{ "_id": "6a10812aacfb0bcc41caeac8", "Package": "pureseqtmr", "Title": "Predict Transmembrane Protein Topology", "Version": "1.4", "Authors@R": "c(\nperson(\"Richèl J.C.\", \"Bilderbeek\", email = \"richel@richelbilderbeek.nl\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-1107-7049\")))", "Description": "Proteins reside in either the cell plasma or in the cell\nmembrane. A membrane protein goes through the membrane at least\nonce. Given the amino acid sequence of a membrane protein, the\ntool 'PureseqTM'\n(, as described\nin \"Efficient And Accurate Prediction Of Transmembrane Topology\nFrom Amino acid sequence only.\", Wang, Qing, et al (2019),\n), can predict the topology of a membrane\nprotein. This package allows one to use 'PureseqTM' from R.", "License": "GPL-3", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.2.3", "URL": "https://github.com/richelbilderbeek/pureseqtmr/", "BugReports": "https://github.com/richelbilderbeek/pureseqtmr/", "VignetteBuilder": "knitr", "SystemRequirements": "PureseqTM\n(https://github.com/PureseqTM/pureseqTM_package)", "Config/pak/sysreqs": "cmake libfontconfig1-dev libfreetype6-dev\nlibfribidi-dev git make libharfbuzz-dev libgit2-dev libicu-dev\nlibjpeg-dev libpng-dev libtiff-dev libuv1-dev libwebp-dev\nlibxml2-dev libssl-dev libx11-dev zlib1g-dev", "Repository": "https://richelbilderbeek.r-universe.dev", "Date/Publication": "2023-04-06 13:18:33 UTC", "RemoteUrl": "https://github.com/richelbilderbeek/pureseqtmr", "RemoteRef": "HEAD", "RemoteSha": "106ebe69748ee0637551326c43adcbfd35a3dafc", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-06 06:05:01 UTC", "User": "root" }, "Author": "Richèl J.C. 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Throws a helpful error message if incomplete, else does nothing", "topics": [ "check_pureseqtm_installation" ] }, { "page": "check_topology", "title": "Check if the topology is valid.", "topics": [ "check_topology" ] }, { "page": "check_topology_str", "title": "Check if the topology string is valid. Will stop if not.", "topics": [ "check_topology_str" ] }, { "page": "convert_tmhmm_to_pureseqtm_topology", "title": "Convert a TMHMM topology to a PureseqTM topology", "topics": [ "convert_tmhmm_to_pureseqtm_topology" ] }, { "page": "count_n_tmhs", "title": "Count the number of TMHs in a topology", "topics": [ "count_n_tmhs" ] }, { "page": "create_pureseqtm_files", "title": "Create the five PureseqTM output files, by running PureseqTM.", "topics": [ "create_pureseqtm_files" ] }, { "page": "create_pureseqtm_proteome_file", "title": "Create the output file of a PureseqTM proteome run", "topics": [ "create_pureseqtm_proteome_file" ] }, { "page": "default_params_doc", "title": "This function does nothing. It is intended to inherit is parameters' documentation.", "topics": [ "default_params_doc" ] }, { "page": "get_default_pureseqtm_folder", "title": "Get the path to the folder where this package installs PureseqTM by default", "topics": [ "get_default_pureseqtm_folder" ] }, { "page": "get_example_filename", "title": "Get the full path to a PureseqTM example file.", "topics": [ "get_example_filename" ] }, { "page": "get_example_filenames", "title": "Get the full path to all PureseqTM example files", "topics": [ "get_example_filenames" ] }, { "page": "get_pureseqtm_url", "title": "Get the URL of the PureseqTM source code", "topics": [ "get_pureseqtm_url" ] }, { "page": "get_pureseqtm_version", "title": "Get the PureseqTM version", "topics": [ "get_pureseqtm_version" ] }, { "page": "install_pureseqtm", "title": "Install PureseqTM to a local folder", "topics": [ "install_pureseqtm" ] }, { "page": "is_on_appveyor", "title": "Determines if the environment is AppVeyor", "topics": [ "is_on_appveyor" ] }, { "page": "is_on_ci", "title": "Determines if the environment is a continuous integration service", "topics": [ "is_on_ci" ] }, { "page": "is_on_github_actions", "title": "Determines if the environment is GitHub Actions", "topics": [ "is_on_github_actions" ] }, { "page": "is_on_travis", "title": "Determines if the environment is Travis CI", "topics": [ "is_on_travis" ] }, { "page": "is_protein_name_line", "title": "Is the line of text the name of a protein, as used within a FASTA filename?", "topics": [ "is_protein_name_line" ] }, { "page": "is_pureseqtm_installed", "title": "Measure if PureseqTM is installed locally", "topics": [ "is_pureseqtm_installed" ] }, { "page": "is_tmh", "title": "Determine if the protein sequence contains at least one transmembrane helix.", "topics": [ "is_tmh" ] }, { "page": "is_topology_line", "title": "Is the line of text the topology, as used within a FASTA filename?", "topics": [ "is_topology_line" ] }, { "page": "is_valid_protein_sequence", "title": "Determine if this a valid protein sequence", "topics": [ "is_valid_protein_sequence" ] }, { "page": "load_fasta_file_as_tibble", "title": "Parse a FASTA file to a table with a 'name' and 'sequence' column", "topics": [ "load_fasta_file_as_tibble" ] }, { "page": "load_fasta_file_as_tibble_cpp", "title": "Parse a FASTA file to a table with a 'name' and 'sequence' column", "topics": [ "load_fasta_file_as_tibble_cpp" ] }, { "page": "load_fasta_file_as_tibble_cpp_raw", "title": "Use Rcpp to load a FASTA file", "topics": [ "load_fasta_file_as_tibble_cpp_raw" ] }, { "page": "load_fasta_file_as_tibble_r", "title": "Parse a FASTA file to a table with a 'name' and 'sequence' column", "topics": [ "load_fasta_file_as_tibble_r" ] }, { "page": "load_topology_file_as_tibble", "title": "Parse a topology ('.topo') file to a table with a 'name' and 'topology' column", "topics": [ "load_topology_file_as_tibble" ] }, { "page": "mock_predict_topologies_from_sequences", "title": "Do a mock prediction directy on a protein sequence, as can be useful in testing Use predict_topologies_from_sequences for doing a real prediction.", "topics": [ "mock_predict_topologies_from_sequences" ] }, { "page": "mock_predict_topology", "title": "Do a mock prediction of the topology of proteins", "topics": [ "mock_predict_topology" ] }, { "page": "parse_pureseqtm_proteome_text", "title": "Parse the output of a call to 'PureseqTM_proteome.sh'", "topics": [ "parse_pureseqtm_proteome_text" ] }, { "page": "plot_topology", "title": "Plot the topology", "topics": [ "plot_topology" ] }, { "page": "predict_topologies_from_sequences", "title": "Run PureseqTM directy on a protein sequence", "topics": [ "predict_topologies_from_sequences" ] }, { "page": "predict_topology", "title": "Predict the topology of proteins from file", "topics": [ "predict_topology" ] }, { "page": "predict_topology_from_sequence", "title": "Run PureseqTM directy on 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