acope3
Ph.D studying mRNA translation dynamics and molecular evolution. B.Sc in Computer Science and Math
Rutgers University
Pinned Repositories
Intragenomic_variation_mutation_bias
A repository presenting the results from our analysis on the effects of intragenomic mutation bias variation within budding yeasts.
RibModelFramework
acope3.github.io
Personal Website
AnaCoDa
AnaCoDa CRAN versions
codon_TASEP
simulate TASEP model with codon-specific elongation rates
Codon_usage_prot_structure_angles
A reanalysis of the results from Rosenberg et al. Nat. Comm. 2022 using simulated data
corHMM
:exclamation: This is a read-only mirror of the CRAN R package repository. corHMM — Analysis of Binary Character Evolution
corHMM-1
Fits a generalized form of the covarion model that allows different transition rate classes on different portions of a phylogeny by treating rate classes as “hidden” states in a Markov process.
Ctherm_PUFs_Revision
CUB_Protein_Structure_Analysis
A repo with analyses for the examining codon usage relating to protein disorder and secondary structure
acope3's Repositories
acope3/Intragenomic_variation_mutation_bias
A repository presenting the results from our analysis on the effects of intragenomic mutation bias variation within budding yeasts.
acope3/RibModelFramework
acope3/RibModelDev
Development repository for the R package ribModel
acope3/acope3.github.io
Personal Website
acope3/AnaCoDa
AnaCoDa CRAN versions
acope3/codon_TASEP
simulate TASEP model with codon-specific elongation rates
acope3/Codon_usage_prot_structure_angles
A reanalysis of the results from Rosenberg et al. Nat. Comm. 2022 using simulated data
acope3/corHMM-1
Fits a generalized form of the covarion model that allows different transition rate classes on different portions of a phylogeny by treating rate classes as “hidden” states in a Markov process.
acope3/Ctherm_PUFs_Revision
acope3/CUB_Protein_Structure_Analysis
A repo with analyses for the examining codon usage relating to protein disorder and secondary structure
acope3/ethereumj
acope3/EVome
Analysis of EVome proteomics data for examining co-secretion of C. elegans proteins
acope3/example-datasets
Example datasets to run with RiboViz
acope3/Example_repo
acope3/GeneExpression_coevolution
A repository for the data and R scripts used for analyzing coevolution of gene expression in a set of fungi
acope3/LaplacesDemon
A complete environment for Bayesian inference within R
acope3/lecture_notes
Lecture Notes on Computational and Mathematical Population Genetics
acope3/new_repository
acope3/papers
working repository for writing papers
acope3/phylolm
acope3/phylometh_continuous
Continuous trait exercise for PhyloMeth
acope3/phylometh_correlated
For correlated traits
acope3/phylometh_discrete
Discrete trait exercise
acope3/phylometh_diversification
Diversification exercise
acope3/phylomethinfo
Website for PhyloMeth course
acope3/popgen-notes
Population genetics notes
acope3/ribotish
Ribo-seq TIS Hunter, predicting translation initiation sites and ORFs using riboseq data
acope3/riboviz
Analysis and Visualization of Ribosome Profiling Data
acope3/Signal_Peptide_Scripts
acope3/Yeast_Nonsense_Error_Analysis
Analysis of nonsense errors using yeast ribosome profiling data from Weinberg et al. Cell Reports 2016.