sjspielman/phyphy

This repository has been archived on 08/Dec/2021
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sjspielman/phyphy

sjspielman

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Python HyPhy: Facilitating HyPhy execution and parsing

pyvolve

Python library to simulate evolutionary sequence data

introverse

Documentation for beginners entering R and the tidyverse

datascience_for_biologists

Course materials for Rowan University Course "Data Science for Biologists"

alignfigR

Create sequence alignment figures in R

UTbiocomputing2015

Peer-led working group in Biological Computing at UT Austin, Spring 2015

leisr_validation

Code accompanying LEISR manuscript

grabbag

Various scripts I have written that seem useful

dragon

Deep time Redox Analysis of the Geobiology Ontology Network

ds4b.materials

Apps and useful student functions for BIOL01301, packaged up

dnds_1rate_2rate

Repository for manuscript "A comparison of one-rate and two-rate inference frameworks for site-specific dN/dS estimation" by SJS, SW, COW.

alignment_filtering

Code and data for "Limited Utility of Residue Masking for Positive-Selection Inference," by SJS, ETD, COW.

mammalian_gpcr_selection

Repository for Data in "Membrane environment imposes unique selection pressures on transmembrane domains of G-protein coupled receptors"

protein_rates_models

Comparing rates across models

datascience_final_assignment

COVID shiny app!!!

sam-kasten-memoirs

English translation of the memoirs of Sam Kasten (Kestin), beloved Yiddish theater comedian

mutsel_benchmark

Repository for " Extensively-parameterized mutation–selection models reliably capture site-specific selective constraint" by SJS and COW.

wmeecv_hsab_analysis

evolfoRces

Simulate population genetics simulations for the classroom

plot-iris

Shiny app for teaching students about different types of quantitative plots