Package: pureseqtmr 1.4.2

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_1.4.2.tar.gz
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pureseqtmr_1.4.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
pureseqtmr/json (API)

# Install 'pureseqtmr' in R:

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

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

Uses libs:

c++– GNU Standard C++ Library v3

On CRAN:

cpp

3.93 score 1 stars 17 scripts 316 downloads 44 exports 117 dependencies

Last updated from:9f8d9f3ab8. Checks:15 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	OK	127
linux-devel-x86_64	OK	159
source / vignettes	OK	211
linux-release-arm64	OK	127
linux-release-x86_64	OK	149
macos-release-arm64	OK	184
macos-release-x86_64	OK	342
macos-oldrel-arm64	OK	94
macos-oldrel-x86_64	OK	190
windows-devel-arm64	OK	469
windows-devel-x86_64	OK	154
windows-release-arm64	OK	335
windows-release-x86_64	OK	116
windows-oldrel-x86_64	OK	133
wasm-release	OK	131

Exports:are_tmhs are_valid_protein_sequences calc_distance_to_tmh_center_from_topology calc_distance_to_tmh_center_from_topology_str check_protein_sequence check_protein_sequences check_pureseqtm_installation check_topology check_topology_str convert_tmhmm_to_pureseqtm_topology count_n_tmhs create_pureseqtm_files create_pureseqtm_proteome_file get_default_pureseqtm_folder get_example_filename get_example_filenames get_pureseqtm_url get_pureseqtm_version install_pureseqtm is_on_appveyor is_on_ci is_on_github_actions is_on_travis is_protein_name_line is_pureseqtm_installed is_tmh is_topology_line is_valid_protein_sequence load_fasta_file_as_tibble load_fasta_file_as_tibble_cpp load_fasta_file_as_tibble_r load_topology_file_as_tibble mock_predict_topologies_from_sequences mock_predict_topology parse_pureseqtm_proteome_text plot_topology predict_topologies_from_sequences predict_topology predict_topology_from_sequence pureseqtmr_report run_pureseqtm_proteome save_tibble_as_fasta_file tally_tmhs uninstall_pureseqtm

Dependencies:askpass base64enc bit bit64 brew brio bslib cachem callr cli clipr commonmark cpp11 crayon credentials curl data.table desc devtools diffobj digest downlit dplyr ellipsis evaluate fansi farver fastmap fontawesome fs generics gert ggplot2 gitcreds glue gtable highr hms htmltools htmlwidgets httpuv httr2 ini isoband jquerylib jsonlite knitr labeling later lifecycle magrittr memoise mime miniUI openssl otel pak Peptides pillar pkgbuild pkgconfig pkgdown pkgload plyr praise prettyunits processx profvis progress promises ps purrr R6 ragg rappdirs rcmdcheck RColorBrewer Rcpp rdtools readr rlang rmarkdown roxygen2 rprojroot rstudioapi rversions S7 sass scales sessioninfo shiny sourcetools stringi stringr sys systemfonts testthat textshaping tibble tidyselect tinytex tzdb urlchecker usethis utf8 vctrs viridisLite vroom waldo whisker withr xfun xml2 xopen xtable yaml zip

Demo

Rendered fromdemo.Rmdusingknitr::rmarkdown

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

Help page	Topics
Are the sequences transmembrance helices?	are_tmhs
Determine if these are all valid protein sequences	are_valid_protein_sequences
Calculate the the distance for each amino acid to the center of the TMH	calc_distance_to_tmh_center_from_topology
Calculate the the distance for each amino acid to the center of the TMH	calc_distance_to_tmh_center_from_topology_str
Use Rcpp to calculate the distance to a TMH center	calc_distance_to_tmh_center_from_topology_str_cpp_stl
Check one protein sequence	check_protein_sequence
Check one or more protein sequences	check_protein_sequences
Checks the installation of PureseqTM. Throws a helpful error message if incomplete, else does nothing	check_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 topology	convert_tmhmm_to_pureseqtm_topology
Count the number of TMHs in a topology	count_n_tmhs
Create the five PureseqTM output files, by running PureseqTM.	create_pureseqtm_files
Create the output file of a PureseqTM proteome run	create_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 default	get_default_pureseqtm_folder
Get the full path to a PureseqTM example file.	get_example_filename
Get the full path to all PureseqTM example files	get_example_filenames
Get the URL of the PureseqTM source code	get_pureseqtm_url
Get the PureseqTM version	get_pureseqtm_version
Install PureseqTM to a local folder	install_pureseqtm
Determines if the environment is AppVeyor	is_on_appveyor
Determines if the environment is a continuous integration service	is_on_ci
Determines if the environment is GitHub Actions	is_on_github_actions
Determines if the environment is Travis CI	is_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 locally	is_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 sequence	is_valid_protein_sequence
Parse a FASTA file to a table with a 'name' and 'sequence' column	load_fasta_file_as_tibble
Parse a FASTA file to a table with a 'name' and 'sequence' column	load_fasta_file_as_tibble_cpp
Use Rcpp to load a FASTA file	load_fasta_file_as_tibble_cpp_raw
Parse a FASTA file to a table with a 'name' and 'sequence' column	load_fasta_file_as_tibble_r
Parse a topology ('.topo') file to a table with a 'name' and 'topology' column	load_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 proteins	mock_predict_topology
Parse the output of a call to 'PureseqTM_proteome.sh'	parse_pureseqtm_proteome_text
Plot the topology	plot_topology
Run PureseqTM directy on a protein sequence	predict_topologies_from_sequences
Predict the topology of proteins from file	predict_topology
Run PureseqTM directy on a protein sequence	predict_topology_from_sequence
Create a pureseqtmr report, to be used when reporting bugs	pureseqtmr_report
Run PureseqTM on a proteome	run_pureseqtm_proteome
Save the first two columns of a tibble as a FASTA file	save_tibble_as_fasta_file
Count the number of transmembrane helices in a topology	tally_tmhs
Uninstall PureseqTM	uninstall_pureseqtm

Package: pureseqtmr 1.4.2

pureseqtmr: Predict Transmembrane Protein Topology

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