Rapid Comparison of Surface Protein Isoform Membrane Topologies Through surfaltr


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Documentation for package ‘surfaltr’ version 1.2.2

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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