Files in currocam/taxa2hmmer
Get more out of homologous sequence search with HMMER
.Rbuildignore
.github/.gitignore
.github/CODE_OF_CONDUCT.md
.github/CONTRIBUTING.md
.github/ISSUE_TEMPLATE/issue_template.md
.github/SUPPORT.md
.github/workflows/R-CMD-check.yaml
.github/workflows/pkgdown.yaml
.gitignore
DESCRIPTION
LICENSE
LICENSE.md
NAMESPACE
R/annotate_with_NCBI_taxid.R
R/calculate_physicochemical_properties.R
R/compat-purrr.R
R/extract_from_HMMER_data_tbl.R
R/pairwise_alignment_sequence_identity.R
R/read_hmmer_from_xml.R
R/search_hmmscan.R
R/search_hmmsearch.R
R/search_jackhmmer.R
R/search_phmmer.R
R/utils-pipe.R
R/utilsHMMER-package.R
R/utils_hmmer.R
R/visualize_MSA_using_ggmsa.R
README.Rmd
README.md
_pkgdown.yml
codecov.yml
cran-comments.md
inst/extdata/HMMER_data_tbl_Sars_CoV.Rds
inst/extdata/spike_pairwise_identities.RDS
man/annotate_with_NCBI_taxid.Rd
man/calculate_physicochemical_properties.Rd
man/extract_from_HMMER_data_tbl.Rd
man/figures/README-unnamed-chunk-4-1.png
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-stable.svg
man/figures/lifecycle-superseded.svg
man/pairwise_alignment_sequence_identity.Rd
man/pipe.Rd
man/read_hmmer_from_xml.Rd
man/search_hmmscan.Rd
man/search_hmmsearch.Rd
man/search_jackhmmer.Rd
man/search_phmmer.Rd
man/utilsHMMER-package.Rd
man/visualize_MSA_using_ggmsa.Rd
tests/testthat.R
tests/testthat/_snaps/calculate_physicochemical_properties/properties.csv
tests/testthat/_snaps/extract_from_HMMER_data_tbl.md
tests/testthat/_snaps/extract_from_HMMER_data_tbl/a-sig-geom-segment.svg
tests/testthat/_snaps/extract_from_HMMER_data_tbl/phmmer_tidy_tbl.csv
tests/testthat/_snaps/extract_from_HMMER_data_tbl/phmmer_tidy_tbl_afa.csv
tests/testthat/_snaps/extract_from_HMMER_data_tbl/phmmer_tidy_tbl_filtered.csv
tests/testthat/_snaps/extract_from_HMMER_data_tbl/tidy_tbl_properties.csv
tests/testthat/_snaps/pairwise_alignment_sequence_identity.md
tests/testthat/_snaps/pairwise_alignment_sequence_identity/a-pairwise-annotated.svg
tests/testthat/_snaps/pairwise_alignment_sequence_identity/a-pairwise-heatmap.svg
tests/testthat/_snaps/pairwise_alignment_sequence_identity/a-pairwise-histogram.svg
tests/testthat/_snaps/visualize_MSA_using_ggmsa/a-msa.svg
tests/testthat/alignment.aln
tests/testthat/fasta.fa
tests/testthat/hmmscan_example.xml
tests/testthat/phmmer_example.afa
tests/testthat/phmmer_example.fa
tests/testthat/phmmer_example.xml
tests/testthat/phmmer_tidy_tbl.csv
tests/testthat/phmmer_tidy_tbl_afa.csv
tests/testthat/phmmer_tidy_tbl_filtered.csv
tests/testthat/properties.csv
tests/testthat/test-annotate_with_NCBI_taxid.R
tests/testthat/test-calculate_physicochemical_properties.R
tests/testthat/test-extract_from_HMMER_data_tbl.R
tests/testthat/test-pairwise_alignment_sequence_identity.R
tests/testthat/test-read_hmmer_from_xml.R
tests/testthat/test-search_hmmscan.R
tests/testthat/test-search_hmmsearch.R
tests/testthat/test-search_jackhmmer.R
tests/testthat/test-search_phmmer.R
tests/testthat/test-visualize_MSA_using_ggmsa.R
tests/testthat/tidy_tbl_properties.csv
utilsHMMER.Rproj
vignettes/.gitignore
vignettes/sars_cov.Rmd
