R: Interface to 'NetMHCIIpan'

# Interface to 'NetMHCIIpan'

## 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