Package: netmhc2pan 1.3.3

netmhc2pan: Interface to 'NetMHCIIpan'

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 <https://services.healthtech.dtu.dk/services/NetMHCIIpan-3.2/> or from the command-line, using a local installation. This package allows to call 'NetMHCIIpan' from R.

Authors:Richèl J.C. Bilderbeek [aut, cre], Lue Ping Zhao [ctb], Byungkuk Min [ctb]

netmhc2pan_1.3.3.tar.gz
netmhc2pan_1.3.3.zip(r-4.7)netmhc2pan_1.3.3.zip(r-4.6)netmhc2pan_1.3.3.zip(r-4.5)
netmhc2pan_1.3.3.tgz(r-4.6-any)netmhc2pan_1.3.3.tgz(r-4.5-any)
netmhc2pan_1.3.3.tar.gz(r-4.7-any)netmhc2pan_1.3.3.tar.gz(r-4.6-any)
netmhc2pan_1.3.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
netmhc2pan/json (API)

# Install 'netmhc2pan' in R:

install.packages('netmhc2pan', repos = c('https://richelbilderbeek.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/richelbilderbeek/netmhc2pan/issues

On CRAN:

4.00 score 2 stars 9 scripts 224 downloads 46 exports 41 dependencies

Last updated from:620be78c23. Checks:5 ERROR, 4 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	ERROR	128
source / vignettes	OK	190
linux-release-x86_64	ERROR	188
macos-release-arm64	OK	134
macos-oldrel-arm64	OK	85
windows-devel	ERROR	80
windows-release	ERROR	96
windows-oldrel	ERROR	89
wasm-release	OK	112

Exports:capitalize_first_char check_alleles check_can_create_file check_fasta_file_sequence_lengths check_netmhc2pan_bin_url check_netmhc2pan_data_url check_netmhc2pan_installation create_temp_fasta_filename create_temp_xls_filename download_netmhc2pan_bin get_default_netmhc2pan_bin_path get_default_netmhc2pan_bin_tarfile_path get_default_netmhc2pan_folder get_default_netmhc2pan_subfolder get_default_netmhc2pan_version get_netmhc2pan_alleles get_netmhc2pan_archive_filename get_netmhc2pan_bin_url get_netmhc2pan_data_url get_netmhc2pan_url install_netmhc2pan install_netmhc2pan_bin install_netmhc2pan_bin_from_file install_netmhc2pan_data install_netmhc2pan_data_from_file install_netmhc2pan_from_files is_netmhc2pan_bin_installed is_netmhc2pan_data_installed is_netmhc2pan_haplotype is_netmhc2pan_installed is_netmhc2pan_set_up is_on_appveyor is_on_ci is_on_github_actions is_on_travis is_tcsh_installed is_url_valid netmhc2pan_report netmhc2pan_self_test predict_ic50 predict_ic50s read_netmhc2pan_xls_output run_netmhc2pan set_up_netmhc2pan to_netmhc2pan_name uninstall_netmhc2pan

Dependencies:ade4 bit bit64 cli clipr cpp11 crayon dplyr generics glue hms lattice lifecycle magrittr MASS nlme pillar pixmap pkgconfig prettyunits progress R6 rappdirs Rcpp RcppArmadillo readr rlang segmented seqinr sessioninfo sp stringi stringr testit tibble tidyselect tzdb utf8 vctrs vroom withr

Binding strength prediction

Rendered fromdemo.Rmdusingknitr::rmarkdown

Last update: 2023-11-07
Started: 2018-12-28

Citation

Development and contributors

Readme and manuals

Help Manual

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