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mhcnuggetsr (version 1.1)

Call MHCnuggets

Description

MHCnuggets () is a Python tool to predict MHC class I and MHC class II epitopes. This package allows one to call MHCnuggets from R.

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Version

Install

install.packages('mhcnuggetsr')

Monthly Downloads

183

Version

1.1

License

GPL-3

Issues

5

Pull Requests

0

Stars

4

Forks

1

Maintainer

Richel Bilderbeek

Last Published

November 4th, 2020

Functions in mhcnuggetsr (1.1)

check_mhcnuggets_installation

Check if MHCnuggets is installed.
check_mhcnuggets_options_names

Check the names of the elements in an mhcnuggets_options list.
default_params_doc

This function does nothing. It is intended to inherit the documentation of the parameters from.
check_mhc_class

Check the MHC class.
get_example_filenames

Get the full path to all MHCnuggets example files
get_mhc_1_haplotypes

Get all the MHC-I haplotypes
install_mhcnuggets

Install the MHCnuggets Python package.
get_trained_mhc_2_haplotypes

Get all the MHC-II haplotypes that have been trained on a model
get_mhcnuggets_version

Get the MHCnuggets version
get_pip_version

Get the version of pip
downgrade_pip

Downgrade pip.
get_mhc_2_haplotypes

Get all the MHC-II haplotypes
mhcnuggetsr

mhcnuggetsr: estimate the topoplogy of membrane proteins
upgrade_pip

Uograde pip.
get_mhcnuggets_url

Get the URL of the MHCnuggets source code
is_on_ci

Determines if the environment is a continuous integration service
set_is_mhcnuggets_installed

Set the MHCnuggets installation state to the desired one
is_on_appveyor

Determines if the environment is AppVeyor
mhcnuggetsr_report

Create a mhcnuggetsr report, to be used when reporting bugs
set_pip_version

Set the version of pip.
uninstall_pip

Install pip.
uninstall_mhcnuggets

Uninstall the MHCnuggets Python package.
get_trained_mhc_1_haplotypes

Get all the MHC-I haplotypes that have been trained on a model
get_python_package_versions

Get the version of all Python packages
install_pip

Install pip.
get_default_mhcnuggets_folder

Get the path to the folder where this package installs MHCnuggets by default
is_pip_installed

Determine if pip is installed
get_example_filename

Get the full path to an MHCnuggets example file
is_on_travis

Determines if the environment is Travis CI
is_mhcnuggets_name

Is this an MHCnuggets name?
is_mhcnuggets_options

Is this a mhcnuggets_options?
is_mhcnuggets_installed

Check if MHCnuggets is installed
to_mhcnuggets_names

Convert one or more standard haplotype name to the MHCnuggets names
to_mhcnuggets_name

Convert a standard haplotype name to the MHCnuggets name
predict_ic50

Predict the IC50 for peptides.
mhcnuggetsr_self_test

Self-test the package
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)
predict_ic50s

Predict the half maximal inhibitory concentrations (aka IC50s) (in nM) of all possible n-mers within a peptide
are_mhcnuggets_names

Are these MHCnuggets names?
create_temp_peptides_path

Create a path to a non-existing temporary file
create_mhcnuggets_options

Create a set of MHCnuggets options.
create_test_mhcnuggets_options

Create testing options for MHCnuggets
check_mhcnuggets_options

Check the MHCnuggets options.