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netmhc2pan (version 1.3.2)

Interface to 'NetMHCIIpan'

Description

The field of immunology benefits from software that can predict which peptide sequences trigger an immune response. 'NetMHCIIpan' is a such a tool: it predicts the binding strength of a short peptide to a Major Histocompatibility Complex class II (MHC-II) molecule. 'NetMHCIIpan' can be used from a web server at or from the command-line, using a local installation. This package allows to call 'NetMHCIIpan' from R.

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Version

Install

install.packages('netmhc2pan')

Monthly Downloads

140

Version

1.3.2

License

GPL-3

Issues

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Repository

https://github.com/richelbilderbeek/netmhc2pan/

Maintainer

Richel Bilderbeek

Last Published

November 8th, 2023

Functions in netmhc2pan (1.3.2)

get_default_netmhc2pan_bin_tarfile_path

Get the default path for the NetMHCIIpan binary tarball file

install_netmhc2pan

Install NetMHCIIpan

Determines if the environment is AppVeyor

get_default_netmhc2pan_bin_path

Get the full path to the default NetMHC2pan binary

is_tcsh_installed

See if tcsh is installed

Is the download URL valid?

install_netmhc2pan_from_files

Install NetMHCIIpan from files.

Determines if the environment is a continuous integration service

download_netmhc2pan_bin

Download the NetMHCIIpan binary

is_netmhc2pan_bin_installed

Measure if NetMHCIIpan binary is installed locally

Predict the IC50s from a sequence

read_netmhc2pan_xls_output

Read MHC2pan output

get_netmhc2pan_alleles

Get a list of the alleles supported by NetMHCIIpan

uninstall_netmhc2pan

Uninstall NetMHCIIpan

install_netmhc2pan_bin

Install the NetMHCIIpan binary to a local folder

is_netmhc2pan_installed

Measure if NetMHCIIpan is installed locally

get_netmhc2pan_archive_filename

Get the filename of the NetMHC2pan archive file

to_netmhc2pan_name

Convert a formal haplotype name to its NetMHC2pan notation

install_netmhc2pan_bin_from_file

Install the NetMHCIIpan binary to a local folder

is_netmhc2pan_set_up

Measure if NetMHCIIpan is set up

netmhc2pan: predict peptide binding strengths using NetMHC2pan

install_netmhc2pan_data

Install the NetMHCIIpan data to a local folder

is_on_github_actions

Determines if the environment is GitHub Actions

install_netmhc2pan_data_from_file

Install the NetMHCIIpan data from file

Predict the IC50 for peptides.

Run NetMHCIIpan

netmhc2pan_report

Show a netmhc2pan report using message, to be used when reporting bugs

Determines if the environment is Travis CI

netmhc2pan_self_test

Test NetMHCIIpan by doing a minimal run.

set_up_netmhc2pan

Install the NetMHCIIpan binary to a local folder

check_netmhc2pan_installation

Checks the installation of NetMHCIIpan.

check_fasta_file_sequence_lengths

Check the lengths of the sequences in a FASTA file

create_temp_xls_filename

Create a .xls file

check_netmhc2pan_bin_url

Check the URL of the NetMHCIIpan binary tarball

capitalize_first_char

Convert the first character to upper case.

check_can_create_file

Check that a file can be created at a certain path.

Check the allele names

check_netmhc2pan_data_url

Check the URL of the NetMHCIIpan binary tarball

create_temp_fasta_filename

Create a .fasta file

default_params_doc

This function does nothing. It is intended to inherit is parameters' documentation.

get_default_netmhc2pan_folder

Get the path to the folder where this package installs NetMHCIIpan by default

is_netmhc2pan_data_installed

Measure if NetMHCIIpan data folder is installed locally

get_netmhc2pan_bin_url

Get the NetMHCIIpan binary download URL.

get_netmhc2pan_url

Deprecated, use get_netmhc2pan_bin_url instead

get_netmhc2pan_data_url

Get the NetMHCIIpan data tarball URL.

get_default_netmhc2pan_version

Get the default NetMHC2pan version used

get_default_netmhc2pan_subfolder

Get the full path to the NetMHC2pan sub-folder

is_netmhc2pan_haplotype

Is the haplotype valid?