Files in maialab/agvgd
An R Implementation of the 'Align-GVGD' Method
.Rbuildignore
.github/.gitignore
.github/workflows/R-CMD-check.yaml
.github/workflows/pkgdown.yaml
.github/workflows/test-coverage.yaml
.gitignore
DESCRIPTION
LICENSE
LICENSE.md
NAMESPACE
NEWS.md
R/again_gapped.R
R/agvgd-package.R
R/agvgd.R
R/align_mat.R
R/alignment_file.R
R/amino_acids.R
R/are_all_one_letter.R
R/are_all_three_letter.R
R/as_matrix.R
R/as_three_letter.R
R/cpv_ranges.R
R/cpv_ranges_after_gaps.R
R/dev.R
R/filter_alignment.R
R/gap_cases.R
R/gap_padding.R
R/gap_streak.R
R/gd.R
R/get_orthologs.R
R/gv.R
R/gvgd_to_class.R
R/import_agvgdweb.R
R/is_poi_a_gap.R
R/line_annotation.R
R/line_start_positions.R
R/matrix_to_list.R
R/max_seq_length.R
R/nr_lines_per_seq.R
R/pad_seq_names.R
R/padding.R
R/poi_to_res.R
R/print_align_mat.R
R/profile_to_alignment.R
R/read_alignment.R
R/read_substitutions.R
R/reference_sequence.R
R/res_to_poi.R
R/safe_rownames.R
R/split_alignment_by_lines.R
R/str_chop.R
R/sysdata.rda
R/utils-pipe.R
R/write_alignment.R
R/write_substitutions.R
README.Rmd
README.md
_pkgdown.yml
agvgd.Rproj
codecov.yml
cran-comments.md
data-raw/alignments.R
data-raw/alignments.ods
data-raw/cpv_ranges.R
inst/extdata/ATM4_Spur.fasta
inst/extdata/BRCA1_Align_Pufferfish.txt
inst/extdata/BRCA2_Puff.fasta
inst/extdata/CHEK2_June_2010.fasta
inst/extdata/MRE11_all.fa
inst/extdata/MSH6_Align_2010a.fa
inst/extdata/NBN_all.fa
inst/extdata/PALB2.fa
inst/extdata/PMS2_Align_2010a.fa
inst/extdata/RAD50_all.fa
inst/extdata/RAD51.fa
inst/extdata/XRCC2_Tadh.fa
inst/extdata/correia_magno2022.txt
inst/extdata/lee2010_sub.txt
inst/extdata/sub.txt
inst/nature.csl
inst/pik3ca.bib
inst/references.bib
man/agvgd-package.Rd
man/agvgd.Rd
man/alignment_file.Rd
man/amino_acids.Rd
man/cpv_ranges.Rd
man/dev.Rd
man/figures/README-pressure-1.png
man/figures/cintesis.svg
man/figures/correia_magno2022_fig02.png
man/figures/dev-def.png
man/figures/dev-def.svg
man/figures/dev-plot-1.png
man/figures/dev-plot-1.svg
man/figures/lee2010_fig03.png
man/figures/logo.svg
man/gd.Rd
man/gv.Rd
man/pipe.Rd
man/poi_to_res.Rd
man/profile_to_alignment.Rd
man/read_agvgdweb_results.Rd
man/read_alignment.Rd
man/read_substitutions.Rd
man/res_to_poi.Rd
man/str_chop.Rd
man/write_alignment.Rd
man/write_substitutions.Rd
notes.md
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
tests/testthat.R
tests/testthat/alignments/agvgd01.tsv
tests/testthat/alignments/agvgd02.tsv
tests/testthat/alignments/agvgd03.tsv
tests/testthat/alignments/agvgd04.tsv
tests/testthat/alignments/agvgd05.tsv
tests/testthat/alignments/agvgd06.tsv
tests/testthat/alignments/agvgd07.tsv
tests/testthat/alignments/agvgd08.tsv
tests/testthat/alignments/agvgd09.tsv
tests/testthat/alignments/agvgd10.tsv
tests/testthat/alignments/agvgd11.tsv
tests/testthat/alignments/agvgd12.tsv
tests/testthat/alignments/agvgd13.tsv
tests/testthat/alignments/agvgd99.tsv
tests/testthat/alignments/align01.fa
tests/testthat/alignments/align02.fa
tests/testthat/alignments/align03.fa
tests/testthat/alignments/align04.fa
tests/testthat/alignments/align05.fa
tests/testthat/alignments/align06.fa
tests/testthat/alignments/align07.fa
tests/testthat/alignments/align08.fa
tests/testthat/alignments/align09.fa
tests/testthat/alignments/align10.fa
tests/testthat/alignments/align11.fa
tests/testthat/alignments/align12.fa
tests/testthat/alignments/align13.fa
tests/testthat/alignments/align99.fa
tests/testthat/alignments/sub.txt
tests/testthat/test-again_gapped.R
tests/testthat/test-agvgd.R
tests/testthat/test-alignment_file.R
tests/testthat/test-are_all_one_letter.R
tests/testthat/test-are_all_three_letter.R
tests/testthat/test-as_matrix_align_mat.R
tests/testthat/test-dev.R
tests/testthat/test-filter_alignment.R
tests/testthat/test-gap_cases.R
tests/testthat/test-gd.R
tests/testthat/test-gv.R
tests/testthat/test-is_align_mat_class.R
tests/testthat/test-matrix_to_list.R
tests/testthat/test-max_gap_streak.R
tests/testthat/test-poi_to_res.R
tests/testthat/test-print_align_mat.R
tests/testthat/test-read_alignment.R
tests/testthat/test-read_substitutions.R
tests/testthat/test-ref_sequence.R
tests/testthat/test-res_to_poi.R
vignettes/.gitignore
vignettes/correia_magno2022.Rmd
vignettes/lee2010.Rmd
