Package: tidysq 1.2.0

Dominik Rafacz

tidysq: Tidy Processing and Analysis of Biological Sequences

A tidy approach to analysis of biological sequences. All processing and data-storage functions are heavily optimized to allow the fastest and most efficient data storage.

Authors:Dominik Rafacz [cre, aut], Michal Burdukiewicz [aut], Laura Bakala [aut], Leon Eyrich Jessen [ctb], Stefan Roediger [ctb], Jadwiga Slowik [ctb], Weronika Puchala [ctb], Katarzyna Sidorczuk [ctb], Filip Pietluch [ctb], Jaroslaw Chilimoniuk [ctb]

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tidysq.pdf |tidysq.html✨
tidysq/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/biogenies/tidysq/issues

Uses libs:
  • c++– GNU Standard C++ Library v3

On CRAN:

bioconductorbioinformaticsbiological-sequencesfastas3sequencestibbletidytidyversevctrs

40 exports 34 stars 2.83 score 37 dependencies 39 scripts 249 downloads

Last updated 3 years agofrom:51103fe76d. Checks:OK: 4 NOTE: 5. Indexed: yes.

TargetResultDate
Doc / VignettesOKAug 28 2024
R-4.5-win-x86_64NOTEAug 28 2024
R-4.5-linux-x86_64NOTEAug 28 2024
R-4.4-win-x86_64NOTEAug 28 2024
R-4.4-mac-x86_64NOTEAug 28 2024
R-4.4-mac-aarch64NOTEAug 28 2024
R-4.3-win-x86_64OKAug 28 2024
R-4.3-mac-x86_64OKAug 28 2024
R-4.3-mac-aarch64OKAug 28 2024

Exports:%has%alphabetas.sqbitecollapsecomplementexport_sqfind_invalid_lettersfind_motifsget_sq_lengthsget_standard_alphabetget_tidysq_optionsimport_sqis_empty_sqis.sqis.sq_amiis.sq_ami_bscis.sq_ami_extis.sq_atpis.sq_dnais.sq_dna_bscis.sq_dna_extis.sq_rnais.sq_rna_bscis.sq_rna_extis.sq_untpasterandom_sqread_fastaremove_ambiguousremove_nareversesqsq_typesq_type<-sqapplysubstitute_letterstranslatetypifywrite_fasta

Dependencies:backportsbriocallrcheckmateclicrayondescdiffobjdigestdplyrevaluatefansifsgenericsgluejsonlitelifecyclemagrittrpillarpkgbuildpkgconfigpkgloadpraiseprocessxpsR6Rcpprematch2rlangrprojroottestthattibbletidyselectutf8vctrswaldowithr

Advanced alphabet techniques

Rendered fromadvanced-alphabet.Rmdusingknitr::rmarkdownon Aug 28 2024.

Last update: 2021-01-21
Started: 2020-12-21

Quick Start

Rendered fromquick-start.Rmdusingknitr::rmarkdownon Aug 28 2024.

Last update: 2022-03-12
Started: 2020-12-20

Readme and manuals

Help Manual

Help pageTopics
tidysq: tidy analysis of biological sequencestidysq-package tidysq
Test sq object for presence of given motifs%has%
Compare sq objects==.sq
Get alphabet of given sq object.alphabet
Convert sq object into character vectoras.character.sq
Convert sq object into matrixas.matrix.sq
Convert an object to sqas.sq as.sq.character as.sq.default
Subset sequences from sq objectsbite bite.sq
Collapse multiple sequences into onecollapse collapse.sq
Create complement sequence from dnasq or rnasq objectcomplement complement.sq_dna_bsc complement.sq_dna_ext complement.sq_rna_bsc complement.sq_rna_ext
Export sq objects into other formatsexport_sq
Find elements which are not suitable for specified type.find_invalid_letters find_invalid_letters.sq
Find given motifsfind_motifs find_motifs.data.frame find_motifs.sq
Get lengths of sequences in sq objectget_sq_lengths
Get standard alphabet for given type.get_standard_alphabet
Obtain current state of tidysq optionsget_tidysq_options tidysq-options
Import sq objects from other objectsimport_sq
Test if sequence is emptyis_empty_sq is_empty_sq.sq
Check if object has specified typeis.sq is.sq_ami is.sq_ami_bsc is.sq_ami_ext is.sq_atp is.sq_dna is.sq_dna_bsc is.sq_dna_ext is.sq_rna is.sq_rna_bsc is.sq_rna_ext is.sq_unt
Paste sequences in string-like fashionpaste paste.sq
Generate random sequencesrandom_sq
Read a FASTA fileread_fasta
Remove sequences that contain ambiguous elementsremove_ambiguous remove_ambiguous.sq
Remove sequences that contain NA valuesremove_na remove_na.sq
Reverse sequencereverse reverse.sq
Construct sq object from character vectorsq
Get type of an sq objectsq_type sq_type.sq sq_type<- sq_type<-.sq
sq: class for keeping biological sequences tidysq-class
Apply function to each sequencesqapply sqapply.sq
Concatenate sq objectssq-concatenate sqconcatenate
Extract parts of a sq objectsq-extract sqextract
Print sq objectsq-print sqprint
Substitute letters in a sequencesubstitute_letters substitute_letters.sq
Convert DNA or RNA into proteins using genetic codetranslate translate.sq_dna_bsc translate.sq_rna_bsc
Set type of an sq objecttypify typify.sq
Save sq to fasta filewrite_fasta write_fasta.data.frame write_fasta.sq