Package: surfaltr 1.19.0

Pooja Gangras

surfaltr: Rapid Comparison of Surface Protein Isoform Membrane Topologies Through surfaltr

Cell surface proteins form a major fraction of the druggable proteome and can be used for tissue-specific delivery of oligonucleotide/cell-based therapeutics. Alternatively spliced surface protein isoforms have been shown to differ in their subcellular localization and/or their transmembrane (TM) topology. Surface proteins are hydrophobic and remain difficult to study thereby necessitating the use of TM topology prediction methods such as TMHMM and Phobius. However, there exists a need for bioinformatic approaches to streamline batch processing of isoforms for comparing and visualizing topologies. To address this gap, we have developed an R package, surfaltr. It pairs inputted isoforms, either known alternatively spliced or novel, with their APPRIS annotated principal counterparts, predicts their TM topologies using TMHMM or Phobius, and generates a customizable graphical output. Further, surfaltr facilitates the prioritization of biologically diverse isoform pairs through the incorporation of three different ranking metrics and through protein alignment functions. Citations for programs mentioned here can be found in the vignette.

Authors:Pooja Gangras [aut, cre], Aditi Merchant [aut]

surfaltr_1.19.0.tar.gz
surfaltr_1.19.0.zip(r-4.7)surfaltr_1.19.0.zip(r-4.6)surfaltr_1.19.0.zip(r-4.5)
surfaltr_1.19.0.tgz(r-4.6-any)surfaltr_1.19.0.tgz(r-4.5-any)
surfaltr_1.19.0.tar.gz(r-4.7-any)surfaltr_1.19.0.tar.gz(r-4.6-any)
surfaltr_1.19.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
surfaltr/json (API)

# Install 'surfaltr' in R:

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

On BioConductor:surfaltr-1.19.0(bioc 3.24)surfaltr-1.18.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

software visualization datarepresentation splicedalignment alignment multiplesequencealignment multiplecomparison

4.00 score 3 scripts 10 exports 97 dependencies

Last updated from:1cadef7389. Checks:8 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	192
linux-devel-x86_64	WARNING	262
source / vignettes	OK	238
linux-release-x86_64	WARNING	251
macos-release-arm64	WARNING	133
macos-oldrel-arm64	WARNING	113
windows-devel	WARNING	160
windows-release	WARNING	165
windows-oldrel	WARNING	173
wasm-release	OK	183

Exports:align_org_prts align_prts check_tmhmm_install get_pairs get_tmhmm graph_from_aas graph_from_ids plot_isoforms run_phobius test_surfaltr

Dependencies:ade4 AnnotationDbi askpass Biobase BiocFileCache BiocGenerics biomaRt Biostrings bit bit64 blob brio cachem callr cli clipr cpp11 crayon curl DBI dbplyr desc diffobj dplyr evaluate farver fastmap filelock fs generics ggplot2 glue gtable hms httr httr2 IRanges isoband jsonlite KEGGREST labeling lattice lifecycle magrittr MASS memoise mime msa MultipleAlignment nlme openssl otel pillar pixmap pkgbuild pkgconfig pkgload png praise prettyunits processx progress protr ps purrr R6 rappdirs RColorBrewer Rcpp RcppArmadillo readr rlang rprojroot RSQLite S4Vectors S7 scales segmented Seqinfo seqinr sp stringi stringr sys testthat tibble tidyr tidyselect tzdb utf8 vctrs viridisLite vroom waldo withr xml2 XVector

Rapid Comparison of Surface Protein Isoform Membrane Topologies Through surfaltr

Rendered fromsurfaltr_vignette.Rmdusingknitr::rmarkdown

Last update: 2022-05-02
Started: 2021-07-30

Help page	Topics
Get aligned amino acid sequences for gene transcripts from multiple organisms	align_org_prts
Get aligned amino acid sequences for gene transcripts	align_prts
Check to make sure TMHMM 2.0 is installed in the file path specified	check_tmhmm_install
Retrieve, Clean, and Format Input Data	clean_data
SurfaltR Amino Acid Test Data- Novel Mouse Retina Isoforms	Crb1
Retrieve Transcript Information from Ensembl for all Primary Transcripts	ensembl_db_retrieval
Reformat transcripts to facilitate fasta file conversion	format_ids
Create fasta file containing amino acid sequences based on user sequences	get_aas
Create csv and fasta files containing information about pairs of transcripts	get_pairs
Query Phobius web server.	get_phobius get_phobius.character get_phobius.data.frame get_phobius.default get_phobius.list
Create fasta file containing amino acid sequences based on IDs	get_prts
Create a data frame with the membrane locations of each amino acid in a protein using TMHMM	get_tmhmm
Create a plot showing membrane locations of each protein based on user provided amino acid sequences	graph_from_aas
Create a plot showing membrane locations of each protein based on transcript IDs	graph_from_ids
Create a plot showing where each amino acid is located within the cell for each primary transcript compared to each alternative transcript	graph_prots
SurfaltR Gene Name and Transcript ID Test Data- Highly Expressed Human Alternative Transcripts	hpa_genes
SurfaltR Gene Name and Transcript ID Test Data- Highly Expressed Mouse Alternative Transcripts	hpa_mouse_genes
Associate Inputted Transcripts with Corresponding Primary Transcripts	merge_trans
Create a plot showing where each amino acid is located within the cell for each primary transcript compared to each alternative transcript	plot_isoforms
Create a data frame with the membrane locations of each amino acid in a sequence	process_tmhmm
Rank the surface proteins by differences in principal and alternative isoforms	rank_prts
Create a data frame with the membrane locations of each amino acid in a protein using Phobius	run_phobius
Split a fasta formatted file.	split_fasta
Test the functionality of surfaltr	test_surfaltr
Retrieve Data from TMHMM and Fix Functionality of TMHMM R Package	tmhmm_fix_path

Package: surfaltr 1.19.0

surfaltr: Rapid Comparison of Surface Protein Isoform Membrane Topologies Through surfaltr

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