Interface to 'NetMHCIIpan'

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Documentation for package ‘netmhc2pan’ version 1.3.2

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

Help Pages

capitalize_first_char	Convert the first character to upper case.
check_alleles	Check the allele names
check_can_create_file	Check that a file can be created at a certain path.
check_fasta_file_sequence_lengths	Check the lengths of the sequences in a FASTA file
check_netmhc2pan_bin_url	Check the URL of the NetMHCIIpan binary tarball
check_netmhc2pan_data_url	Check the URL of the NetMHCIIpan binary tarball
check_netmhc2pan_installation	Checks the installation of NetMHCIIpan.
create_temp_fasta_filename	Create a '.fasta' file
create_temp_xls_filename	Create a '.xls' file
default_params_doc	This function does nothing. It is intended to inherit is parameters' documentation.
download_netmhc2pan_bin	Download the NetMHCIIpan binary
get_default_netmhc2pan_bin_path	Get the full path to the default NetMHC2pan binary
get_default_netmhc2pan_bin_tarfile_path	Get the default path for the NetMHCIIpan binary tarball file
get_default_netmhc2pan_folder	Get the path to the folder where this package installs NetMHCIIpan by default
get_default_netmhc2pan_subfolder	Get the full path to the NetMHC2pan sub-folder
get_default_netmhc2pan_version	Get the default NetMHC2pan version used
get_netmhc2pan_alleles	Get a list of the alleles supported by NetMHCIIpan
get_netmhc2pan_archive_filename	Get the filename of the NetMHC2pan archive file
get_netmhc2pan_bin_url	Get the NetMHCIIpan binary download URL.
get_netmhc2pan_data_url	Get the NetMHCIIpan data tarball URL.
get_netmhc2pan_url	Deprecated, use get_netmhc2pan_bin_url instead
install_netmhc2pan	Install NetMHCIIpan
install_netmhc2pan_bin	Install the NetMHCIIpan binary to a local folder
install_netmhc2pan_bin_from_file	Install the NetMHCIIpan binary to a local folder
install_netmhc2pan_data	Install the NetMHCIIpan data to a local folder
install_netmhc2pan_data_from_file	Install the NetMHCIIpan data from file
install_netmhc2pan_from_files	Install NetMHCIIpan from files.
is_netmhc2pan_bin_installed	Measure if NetMHCIIpan binary is installed locally
is_netmhc2pan_data_installed	Measure if NetMHCIIpan data folder is installed locally
is_netmhc2pan_haplotype	Is the haplotype valid?
is_netmhc2pan_installed	Measure if NetMHCIIpan is installed locally
is_netmhc2pan_set_up	Measure if NetMHCIIpan is set up
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_tcsh_installed	See if tcsh is installed
is_url_valid	Is the download URL valid?
netmhc2pan	netmhc2pan: predict peptide binding strengths using NetMHC2pan
netmhc2pan_report	Show a 'netmhc2pan' report using message, to be used when reporting bugs
netmhc2pan_self_test	Test NetMHCIIpan by doing a minimal run.
predict_ic50	Predict the IC50 for peptides.
predict_ic50s	Predict the IC50s from a sequence
read_netmhc2pan_xls_output	Read MHC2pan output
run_netmhc2pan	Run NetMHCIIpan
set_up_netmhc2pan	Install the NetMHCIIpan binary to a local folder
to_netmhc2pan_name	Convert a formal haplotype name to its NetMHC2pan notation
uninstall_netmhc2pan	Uninstall NetMHCIIpan