# Rapid Comparison of Surface Protein Isoform Membrane Topologies Through surfaltr

## Documentation for package ‘surfaltr’ version 1.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## 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