Man pages for pureseqtmr
Predict Transmembrane Protein Topology
| are_tmhs | Are the sequences transmembrance helices? |
| are_valid_protein_sequences | Determine if these are all valid protein sequences |
| calc_distance_to_tmh_center_from_topology | Calculate the the distance for each amino acid to the center... |
| calc_distance_to_tmh_center_from_topology_str | Calculate the the distance for each amino acid to the center... |
| calc_distance_to_tmh_center_from_topology_str_cpp_stl | Use Rcpp to calculate the distance to a TMH center |
| check_protein_sequence | Check one protein sequence |
| check_protein_sequences | Check one or more protein sequences |
| check_pureseqtm_installation | Checks the installation of PureseqTM. Throws a helpful error... |
| check_topology | Check if the topology is valid. |
| check_topology_str | Check if the topology string is valid. Will stop if not. |
| convert_tmhmm_to_pureseqtm_topology | Convert a TMHMM topology to a PureseqTM topology |
| count_n_tmhs | Count the number of TMHs in a topology |
| create_pureseqtm_files | Create the five PureseqTM output files, by running PureseqTM. |
| create_pureseqtm_proteome_file | Create the output file of a PureseqTM proteome run |
| default_params_doc | This function does nothing. It is intended to inherit is... |
| get_default_pureseqtm_folder | Get the path to the folder where this package installs... |
| get_example_filename | Get the full path to a PureseqTM example file. |
| get_example_filenames | Get the full path to all PureseqTM example files |
| get_pureseqtm_url | Get the URL of the PureseqTM source code |
| get_pureseqtm_version | Get the PureseqTM version |
| install_pureseqtm | Install PureseqTM to a local folder |
| is_on_appveyor | Determines if the environment is AppVeyor |
| is_on_ci | Determines if the environment is a continuous integration... |
| is_on_github_actions | Determines if the environment is GitHub Actions |
| is_on_travis | Determines if the environment is Travis CI |
| is_protein_name_line | Is the line of text the name of a protein, as used within a... |
| is_pureseqtm_installed | Measure if PureseqTM is installed locally |
| is_tmh | Determine if the protein sequence contains at least one... |
| is_topology_line | Is the line of text the topology, as used within a FASTA... |
| is_valid_protein_sequence | Determine if this a valid protein sequence |
| load_fasta_file_as_tibble | Parse a FASTA file to a table with a 'name' and 'sequence'... |
| load_fasta_file_as_tibble_cpp | Parse a FASTA file to a table with a 'name' and 'sequence'... |
| load_fasta_file_as_tibble_cpp_raw | Use Rcpp to load a FASTA file |
| load_fasta_file_as_tibble_r | Parse a FASTA file to a table with a 'name' and 'sequence'... |
| load_topology_file_as_tibble | Parse a topology ('.topo') file to a table with a 'name' and... |
| mock_predict_topologies_from_sequences | Do a mock prediction directy on a protein sequence, as can be... |
| mock_predict_topology | Do a mock prediction of the topology of proteins |
| parse_pureseqtm_proteome_text | Parse the output of a call to 'PureseqTM_proteome.sh' |
| plot_topology | Plot the topology |
| predict_topologies_from_sequences | Run PureseqTM directy on a protein sequence |
| predict_topology | Predict the topology of proteins from file |
| predict_topology_from_sequence | Run PureseqTM directy on a protein sequence |
| pureseqtmr | pureseqtmr: estimate the topoplogy of membrane proteins |
| pureseqtmr_report | Create a pureseqtmr report, to be used when reporting bugs |
| run_pureseqtm_proteome | Run PureseqTM on a proteome |
| save_tibble_as_fasta_file | Save the first two columns of a tibble as a FASTA file |
| tally_tmhs | Count the number of transmembrane helices in a topology |
| uninstall_pureseqtm | Uninstall PureseqTM |
