Package: pureseqtmr 1.4

Richèl J.C. Bilderbeek

pureseqtmr: Predict Transmembrane Protein Topology

Proteins reside in either the cell plasma or in the cell membrane. A membrane protein goes through the membrane at least once. Given the amino acid sequence of a membrane protein, the tool 'PureseqTM' (<https://github.com/PureseqTM/pureseqTM_package>, as described in "Efficient And Accurate Prediction Of Transmembrane Topology From Amino acid sequence only.", Wang, Qing, et al (2019), <doi:10.1101/627307>), can predict the topology of a membrane protein. This package allows one to use 'PureseqTM' from R.

Authors:Richèl J.C. Bilderbeek [aut, cre]

pureseqtmr_1.4.tar.gz
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pureseqtmr.pdf |pureseqtmr.html✨
pureseqtmr/json (API)

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

Peer review:

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

Uses libs:
  • c++– GNU Standard C++ Library v3

On CRAN:

3.90 score 1 stars 16 scripts 256 downloads 44 exports 123 dependencies

Last updated 2 years agofrom:106ebe6974. Checks:OK: 9. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 31 2024
R-4.5-win-x86_64OKOct 31 2024
R-4.5-linux-x86_64OKOct 31 2024
R-4.4-win-x86_64OKOct 31 2024
R-4.4-mac-x86_64OKOct 31 2024
R-4.4-mac-aarch64OKOct 31 2024
R-4.3-win-x86_64OKOct 31 2024
R-4.3-mac-x86_64OKOct 31 2024
R-4.3-mac-aarch64OKOct 31 2024

Exports:are_tmhsare_valid_protein_sequencescalc_distance_to_tmh_center_from_topologycalc_distance_to_tmh_center_from_topology_strcheck_protein_sequencecheck_protein_sequencescheck_pureseqtm_installationcheck_topologycheck_topology_strconvert_tmhmm_to_pureseqtm_topologycount_n_tmhscreate_pureseqtm_filescreate_pureseqtm_proteome_fileget_default_pureseqtm_folderget_example_filenameget_example_filenamesget_pureseqtm_urlget_pureseqtm_versioninstall_pureseqtmis_on_appveyoris_on_ciis_on_github_actionsis_on_travisis_protein_name_lineis_pureseqtm_installedis_tmhis_topology_lineis_valid_protein_sequenceload_fasta_file_as_tibbleload_fasta_file_as_tibble_cppload_fasta_file_as_tibble_rload_topology_file_as_tibblemock_predict_topologies_from_sequencesmock_predict_topologyparse_pureseqtm_proteome_textplot_topologypredict_topologies_from_sequencespredict_topologypredict_topology_from_sequencepureseqtmr_reportrun_pureseqtm_proteomesave_tibble_as_fasta_filetally_tmhsuninstall_pureseqtm

Dependencies:askpassbase64encbitbit64brewbriobslibcachemcallrclicliprcolorspacecommonmarkcpp11crayoncredentialscurldata.tabledescdevtoolsdiffobjdigestdownlitdplyrellipsisevaluatefansifarverfastmapfontawesomefsgenericsgertggplot2ghgitcredsgluegtablehighrhmshtmltoolshtmlwidgetshttpuvhttr2iniisobandjquerylibjsonliteknitrlabelinglaterlatticelifecyclemagrittrMASSMatrixmemoisemgcvmimeminiUImunsellnlmeopensslPeptidespillarpkgbuildpkgconfigpkgdownpkgloadplyrpraiseprettyunitsprocessxprofvisprogresspromisespspurrrR6raggrappdirsrcmdcheckRColorBrewerRcppreadrrematch2remotesrlangrmarkdownroxygen2rprojrootrstudioapirversionssassscalessessioninfoshinysourcetoolsstringistringrsyssystemfontstestthattextshapingtibbletidyselecttinytextzdburlcheckerusethisutf8vctrsviridisLitevroomwaldowhiskerwithrxfunxml2xopenxtableyamlzip

Demo

Rendered fromdemo.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2021-01-18
Started: 2020-05-21

Readme and manuals

Help Manual

Help pageTopics
Are the sequences transmembrance helices?are_tmhs
Determine if these are all valid protein sequencesare_valid_protein_sequences
Calculate the the distance for each amino acid to the center of the TMHcalc_distance_to_tmh_center_from_topology
Calculate the the distance for each amino acid to the center of the TMHcalc_distance_to_tmh_center_from_topology_str
Use Rcpp to calculate the distance to a TMH centercalc_distance_to_tmh_center_from_topology_str_cpp_stl
Check one protein sequencecheck_protein_sequence
Check one or more protein sequencescheck_protein_sequences
Checks the installation of PureseqTM. Throws a helpful error message if incomplete, else does nothingcheck_pureseqtm_installation
Check if the topology is valid.check_topology
Check if the topology string is valid. Will stop if not.check_topology_str
Convert a TMHMM topology to a PureseqTM topologyconvert_tmhmm_to_pureseqtm_topology
Count the number of TMHs in a topologycount_n_tmhs
Create the five PureseqTM output files, by running PureseqTM.create_pureseqtm_files
Create the output file of a PureseqTM proteome runcreate_pureseqtm_proteome_file
This function does nothing. It is intended to inherit is parameters' documentation.default_params_doc
Get the path to the folder where this package installs PureseqTM by defaultget_default_pureseqtm_folder
Get the full path to a PureseqTM example file.get_example_filename
Get the full path to all PureseqTM example filesget_example_filenames
Get the URL of the PureseqTM source codeget_pureseqtm_url
Get the PureseqTM versionget_pureseqtm_version
Install PureseqTM to a local folderinstall_pureseqtm
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
Is the line of text the name of a protein, as used within a FASTA filename?is_protein_name_line
Measure if PureseqTM is installed locallyis_pureseqtm_installed
Determine if the protein sequence contains at least one transmembrane helix.is_tmh
Is the line of text the topology, as used within a FASTA filename?is_topology_line
Determine if this a valid protein sequenceis_valid_protein_sequence
Parse a FASTA file to a table with a 'name' and 'sequence' columnload_fasta_file_as_tibble
Parse a FASTA file to a table with a 'name' and 'sequence' columnload_fasta_file_as_tibble_cpp
Use Rcpp to load a FASTA fileload_fasta_file_as_tibble_cpp_raw
Parse a FASTA file to a table with a 'name' and 'sequence' columnload_fasta_file_as_tibble_r
Parse a topology ('.topo') file to a table with a 'name' and 'topology' columnload_topology_file_as_tibble
Do a mock prediction directy on a protein sequence, as can be useful in testing Use predict_topologies_from_sequences for doing a real prediction.mock_predict_topologies_from_sequences
Do a mock prediction of the topology of proteinsmock_predict_topology
Parse the output of a call to 'PureseqTM_proteome.sh'parse_pureseqtm_proteome_text
Plot the topologyplot_topology
Run PureseqTM directy on a protein sequencepredict_topologies_from_sequences
Predict the topology of proteins from filepredict_topology
Run PureseqTM directy on a protein sequencepredict_topology_from_sequence
pureseqtmr: estimate the topoplogy of membrane proteinspureseqtmr
Create a pureseqtmr report, to be used when reporting bugspureseqtmr_report
Run PureseqTM on a proteomerun_pureseqtm_proteome
Save the first two columns of a tibble as a FASTA filesave_tibble_as_fasta_file
Count the number of transmembrane helices in a topologytally_tmhs
Uninstall PureseqTMuninstall_pureseqtm