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 |
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 |