Predict Transmembrane Protein Topology

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Documentation for package ‘pureseqtmr’ version 1.2

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are_tmhs Are the sequences transmembrance helices?
check_pureseqtm_installation Checks the installation of PureseqTM. Throws a helpful error message if incomplete, else does nothing
check_topology Check if the topology is valid.
create_pureseqtm_files Create the five PureseqTM output files, by running PureseqTM.
create_pureseqtm_proteome_file Create the output file of a PureseqTM proteome run
default_params_doc This function does nothing. It is intended to inherit is parameters' documentation.
get_default_pureseqtm_folder Get the path to the folder where this package installs PureseqTM by default
get_example_filename Get the full path to a PureseqTM example file.
get_example_filenames Get the full path to all PureseqTM example files
get_pureseqtm_url Get the URL of the PureseqTM source code
get_pureseqtm_version Get the PureseqTM version
install_pureseqtm Install PureseqTM to a local folder
is_on_appveyor Determines if the environment is AppVeyor
is_on_ci Determines if the environment is a continuous integration service
is_on_travis Determines if the environment is Travis CI
is_protein_name_line Is the line of text the name of a protein, as used within a FASTA filename?
is_pureseqtm_installed Measure if PureseqTM is installed locally
is_tmh Determine if the protein sequence contains at least one transmembrane helix.
is_topology_line Is the line of text the topology, as used within a FASTA filename?
plot_topology Plot the topology
predict_topology Predict the topology of a proteome
predict_topology_from_sequence Run PureseqTM directy on a protein sequence
pureseqtmr pureseqtmr: estimate the topoplogy of membrane proteins
pureseqtmr_report Create a pureseqtmr report, to be used when reporting bugs
run_pureseqtm_proteome Run PureseqTM on a proteome
tally_tmhs Count the number of transmembrane helices in a topology
uninstall_pureseqtm Uninstall PureseqTM