Rapid Comparison of Surface Protein Isoform Membrane Topologies Through surfaltr

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Documentation for package ‘surfaltr’ version 1.11.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

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