Files in currocam/toolkit4pySCA
A set of useful functions for performing an Statistical Coupling Analysis from scratch in R and using pySCA

.Rbuildignore

.github/.gitignore

.github/workflows/R-CMD-check.yaml

.gitignore

DESCRIPTION

LICENSE

NAMESPACE

R/SCA_correlation_matrix_data.R R/SCA_positional_coevolution_matrix_components_data.R R/SCA_positional_coevolution_matrix_eigenvalues_data.R R/data.R R/data_pySCA.R R/download_tax_from_ncbi.R R/extract_tidy_df_from_hmmer.R R/extract_tidy_domains_from_xml.R R/extract_tidy_hits_from_xml.R R/extract_tidy_stats_from_xml.R R/global_similarity_matrix_data.R R/import_pySCA_module_using_reticulate.R R/pairwise_sequence_identities_data.R R/position_specific_conservation_data.R R/post_request_to_phmer.R R/quick_AA_search_using_phmmer.R R/read_pySCA_pickle.R R/sequence_correlation_matrix_projections_data.R R/utils-pipe.R R/write_sectors_for_pymol.R README.Rmd README.md data-raw/HBG2_HUMAN.R

data/phmmer_HBG2_HUMAN.rda

data/pySCA_HBG2_HUMAN.rda

inst/extdata/HBG2_HUMAN.ClustalW.aln

inst/python/pysca/__init__.py

inst/python/pysca/scaTools.py

inst/python/pysca/settings.py

man/SCA_correlation_matrix_data.Rd man/SCA_positional_coevolution_matrix_components_data.Rd man/SCA_positional_coevolution_matrix_eigenvalues_data.Rd man/download_tax_from_ncbi.Rd man/eigenspectrum_SCA_positional_coevolution_matrix_plot.Rd man/extract_tidy_df_from_hmmer.Rd man/extract_tidy_domains_from_xml.Rd man/extract_tidy_hits_from_xml.Rd man/extract_tidy_stats_from_xml.Rd

man/figures/README-hist_ph_desc_hmmer-1.png

man/figures/README-unnamed-chunk-10-1.png

man/figures/README-unnamed-chunk-11-1.png

man/figures/README-unnamed-chunk-12-1.png

man/figures/README-unnamed-chunk-13-1.png

man/figures/README-unnamed-chunk-14-1.png

man/figures/README-unnamed-chunk-2-1.png

man/global_similarity_matrix_data.Rd man/global_similarity_matrix_heatmap.Rd man/import_pySCA_module_using_reticulate.Rd man/pairwise_sequence_identities_data.Rd man/pairwise_sequence_identities_hist.Rd man/phmmer_HBG2_HUMAN.Rd man/pipe.Rd man/position_specific_conservation_data.Rd man/position_specific_conservation_plot.Rd man/post_request_to_phmer.Rd man/pySCA_HBG2_HUMAN.Rd man/quick_AA_search_using_phmmer.Rd man/read_pySCA_pickle.Rd man/sequence_correlation_matrix_projections_data.Rd man/sequence_correlation_matrix_projections_plot.Rd man/write_sectors_for_pymol.Rd tests/testthat.R

tests/testthat/2abl_A_pdb.xml

tests/testthat/2abl_A_swissprot.xml

tests/testthat/test-SCA_correlation_matrix_data.R tests/testthat/test-SCA_positional_coevolution_matrix_components_data.R tests/testthat/test-SCA_positional_coevolution_matrix_eigenvalues_data.R tests/testthat/test-download_tax_from_ncbi.R tests/testthat/test-extract_tidy_df_from_hmmer.R tests/testthat/test-extract_tidy_domains_from_xml.R tests/testthat/test-extract_tidy_hits_from_xml.R tests/testthat/test-extract_tidy_stats_from_xml.R tests/testthat/test-global_similarity_matrix_data.R tests/testthat/test-import_pySCA_module_using_reticulate.R tests/testthat/test-pairwise_sequence_identities_data.R tests/testthat/test-position_specific_conservation_data.R tests/testthat/test-post_request_to_phmer.R tests/testthat/test-quick_AA_search_using_phmmer.R tests/testthat/test-sequence_correlation_matrix_projections_data.R

toolkit4pySCA.Rproj

currocam/toolkit4pySCA documentation built on April 7, 2022, 8:17 p.m.

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