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 |