Files in michbur/tidysq
Tidy Processing and Analysis of Biological Sequences

.Rbuildignore
.github/.gitignore
.github/ISSUE_TEMPLATE/bug_report.md .github/ISSUE_TEMPLATE/feature_request.md
.github/workflows/check-bioc.yml
.gitignore
DESCRIPTION
NAMESPACE
NEWS.md R/RcppExports.R R/alphabet.R R/bite.R R/catch-routine-registration.R R/collapse.R R/complement.R R/doc-sq-class.R R/doc-tidysq.R R/export_sq.R R/find_invalid_letters.R R/find_motifs.R R/has.R R/import_sq.R R/is_empty_sq.R R/paste.R R/random_sq.R R/read_fasta.R R/remove_ambiguous.R R/remove_na.R R/reverse.R R/sq.R R/sqapply.R R/substitute_letters.R
R/sysdata.rda
R/translate.R R/typify.R R/util-checkmate-functions.R R/util-format.R R/util-methods.R R/util-options.R R/util-pack.R R/util-print.R R/util-type.R R/util-unpack.R R/util-vctrs-cast.R R/util-vctrs-names.R R/util-vctrs-prototypes.R R/write_fasta.R R/zzz.R README.Rmd README.md
_pkgdown.yml
codecov.yml
cran-comments.md
docs/404.html
docs/apple-touch-icon-120x120.png
docs/apple-touch-icon-152x152.png
docs/apple-touch-icon-180x180.png
docs/apple-touch-icon-60x60.png
docs/apple-touch-icon-76x76.png
docs/apple-touch-icon.png
docs/articles/advanced-alphabet.html
docs/articles/advanced-alphabet_files/header-attrs-2.9/header-attrs.js
docs/articles/index.html
docs/articles/quick-start.html
docs/articles/quick-start_files/header-attrs-2.9/header-attrs.js
docs/authors.html
docs/bootstrap-toc.css
docs/bootstrap-toc.js
docs/docsearch.css
docs/docsearch.js
docs/favicon-16x16.png
docs/favicon-32x32.png
docs/favicon.ico
docs/index.html
docs/link.svg
docs/logo.png
docs/news/index.html
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/AAindex.html
docs/reference/BLOSUM50.html
docs/reference/BLOSUM50_enc.html
docs/reference/BLOSUM50_pca.html
docs/reference/BLOSUM62.html
docs/reference/BLOSUM62_enc.html
docs/reference/BLOSUM62_pca.html
docs/reference/Rplot001.png
docs/reference/alphabet.html
docs/reference/aminoacids_df.html
docs/reference/as.character.sq.html
docs/reference/as.matrix.sq.html
docs/reference/as.sq.html
docs/reference/bg_freqs.html
docs/reference/bite.html
docs/reference/c.sq.html
docs/reference/clean.html
docs/reference/collapse.html
docs/reference/complement.html
docs/reference/construct_sq.html
docs/reference/count_kmers.html
docs/reference/encode.html
docs/reference/encsq_to_list.html
docs/reference/equals-.sq.html
docs/reference/export_sq.html
docs/reference/extract_kmers.html
docs/reference/fast-mode.html
docs/reference/figures/lifecycle-archived.svg
docs/reference/figures/lifecycle-defunct.svg
docs/reference/figures/lifecycle-deprecated.svg
docs/reference/figures/lifecycle-experimental.svg
docs/reference/figures/lifecycle-maturing.svg
docs/reference/figures/lifecycle-questioning.svg
docs/reference/figures/lifecycle-soft-deprecated.svg
docs/reference/figures/lifecycle-stable.svg
docs/reference/figures/lifecycle-superseded.svg
docs/reference/figures/logo.png
docs/reference/find_invalid_letters.html
docs/reference/find_motifs.html
docs/reference/get_invalid_letters.html
docs/reference/get_sq_alphabet.html
docs/reference/get_sq_lengths.html
docs/reference/get_sq_type.html
docs/reference/get_standard_alphabet.html
docs/reference/get_tidysq_options.html
docs/reference/grapes-has-grapes.html
docs/reference/import_sq.html
docs/reference/index.html
docs/reference/is.sq.html
docs/reference/is_empty_sq.html
docs/reference/is_null_sq.html
docs/reference/nucleotides_df.html
docs/reference/paste.html
docs/reference/print.sq.html
docs/reference/random_sq.html
docs/reference/read_fasta.html
docs/reference/remove_ambiguous.html
docs/reference/remove_na.html
docs/reference/reverse.html
docs/reference/sq-class.html
docs/reference/sq.html
docs/reference/sq_type.html
docs/reference/sqapply.html
docs/reference/sqconcatenate.html
docs/reference/sqextract.html
docs/reference/sqprint.html
docs/reference/substitute_letters.html
docs/reference/tidysq-options.html
docs/reference/tidysq-package.html
docs/reference/translate.html
docs/reference/typify.html
docs/reference/write_fasta.html
inst/WORDLIST
inst/examples/example_aa.fasta
inst/include/tidysq.h
inst/include/tidysq/Alphabet.h
inst/include/tidysq/ProtoSequence.h
inst/include/tidysq/ProtoSequenceInputInterpreter.h
inst/include/tidysq/ProtoSq.h
inst/include/tidysq/Proxy.h
inst/include/tidysq/Rcpp-export.h
inst/include/tidysq/Rcpp-import.h
inst/include/tidysq/Sequence.h
inst/include/tidysq/Sq.h
inst/include/tidysq/collapse.h
inst/include/tidysq/constants/WarningLevel.h
inst/include/tidysq/constants/ambiguous_maps.h
inst/include/tidysq/constants/complement_tables.h
inst/include/tidysq/constants/io.h
inst/include/tidysq/constants/standard_letters.h
inst/include/tidysq/constants/translate_tables.h
inst/include/tidysq/find_motifs.h
inst/include/tidysq/internal/LetterTree.h
inst/include/tidysq/internal/Motif.h
inst/include/tidysq/internal/MotifFrame.h
inst/include/tidysq/internal/obtain_alphabet.h
inst/include/tidysq/internal/pack.h
inst/include/tidysq/internal/unpack_common.h
inst/include/tidysq/internal/unpack_multichar.h
inst/include/tidysq/io/read_fasta.h
inst/include/tidysq/io/write_fasta.h
inst/include/tidysq/ops/Operation.h
inst/include/tidysq/ops/apply_R_function.h
inst/include/tidysq/ops/bite.h
inst/include/tidysq/ops/complement.h
inst/include/tidysq/ops/find_invalid_letters.h
inst/include/tidysq/ops/has.h
inst/include/tidysq/ops/pack.h
inst/include/tidysq/ops/random_sq.h
inst/include/tidysq/ops/remove_NA.h
inst/include/tidysq/ops/remove_ambiguous.h
inst/include/tidysq/ops/remove_on_condition.h
inst/include/tidysq/ops/reverse.h
inst/include/tidysq/ops/skip.h
inst/include/tidysq/ops/substitute_letters.h
inst/include/tidysq/ops/translate.h
inst/include/tidysq/ops/typify.h
inst/include/tidysq/ops/unpack.h
inst/include/tidysq/paste.h
inst/include/tidysq/sq-types.h
inst/include/tidysq/sqapply.h
inst/include/tidysq/tidysq-typedefs.h
inst/include/tidysq/util/ResultWrapper.h
inst/include/tidysq/util/calculate_length.h
inst/include/tidysq/util/find_common_size.h
inst/include/tidysq/util/handle_warning_message.h
inst/include/tidysq/util/match_letter.h
inst/include/tidysq/util/obtain_alphabet.h
inst/include/tidysq/util/random.h
inst/include/tidysq/util/transform-common.h
man/alphabet.Rd man/as.character.sq.Rd man/as.matrix.sq.Rd man/as.sq.Rd man/bite.Rd man/collapse.Rd man/complement.Rd man/equals-.sq.Rd man/export_sq.Rd
man/figures/lifecycle-archived.svg
man/figures/lifecycle-defunct.svg
man/figures/lifecycle-deprecated.svg
man/figures/lifecycle-experimental.svg
man/figures/lifecycle-maturing.svg
man/figures/lifecycle-questioning.svg
man/figures/lifecycle-soft-deprecated.svg
man/figures/lifecycle-stable.svg
man/figures/lifecycle-superseded.svg
man/figures/logo.png
man/find_invalid_letters.Rd man/find_motifs.Rd man/get_sq_lengths.Rd man/get_standard_alphabet.Rd man/get_tidysq_options.Rd man/grapes-has-grapes.Rd man/import_sq.Rd man/is.sq.Rd man/is_empty_sq.Rd man/paste.Rd man/random_sq.Rd man/read_fasta.Rd man/remove_ambiguous.Rd man/remove_na.Rd man/reverse.Rd man/roxygen/meta.R man/roxygen/templates/NA_letter.R man/roxygen/templates/alphabet.R man/roxygen/templates/by_letter.R man/roxygen/templates/dest_type.R man/roxygen/templates/ignore_case.R man/roxygen/templates/motif_details.R man/roxygen/templates/name.R man/roxygen/templates/on_warning.R man/roxygen/templates/safe_mode.R man/roxygen/templates/three-dots.R man/roxygen/templates/x.R man/sq-class.Rd man/sq.Rd man/sq_type.Rd man/sqapply.Rd man/sqconcatenate.Rd man/sqextract.Rd man/sqprint.Rd man/substitute_letters.Rd man/tidysq-package.Rd man/translate.Rd man/typify.Rd man/write_fasta.Rd
pkgdown/favicon/apple-touch-icon-120x120.png
pkgdown/favicon/apple-touch-icon-152x152.png
pkgdown/favicon/apple-touch-icon-180x180.png
pkgdown/favicon/apple-touch-icon-60x60.png
pkgdown/favicon/apple-touch-icon-76x76.png
pkgdown/favicon/apple-touch-icon.png
pkgdown/favicon/favicon-16x16.png
pkgdown/favicon/favicon-32x32.png
pkgdown/favicon/favicon.ico
renv.lock
renv/.gitignore
renv/activate.R
renv/settings.dcf
src/Makevars
src/Makevars.win
src/RcppExports.cpp
src/apply_R_function.cpp
src/bite.cpp
src/collapse.cpp
src/complement.cpp
src/find_invalid_letters.cpp
src/find_motifs.cpp
src/get_standard_alphabet.cpp
src/guess_standard_alph.cpp
src/has.cpp
src/obtain_alphabet.cpp
src/pack.cpp
src/paste.cpp
src/random_sq.cpp
src/read_fasta.cpp
src/remove_NA.cpp
src/remove_ambiguous.cpp
src/reverse.cpp
src/sqapply.cpp
src/substitute_letters.cpp
src/test-pack.cpp
src/test-runner.cpp
src/translate.cpp
src/typify.cpp
src/unpack.cpp
src/write_fasta.cpp
tests/spelling.R tests/testthat.R tests/testthat/test-alphabet.R tests/testthat/test-bite.R tests/testthat/test-casting.R tests/testthat/test-collapse.R tests/testthat/test-complement.R tests/testthat/test-concatenate.R tests/testthat/test-cpp.R tests/testthat/test-export_sq.R tests/testthat/test-find_invalid_letters.R tests/testthat/test-find_motifs.R tests/testthat/test-has.R tests/testthat/test-io.R tests/testthat/test-is.R tests/testthat/test-is_empty_sq.R tests/testthat/test-options.R tests/testthat/test-pack-unpack.R tests/testthat/test-paste.R tests/testthat/test-pkg-Biostrings.R tests/testthat/test-pkg-ape.R tests/testthat/test-pkg-bioseq.R tests/testthat/test-pkg-seqinr.R tests/testthat/test-random_sq.R tests/testthat/test-remove_ambiguous.R tests/testthat/test-remove_na.R tests/testthat/test-reverse.R tests/testthat/test-sq.R tests/testthat/test-sq_type.R tests/testthat/test-sqapply.R tests/testthat/test-substitute_letters.R tests/testthat/test-translate.R tests/testthat/test-typify.R tests/testthat/test-vctrs-ptype2.R tests/testthat/test-warnings.R
vignettes/.gitignore
vignettes/advanced-alphabet.Rmd vignettes/quick-start.Rmd
michbur/tidysq documentation built on Oct. 22, 2021, 9:21 p.m.