Package: surfaltr 1.11.0

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]

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NEWS

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

Peer review:

On BioConductor:surfaltr-1.11.0(bioc 3.20)surfaltr-1.10.0(bioc 3.19)

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

bioconductor-package

10 exports 0.49 score 105 dependencies

Last updated 2 months agofrom:f4c0d774cf

Exports:align_org_prtsalign_prtscheck_tmhmm_installget_pairsget_tmhmmgraph_from_aasgraph_from_idsplot_isoformsrun_phobiustest_surfaltr

Dependencies:ade4AnnotationDbiaskpassBiobaseBiocFileCacheBiocGenericsbiomaRtBiostringsbitbit64blobbriocachemcallrclicliprcolorspacecpp11crayoncurlDBIdbplyrdescdiffobjdigestdplyrevaluatefansifarverfastmapfilelockfsgenericsGenomeInfoDbGenomeInfoDbDataggplot2gluegtablehmshttrhttr2IRangesisobandjsonliteKEGGRESTlabelinglatticelifecyclemagrittrMASSMatrixmemoisemgcvmimemsamunsellnlmeopensslpillarpixmappkgbuildpkgconfigpkgloadplogrpngpraiseprettyunitsprocessxprogressprotrpspurrrR6rappdirsRColorBrewerRcppRcppArmadilloreadrrematch2rlangrprojrootRSQLiteS4VectorsscalessegmentedseqinrspstringistringrsystestthattibbletidyrtidyselecttzdbUCSC.utilsutf8vctrsviridisLitevroomwaldowithrxml2XVectorzlibbioc

Rapid Comparison of Surface Protein Isoform Membrane Topologies Through surfaltr

Rendered fromsurfaltr_vignette.Rmdusingknitr::rmarkdownon Jun 11 2024.

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

Readme and manuals

Help Manual

Help pageTopics
Get aligned amino acid sequences for gene transcripts from multiple organismsalign_org_prts
Get aligned amino acid sequences for gene transcriptsalign_prts
Check to make sure TMHMM 2.0 is installed in the file path specifiedcheck_tmhmm_install
Retrieve, Clean, and Format Input Dataclean_data
SurfaltR Amino Acid Test Data- Novel Mouse Retina IsoformsCrb1
Retrieve Transcript Information from Ensembl for all Primary Transcriptsensembl_db_retrieval
Reformat transcripts to facilitate fasta file conversionformat_ids
Create fasta file containing amino acid sequences based on user sequencesget_aas
Create csv and fasta files containing information about pairs of transcriptsget_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 IDsget_prts
Create a data frame with the membrane locations of each amino acid in a protein using TMHMMget_tmhmm
Create a plot showing membrane locations of each protein based on user provided amino acid sequencesgraph_from_aas
Create a plot showing membrane locations of each protein based on transcript IDsgraph_from_ids
Create a plot showing where each amino acid is located within the cell for each primary transcript compared to each alternative transcriptgraph_prots
SurfaltR Gene Name and Transcript ID Test Data- Highly Expressed Human Alternative Transcriptshpa_genes
SurfaltR Gene Name and Transcript ID Test Data- Highly Expressed Mouse Alternative Transcriptshpa_mouse_genes
Associate Inputted Transcripts with Corresponding Primary Transcriptsmerge_trans
Create a plot showing where each amino acid is located within the cell for each primary transcript compared to each alternative transcriptplot_isoforms
Create a data frame with the membrane locations of each amino acid in a sequenceprocess_tmhmm
Rank the surface proteins by differences in principal and alternative isoformsrank_prts
Create a data frame with the membrane locations of each amino acid in a protein using Phobiusrun_phobius
Split a fasta formatted file.split_fasta
Test the functionality of surfaltrtest_surfaltr
Retrieve Data from TMHMM and Fix Functionality of TMHMM R Packagetmhmm_fix_path