Crb1                    SurfaltR Amino Acid Test Data- Novel Mouse
                        Retina Isoforms
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
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_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
