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 |