Call MHCnuggets

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Documentation for package ‘mhcnuggetsr’ version 1.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

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.