Matt Johnson's repositories
bmi203_final
final project for bmi203
BMI203_HW1
homework 1 for algorithms
BMI203_HW3
Smith-Waterman algorithm
BMI206
Individual Analysis
Bootstrap_averager
Takes Newick format trees and computes average bootstrap of entire tree
DefenseHotspot
anti-phage defense hotspots
example
example python project with continuous integration testing
FastaRand
Randomizes FASTA sequences
flipGenbank
flips genbank
Gray-Matter
Neural network that searches for remote gene families using word embeddings
HW2
BMI203 HW2
NasChase
Finds occurrences of Nasonia chases from trajectory data - to be incorporated into NasTracks
NasTracks
ShinyApp that analyzes idTracker data for Nasonia wasps and produces graphs
nastracks-demo-data
sample trajectory data
Protein-cutter
Cuts out conserved motifs from protein families for use in building phylogenetic motif trees
SAMS
Large regular expression that scores and detects SIM/SMR genes
SpacerMakerCas13b
Ranks spacers based on PFS rules and RNAplfold RNA accessibility described in Smargon et al. Cell 2017.
synet
anti-CRISPR "guilt by association network
synet_app
Dash app for synet