are_mhcnuggets_names |
Are these MHCnuggets names? |
check_mhcnuggets_installation |
Check if MHCnuggets is installed. |
check_mhcnuggets_options |
Check the MHCnuggets options. |
check_mhcnuggets_options_names |
Check the names of the elements in an 'mhcnuggets_options' list. |
check_mhc_class |
Check the MHC class. |
create_mhcnuggets_options |
Create a set of MHCnuggets options. |
create_temp_peptides_path |
Create a path to a non-existing temporary file |
create_test_mhcnuggets_options |
Create testing options for MHCnuggets |
default_params_doc |
This function does nothing. It is intended to inherit the documentation of the parameters from. |
downgrade_pip |
Downgrade pip. |
get_default_mhcnuggets_folder |
Get the path to the folder where this package installs MHCnuggets by default |
get_example_filename |
Get the full path to an MHCnuggets example file |
get_example_filenames |
Get the full path to all MHCnuggets example files |
get_mhcnuggets_url |
Get the URL of the MHCnuggets source code |
get_mhcnuggets_version |
Get the MHCnuggets version |
get_mhc_1_haplotypes |
Get all the MHC-I haplotypes |
get_mhc_2_haplotypes |
Get all the MHC-II haplotypes |
get_pip_version |
Get the version of pip |
get_python_package_versions |
Get the version of all Python packages |
get_trained_mhc_1_haplotypes |
Get all the MHC-I haplotypes that have been trained on a model |
get_trained_mhc_2_haplotypes |
Get all the MHC-II haplotypes that have been trained on a model |
install_mhcnuggets |
Install the 'MHCnuggets' 'Python' package. |
install_pip |
Install pip. |
is_mhcnuggets_installed |
Check if MHCnuggets is installed |
is_mhcnuggets_name |
Is this an MHCnuggets name? |
is_mhcnuggets_options |
Is this a 'mhcnuggets_options'? |
is_on_appveyor |
Determines if the environment is AppVeyor |
is_on_ci |
Determines if the environment is a continuous integration service |
is_on_travis |
Determines if the environment is Travis CI |
is_pip_installed |
Determine if pip is installed |
mhcnuggetsr |
mhcnuggetsr: estimate the topoplogy of membrane proteins |
mhcnuggetsr_report |
Create a mhcnuggetsr report, to be used when reporting bugs |
mhcnuggetsr_self_test |
Self-test the package |
predict_ic50 |
Predict the IC50 for peptides. |
predict_ic50s |
Predict the half maximal inhibitory concentrations (aka IC50s) (in nM) of all possible n-mers within a peptide |
predict_ic50_from_file |
Predict the half maximal inhibitory concentration (aka IC50) (in nM) for one or more peptides as saved in a file. Each peptide must be 15 amino acids at most (use predict_ic50s to predict the IC50s for longer peptides) |
set_is_mhcnuggets_installed |
Set the MHCnuggets installation state to the desired one |
set_pip_version |
Set the version of pip. |
to_mhcnuggets_name |
Convert a standard haplotype name to the MHCnuggets name |
to_mhcnuggets_names |
Convert one or more standard haplotype name to the MHCnuggets names |
uninstall_mhcnuggets |
Uninstall the MHCnuggets Python package. |
uninstall_pip |
Install pip. |
upgrade_pip |
Uograde pip. |