| 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 |