Man pages for richelbilderbeek/tmhmm
Interface to TMHMM
| are_tmhs | Are the sequences TMHs? |
| are_topology_sequences | Are all the one or more topology sequences valid? |
| check_tmhmm_installation | Checks the installation of TMHMM. Throws a helpful error... |
| check_topology | Check if the topology is valid. |
| default_params_doc | This function does nothing. It is intended to inherit is... |
| fasta_text_to_tibble | Convert FASTA text to a tibble |
| get_default_tmhmm_bin_path | Get the default path to the TMHMM binary |
| get_default_tmhmm_folder | Get the path to the folder where this package installs TMHMM... |
| get_tmhmm_url | Get an URL to download TMHMM from. These URLs expire. |
| install_tmhmm | Install NetMHC2pan to a local folder |
| install_tmhmm_bin | Install the NetMHC2pan binary to a local folder |
| is_locatome_line | Is the topology sequence valid? |
| 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_tmh | Determine if the protein sequence contains at least one TMH. |
| is_tmhmm_bin_installed | Measure if TMHMM binary is installed locally |
| is_tmhmm_installed | Measure if TMHMM is installed locally |
| is_tmhmm_result | Is the text a TMHMM result text? |
| is_tmhmm_set_up | Determine if TMHMM is set up |
| is_topology_sequence | Is the topology sequence valid? |
| is_topology_text | Is the text a topology text? |
| is_url_valid | Is the download URL valid? |
| locatome_to_df | Convert a multi-line locatome to a tidy data frame |
| mock_predict_topology_from_sequence | Mock the topology prediction. |
| mock_run_tmhmm | Mock run_tmhmm |
| mock_run_tmhmm_to_file | Mock run_tmhmm_to_file |
| parse_fasta_file | Parse a FASTA file to a table with a 'name' and 'sequence'... |
| plot_locatome | Plot the topology from text |
| plot_topology | Plot the topology |
| plot_topology_text | Plot the topology from text |
| predict_topologies_from_sequences | Run TMHMM directy on a protein sequence |
| predict_topology | Predict the topology of a membrane protein |
| predict_topology_from_sequence | Run TMHMM directy on a protein sequence |
| run_tmhmm | Run TMHMM on a FASTA file with one or more proteins. |
| run_tmhmm_on_one_protein_fasta_file | Run TMHMM on a FASTA file with one protein |
| run_tmhmm_on_sequence | Run TMHMM directy on a protein sequence |
| run_tmhmm_to_file | Creates a FASTA-like file, that has the locations of the... |
| set_up_tmhmm | Set up TMHMM |
| tally_locatome | Tally each location in a locatome |
| tally_tmhs | Count the number of transmembrane helices in a topology |
| tmhmm | tmhmm: estimate the topoplogy of membrane proteins |
| tmhmm_self_test | Self-test the TMHMM installation |
| uninstall_tmhmm | Uninstall TMHMM |
