwise distance
tales_group_kmedoids(): Group TALEs by k-medoids clustering of their pairwise distance
tales_tale_distances(): Pairwise distances between TALE arrays
validate_pairwise_distances(): Validate a pairwise distance table

Alignment

Multiple alignment of TALE arrays and consensus over it.

as.matrix(<tales_msa>): Render a TALE alignment as a matrix
is_tales_msa(): Is this a tales_msa object?
tales_align(): Align the repeat arrays of a tales object
tales_consensus(): Compute a consensus from a TALE msa
tales_consensus_match(): Do elements in a TALE msa match the consensus?
tales_msa(): Create a tales_msa object
tales_msa_params(): Settings a TALE alignment was made with
tales_msa_width(): Width of a TALE alignment
validate_tales_msa(): Validate a tales_msa object

Projections and conversions

Views derived from a tales object, and format conversions between them.

tales_coded_strings(): Domain-coded strings, one per TALE array
tales_domain_codes(): The domain code lookup table
tales_get_dna_seq(): Whole-array DNA sequence, one per TALE array
tales_get_protein_seq(): Whole-array protein sequence, one per TALE array
tales_rvd_strings(): RVD strings, one per TALE array
tales_to_universalmotif(): Convert a tales object to a list of predicted DNA-binding-specificity PWMs

Plots

Visualising alignments, array composition and talome content.

plot(<tales>): Plot the domain composition of a set of TALE arrays
plot(<tales_msa>): Plot a multiple alignment of TALEs
plot_target_preds(): Plot TALE RVD sequences along a potential DNA target region
talomes_heatmap(): Heatmap of RVD sequence variants across strains and TALE groups

Target prediction

Predicting EBEs in a promoter set, and plotting the result.

plot_target_preds(): Plot TALE RVD sequences along a potential DNA target region
preditale(): Run TALE target predictions on DNA sequence(s) using PrediTale
tales_predict_targets(): Predict TALE target boxes
talvez(): Run TALE target predictions on DNA sequence(s) using Talvez

Setting up

Checking, building and downloading the external tools tantale drives, and the example genomes.

tantale_setup(): Check, and optionally build, tantale's external dependencies
tantale_genome(): Path to one of the example genomes

Package documentation

Package-level documentation.

tantale tantale-package: tantale: Transcription Activator-Like Effectors (TALEs) tools

External tool wrappers

Wrappers around AnnoTALE programs.

run_annotale_assign(): Assign TALEs to AnnoTALE's published classes
run_annotale_build(): Run the "build" stage of AnnoTALE
run_annotale_load_classes(): Download AnnoTALE's catalogue of TALE classes
run_annotale_predict(): Runs the "predict" and "analyze" steps of AnnoTALE on a fasta file