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 of the TMH
calc_distance_to_tmh_center_from_topology_str
                        Calculate the the distance for each amino acid
                        to the center of the TMH
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 message if incomplete, else does
                        nothing
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 parameters' documentation.
get_default_pureseqtm_folder
                        Get the path to the folder where this package
                        installs PureseqTM by default
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 service
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 FASTA filename?
is_pureseqtm_installed
                        Measure if PureseqTM is installed locally
is_tmh                  Determine if the protein sequence contains at
                        least one transmembrane helix.
is_topology_line        Is the line of text the topology, as used
                        within a FASTA filename?
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' column
load_fasta_file_as_tibble_cpp
                        Parse a FASTA file to a table with a 'name' and
                        'sequence' column
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' column
load_topology_file_as_tibble
                        Parse a topology ('.topo') file to a table with
                        a 'name' and 'topology' column
mock_predict_topologies_from_sequences
                        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.
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_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
