Files in currocam/HMMERutils
HMMERutils
.Rbuildignore
.Rprofile
.github/.gitignore
.github/CODE_OF_CONDUCT.md
.github/CONTRIBUTING.md
.github/ISSUE_TEMPLATE/issue_template.md
.github/SUPPORT.md
.github/workflows/check-bioc.yml
.github/workflows/pr.yml
.gitignore
DESCRIPTION
NAMESPACE
NEWS.md
R/HMMER.R
R/add_physicochemical_properties_to_HMMER_tbl.R
R/add_sequences_to_hmmer_tbl.R
R/add_taxa_to_hmmer_tbl.R
R/annotate_with_ncbi.R
R/data.R
R/extract_from_hmmer.R
R/filter_hmmer.R
R/globals.R
R/hmmer_evalues_cleveland_dot_plot.R
R/pairwise_alignment.R
R/parse_fasta_header.R
R/read_hmmer_from_json.R
R/search_hmmscan.R
R/search_hmmsearch.R
R/search_phmmer.R
R/utils-pipe.R
R/utils.R
README.Rmd
README.md
_pkgdown.yml
codecov.yml
data-raw/2abl_phmmer.R
data/hmmscan_2abl.rda
data/phmmer_2abl.rda
docs/404.html
docs/CODE_OF_CONDUCT.html
docs/CONTRIBUTING.html
docs/SUPPORT.html
docs/articles/HMMERutils.html
docs/articles/HMMERutils_files/figure-html/boxplot-1.png
docs/articles/HMMERutils_files/figure-html/e-values-1.png
docs/articles/HMMERutils_files/figure-html/hist-1.png
docs/articles/HMMERutils_files/figure-html/taxa_plot-1.png
docs/articles/HMMERutils_files/figure-html/unnamed-chunk-2-1.png
docs/articles/index.html
docs/authors.html
docs/bootstrap-toc.css
docs/bootstrap-toc.js
docs/docsearch.css
docs/docsearch.js
docs/index.html
docs/link.svg
docs/news/index.html
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/Rplot001.png
docs/reference/add_physicochemical_properties_to_HMMER_tbl.html
docs/reference/add_sequences_to_hmmer_tbl.html
docs/reference/add_taxa_to_hmmer_tbl.html
docs/reference/annotate_with_NCBI_taxid.html
docs/reference/extract_from_hmmer.html
docs/reference/figures/README-e-values-1.png
docs/reference/figures/README-pairwise_arcg-1.png
docs/reference/figures/README-pairwise_ph-1.png
docs/reference/filter_hmmer.html
docs/reference/hmmer_evalues_cleveland_dot_plot-1.png
docs/reference/hmmer_evalues_cleveland_dot_plot.html
docs/reference/hmmscan_2abl.html
docs/reference/index.html
docs/reference/pairwise_alignment_sequence_identity.html
docs/reference/pairwise_sequence_identity_heatmap-1.png
docs/reference/pairwise_sequence_identity_heatmap.html
docs/reference/pairwise_sequence_identity_histogram-1.png
docs/reference/pairwise_sequence_identity_histogram.html
docs/reference/parse_fasta_headers.html
docs/reference/phmmer_2abl.html
docs/reference/pipe.html
docs/reference/read_hmmer_from_json.html
docs/reference/search_hmmscan.html
docs/reference/search_hmmsearch.html
docs/reference/search_phmmer.html
docs/sitemap.xml
inst/CITATION
inst/extdata/alignment.fasta
inst/extdata/phmmer_2abl.xml
man/add_physicochemical_properties_to_HMMER_tbl.Rd
man/add_sequences_to_hmmer_tbl.Rd
man/add_taxa_to_hmmer_tbl.Rd
man/annotate_with_NCBI_taxid.Rd
man/extract_from_hmmer.Rd
man/figures/README-e-values-1.png
man/figures/README-pairwise_arcg-1.png
man/figures/README-pairwise_ph-1.png
man/filter_hmmer.Rd
man/hmmer_evalues_cleveland_dot_plot.Rd
man/hmmscan_2abl.Rd
man/pairwise_alignment_sequence_identity.Rd
man/pairwise_sequence_identity_heatmap.Rd
man/pairwise_sequence_identity_histogram.Rd
man/parse_fasta_headers.Rd
man/phmmer_2abl.Rd
man/pipe.Rd
man/read_hmmer_from_json.Rd
man/search_hmmscan.Rd
man/search_hmmsearch.Rd
man/search_phmmer.Rd
renv.lock
renv/.gitignore
renv/activate.R
renv/settings.dcf
tests/testthat.R
tests/testthat/Rplots.pdf
tests/testthat/_snaps/HMMER.md
tests/testthat/_snaps/extract_from_hmmer.md
tests/testthat/_snaps/filter_hmmer.md
tests/testthat/_snaps/hmmer_evalues_cleveland_dot_plot/a-cleveland-dot-plot.svg
tests/testthat/_snaps/pairwise_aligment.md
tests/testthat/_snaps/pairwise_aligment/base-graphics-heatmap.svg
tests/testthat/_snaps/pairwise_aligment/base-graphics-histogram.svg
tests/testthat/alignment.fasta
tests/testthat/test-HMMER.R
tests/testthat/test-add_properties.R
tests/testthat/test-add_sequences_to_hmmer_tbl.R
tests/testthat/test-add_taxa_to_hmmer_tbl.R
tests/testthat/test-annotate_with_ncbi.r
tests/testthat/test-extract_from_hmmer.R
tests/testthat/test-filter_hmmer.R
tests/testthat/test-hmmer_evalues_cleveland_dot_plot.R
tests/testthat/test-pairwise_aligment.R
tests/testthat/test-parse_fasta_headers.R
tests/testthat/test-search_functions.R
tests/testthat/www.ebi.ac.uk/Tools/hmmer/search/hmmscan-21c435-POST.json
tests/testthat/www.ebi.ac.uk/Tools/hmmer/search/hmmscan-a25689-POST.R
tests/testthat/www.ebi.ac.uk/Tools/hmmer/search/hmmscan-aca693-POST.R
tests/testthat/www.ebi.ac.uk/Tools/hmmer/search/hmmscan-d48b2c-POST.json
tests/testthat/www.ebi.ac.uk/Tools/hmmer/search/hmmsearch-2be88e-POST.json
tests/testthat/www.ebi.ac.uk/Tools/hmmer/search/hmmsearch-438819-POST.R
tests/testthat/www.ebi.ac.uk/Tools/hmmer/search/hmmsearch-a25689-POST.R
tests/testthat/www.ebi.ac.uk/Tools/hmmer/search/hmmsearch-ae7991-POST.json
tests/testthat/www.ebi.ac.uk/Tools/hmmer/search/phmmer-21c435-POST.R
tests/testthat/www.ebi.ac.uk/Tools/hmmer/search/phmmer-8ebe88-POST.json
tests/testthat/www.ebi.ac.uk/Tools/hmmer/search/phmmer-a25689-POST.json
tests/testthat/www.ebi.ac.uk/Tools/hmmer/search/phmmer-fb0fc7-POST.R
vignettes/.gitignore
vignettes/HMMERutils.Rmd
