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tmhmm (version 1.3)

Interface to TMHMM

Description

Predicting the topology of membrane proteins is part of the field of computational biology. 'TMHMM' is a program to predict transmembrane helices in proteins. 'TMHMM' can be called from a website and/or locally using Bash. This package allows to install and call TMHMM from R and parse its results.

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Version

Install

install.packages('tmhmm')

Monthly Downloads

3

Version

1.3

License

GPL-3

Issues

2

Pull Requests

0

Stars

6

Forks

0

Maintainer

Richel Bilderbeek

Last Published

November 18th, 2020

Functions in tmhmm (1.3)

check_topology

Check if the topology is valid.
is_tmh

Determine if the protein sequence contains at least one TMH.
default_params_doc

This function does nothing. It is intended to inherit is parameters' documentation.
is_tmhmm_bin_installed

Measure if TMHMM binary is installed locally
tmhmm

tmhmm: estimate the topoplogy of membrane proteins
uninstall_tmhmm

Uninstall TMHMM
tmhmm_self_test

Self-test the TMHMM installation
get_tmhmm_url

Get an URL to download TMHMM from. These URLs expire.
install_tmhmm

Install NetMHC2pan to a local folder
are_tmhs

Are the sequences TMHs?
is_tmhmm_set_up

Determine if TMHMM is set up
is_url_valid

Is the download URL valid?
run_tmhmm

Run TMHMM
run_tmhmm_to_file

Creates a FASTA-like file, that has the locations of the amino acids.
set_up_tmhmm

Set up TMHMM
is_tmhmm_result

Is the text a TMHMM result text?
get_default_tmhmm_folder

Get the path to the folder where this package installs TMHMM by default
run_tmhmm_on_sequence

Run TMHMM directy on a protein sequence
is_tmhmm_installed

Measure if TMHMM is installed locally
get_default_tmhmm_bin_path

Get the default path to the TMHMM binary
check_tmhmm_installation

Checks the installation of TMHMM. Throws a helpful error message if incomplete, else does nothing
locatome_to_df

Convert a multi-line locatome to a tidy data frame
plot_locatome

Plot the locatome
is_locatome_line

Is the line of text the locatome, as used within a FASTA filename?
is_protein_name_line

Is the line of text the name of a protein, as used within a FASTA filename?
install_tmhmm_bin

Install the NetMHC2pan binary to a local folder
is_on_travis

Determines if the environment is Travis CI
tally_locatome

Tally each location in a locatome
tally_tmhs

Count the number of transmembrane helices in a topology