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pureseqtmr  

Predict Transmembrane Protein Topology
View on CRAN: Click here


Download and install pureseqtmr package within the R console
Install from CRAN:
install.packages("pureseqtmr")

Install from Github:
library("remotes")
install_github("cran/pureseqtmr")

Install by package version:
library("remotes")
install_version("pureseqtmr", "1.4")



Attach the package and use:
library("pureseqtmr")
Maintained by
Richèl J.C. Bilderbeek
[Scholar Profile | Author Map]
First Published: 2020-07-30
Latest Update: 2023-04-06
Description:
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' (, as described in "Efficient And Accurate Prediction Of Transmembrane Topology From Amino acid sequence only.", Wang, Qing, et al (2019), ), can predict the topology of a membrane protein. This package allows one to use 'PureseqTM' from R.
How to cite:
Richèl J.C. Bilderbeek (2020). pureseqtmr: Predict Transmembrane Protein Topology. R package version 1.4, https://cran.r-project.org/web/packages/pureseqtmr. Accessed 07 May. 2025.
Previous versions and publish date:
1.2 (2020-07-30 12:50)
Other packages that cited pureseqtmr R package
View pureseqtmr citation profile
Other R packages that pureseqtmr depends, imports, suggests or enhances
Complete documentation for pureseqtmr
Functions, R codes and Examples using the pureseqtmr R package
Some associated functions: are_tmhs . are_valid_protein_sequences . calc_distance_to_tmh_center_from_topology . calc_distance_to_tmh_center_from_topology_str . calc_distance_to_tmh_center_from_topology_str_cpp_stl . 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 . default_params_doc . 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_cpp_raw . 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 . pureseqtmr_report . run_pureseqtm_proteome . save_tibble_as_fasta_file . tally_tmhs . uninstall_pureseqtm . 
Some associated R codes: RcppExports.R . are_tmhs.R . are_valid_protein_sequences.R . calc_distance_to_tmh_center_from_topology.R . calc_distance_to_tmh_center_from_topology_str.R . check_protein_sequence.R . check_protein_sequences.R . check_pureseqtm_installation.R . check_topology.R . check_topology_str.R . convert_tmhmm_to_pureseqtm_topology.R . count_n_tmhs.R . create_pureseqtm_files.R . create_pureseqtm_proteome_file.R . default_params_doc.R . get_default_pureseqtm_folder.R . get_example_filename.R . get_example_filenames.R . get_pureseqtm_url.R . get_pureseqtm_version.R . install_pureseqtm.R . is_on_ci.R . is_protein_name_line.R . is_pureseqtm_installed.R . is_tmh.R . is_topology_line.R . is_valid_protein_sequence.R . load_fasta_file_as_tibble.R . load_fasta_file_as_tibble_cpp.R . load_fasta_file_as_tibble_r.R . load_topology_file_as_tibble.R . mock_predict_topologies_from_sequences.R . mock_predict_topology.R . parse_pureseqtm_proteome_text.R . plot_topology.R . predict_topologies_from_sequences.R . predict_topology.R . predict_topology_from_sequence.R . pureseqtmr.R . pureseqtmr_report.R . run_pureseqtm_proteome.R . save_tibble_as_fasta_file.R . tally_tmhs.R . uninstall_pureseqtm.R . use_rcpp.R .  Full pureseqtmr package functions and examples
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