Man pages for pureseqtmr
Predict Transmembrane Protein Topology

are_tmhsAre the sequences transmembrance helices?
are_valid_protein_sequencesDetermine if these are all valid protein sequences
calc_distance_to_tmh_center_from_topologyCalculate the the distance for each amino acid to the center...
calc_distance_to_tmh_center_from_topology_strCalculate the the distance for each amino acid to the center...
calc_distance_to_tmh_center_from_topology_str_cpp_stlUse Rcpp to calculate the distance to a TMH center
check_protein_sequenceCheck one protein sequence
check_protein_sequencesCheck one or more protein sequences
check_pureseqtm_installationChecks the installation of PureseqTM. Throws a helpful error...
check_topologyCheck if the topology is valid.
check_topology_strCheck if the topology string is valid. Will stop if not.
convert_tmhmm_to_pureseqtm_topologyConvert a TMHMM topology to a PureseqTM topology
count_n_tmhsCount the number of TMHs in a topology
create_pureseqtm_filesCreate the five PureseqTM output files, by running PureseqTM.
create_pureseqtm_proteome_fileCreate the output file of a PureseqTM proteome run
default_params_docThis function does nothing. It is intended to inherit is...
get_default_pureseqtm_folderGet the path to the folder where this package installs...
get_example_filenameGet the full path to a PureseqTM example file.
get_example_filenamesGet the full path to all PureseqTM example files
get_pureseqtm_urlGet the URL of the PureseqTM source code
get_pureseqtm_versionGet the PureseqTM version
install_pureseqtmInstall PureseqTM to a local folder
is_on_appveyorDetermines if the environment is AppVeyor
is_on_ciDetermines if the environment is a continuous integration...
is_on_github_actionsDetermines if the environment is GitHub Actions
is_on_travisDetermines if the environment is Travis CI
is_protein_name_lineIs the line of text the name of a protein, as used within a...
is_pureseqtm_installedMeasure if PureseqTM is installed locally
is_tmhDetermine if the protein sequence contains at least one...
is_topology_lineIs the line of text the topology, as used within a FASTA...
is_valid_protein_sequenceDetermine if this a valid protein sequence
load_fasta_file_as_tibbleParse a FASTA file to a table with a 'name' and 'sequence'...
load_fasta_file_as_tibble_cppParse a FASTA file to a table with a 'name' and 'sequence'...
load_fasta_file_as_tibble_cpp_rawUse Rcpp to load a FASTA file
load_fasta_file_as_tibble_rParse a FASTA file to a table with a 'name' and 'sequence'...
load_topology_file_as_tibbleParse a topology ('.topo') file to a table with a 'name' and...
mock_predict_topologies_from_sequencesDo a mock prediction directy on a protein sequence, as can be...
mock_predict_topologyDo a mock prediction of the topology of proteins
parse_pureseqtm_proteome_textParse the output of a call to ''
plot_topologyPlot the topology
predict_topologies_from_sequencesRun PureseqTM directy on a protein sequence
predict_topologyPredict the topology of proteins from file
predict_topology_from_sequenceRun PureseqTM directy on a protein sequence
pureseqtmrpureseqtmr: estimate the topoplogy of membrane proteins
pureseqtmr_reportCreate a pureseqtmr report, to be used when reporting bugs
run_pureseqtm_proteomeRun PureseqTM on a proteome
save_tibble_as_fasta_fileSave the first two columns of a tibble as a FASTA file
tally_tmhsCount the number of transmembrane helices in a topology
uninstall_pureseqtmUninstall PureseqTM
pureseqtmr documentation built on April 6, 2023, 5:20 p.m.