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-4.5)netmhc2pan_1.3.3.zip(r-4.4)netmhc2pan_1.3.3.zip(r-4.3)
netmhc2pan_1.3.3.tgz(r-4.4-any)netmhc2pan_1.3.3.tgz(r-4.3-any)
netmhc2pan_1.3.3.tar.gz(r-4.5-noble)netmhc2pan_1.3.3.tar.gz(r-4.4-noble)
netmhc2pan_1.3.3.tgz(r-4.4-emscripten)netmhc2pan_1.3.3.tgz(r-4.3-emscripten)
netmhc2pan.pdf |netmhc2pan.html✨
netmhc2pan/json (API)

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

Peer review:

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

On CRAN:

4.00 score 1 stars 8 scripts 187 downloads 46 exports 42 dependencies

Last updated 4 months agofrom:620be78c23. Checks:OK: 3 ERROR: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 07 2024
R-4.5-winERRORNov 07 2024
R-4.5-linuxERRORNov 07 2024
R-4.4-winERRORNov 07 2024
R-4.4-macOKNov 07 2024
R-4.3-winERRORNov 07 2024
R-4.3-macOKNov 07 2024

Exports:capitalize_first_charcheck_allelescheck_can_create_filecheck_fasta_file_sequence_lengthscheck_netmhc2pan_bin_urlcheck_netmhc2pan_data_urlcheck_netmhc2pan_installationcreate_temp_fasta_filenamecreate_temp_xls_filenamedownload_netmhc2pan_binget_default_netmhc2pan_bin_pathget_default_netmhc2pan_bin_tarfile_pathget_default_netmhc2pan_folderget_default_netmhc2pan_subfolderget_default_netmhc2pan_versionget_netmhc2pan_allelesget_netmhc2pan_archive_filenameget_netmhc2pan_bin_urlget_netmhc2pan_data_urlget_netmhc2pan_urlinstall_netmhc2paninstall_netmhc2pan_bininstall_netmhc2pan_bin_from_fileinstall_netmhc2pan_datainstall_netmhc2pan_data_from_fileinstall_netmhc2pan_from_filesis_netmhc2pan_bin_installedis_netmhc2pan_data_installedis_netmhc2pan_haplotypeis_netmhc2pan_installedis_netmhc2pan_set_upis_on_appveyoris_on_ciis_on_github_actionsis_on_travisis_tcsh_installedis_url_validnetmhc2pan_reportnetmhc2pan_self_testpredict_ic50predict_ic50sread_netmhc2pan_xls_outputrun_netmhc2panset_up_netmhc2panto_netmhc2pan_nameuninstall_netmhc2pan

Dependencies:ade4bitbit64clicliprcpp11crayondplyrfansigenericsgluehmslatticelifecyclemagrittrMASSnlmepillarpixmappkgconfigprettyunitsprogressR6rappdirsRcppRcppArmadilloreadrrlangsegmentedseqinrsessioninfospstringistringrtestittibbletidyselecttzdbutf8vctrsvroomwithr

Binding strength prediction

Richel J.C. Bilderbeek

Rendered fromdemo.Rmdusingknitr::rmarkdownon Nov 07 2024.

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

Readme and manuals

Help Manual

Help pageTopics
Convert the first character to upper case.capitalize_first_char
Check the allele namescheck_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 filecheck_fasta_file_sequence_lengths
Check the URL of the NetMHCIIpan binary tarballcheck_netmhc2pan_bin_url
Check the URL of the NetMHCIIpan binary tarballcheck_netmhc2pan_data_url
Checks the installation of NetMHCIIpan.check_netmhc2pan_installation
Create a '.fasta' filecreate_temp_fasta_filename
Create a '.xls' filecreate_temp_xls_filename
This function does nothing. It is intended to inherit is parameters' documentation.default_params_doc
Download the NetMHCIIpan binarydownload_netmhc2pan_bin
Get the full path to the default NetMHC2pan binaryget_default_netmhc2pan_bin_path
Get the default path for the NetMHCIIpan binary tarball fileget_default_netmhc2pan_bin_tarfile_path
Get the path to the folder where this package installs NetMHCIIpan by defaultget_default_netmhc2pan_folder
Get the full path to the NetMHC2pan sub-folderget_default_netmhc2pan_subfolder
Get the default NetMHC2pan version usedget_default_netmhc2pan_version
Get a list of the alleles supported by NetMHCIIpanget_netmhc2pan_alleles
Get the filename of the NetMHC2pan archive fileget_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 insteadget_netmhc2pan_url
Install NetMHCIIpaninstall_netmhc2pan
Install the NetMHCIIpan binary to a local folderinstall_netmhc2pan_bin
Install the NetMHCIIpan binary to a local folderinstall_netmhc2pan_bin_from_file
Install the NetMHCIIpan data to a local folderinstall_netmhc2pan_data
Install the NetMHCIIpan data from fileinstall_netmhc2pan_data_from_file
Install NetMHCIIpan from files.install_netmhc2pan_from_files
Measure if NetMHCIIpan binary is installed locallyis_netmhc2pan_bin_installed
Measure if NetMHCIIpan data folder is installed locallyis_netmhc2pan_data_installed
Is the haplotype valid?is_netmhc2pan_haplotype
Measure if NetMHCIIpan is installed locallyis_netmhc2pan_installed
Measure if NetMHCIIpan is set upis_netmhc2pan_set_up
Determines if the environment is AppVeyoris_on_appveyor
Determines if the environment is a continuous integration serviceis_on_ci
Determines if the environment is GitHub Actionsis_on_github_actions
Determines if the environment is Travis CIis_on_travis
See if tcsh is installedis_tcsh_installed
Is the download URL valid?is_url_valid
netmhc2pan: predict peptide binding strengths using NetMHC2pannetmhc2pan
Show a 'netmhc2pan' report using message, to be used when reporting bugsnetmhc2pan_report
Test NetMHCIIpan by doing a minimal run.netmhc2pan_self_test
Predict the IC50 for peptides.predict_ic50
Predict the IC50s from a sequencepredict_ic50s
Read MHC2pan outputread_netmhc2pan_xls_output
Run NetMHCIIpanrun_netmhc2pan
Install the NetMHCIIpan binary to a local folderset_up_netmhc2pan
Convert a formal haplotype name to its NetMHC2pan notationto_netmhc2pan_name
Uninstall NetMHCIIpanuninstall_netmhc2pan