Pinned Repositories
as.color
R package to assign random colors to unique items in a vector
cds_fold
Outputs the 0-fold and 4-fold sites from a gff and reference genome.
git-tooty
slides and material for joint lab meeting presentation
gpfreqs
lasthenia_docker
Containerized repo for reproducing results in Grow where you thrive, or where only you can survive? An analysis of performance curve evolution in a clade with diverse habitat affinities."
performr
pomodoror
A silly R package to help you write more
rdmc
R package implementing convergent adaptation models of Lee and Coop (2017)
shiny_popgen
Shiny apps for teaching Population Genetics
tidy_vcf
Converts a sample of sites from standard VCF table into tidy format for easy summary stats and plotting.
silastittes's Repositories
silastittes/shiny_popgen
Shiny apps for teaching Population Genetics
silastittes/cds_fold
Outputs the 0-fold and 4-fold sites from a gff and reference genome.
silastittes/performr
silastittes/rdmc
R package implementing convergent adaptation models of Lee and Coop (2017)
silastittes/tidy_vcf
Converts a sample of sites from standard VCF table into tidy format for easy summary stats and plotting.
silastittes/gpfreqs
silastittes/random_seqmask
Input a fasta of sequence, masks each sequence randomly according to input parameters. Allows identical masking across the input sequences or random masking.
silastittes/abc-nam
silastittes/abc_maize
silastittes/analysis2
Analysis for the second consortium paper.
silastittes/analysis2_manuscript
manuscript repo for the paper describing selection additions and analysis
silastittes/cv
My Curriculum vitae
silastittes/degenotate
silastittes/DFE-alpha_CLI
A wrapper for running the DFE-alpha software
silastittes/diploSHIC
silastittes/dna-seq-gatk-variant-calling
silastittes/ms_sub
silastittes/msmc2_to_usfs
silastittes/panand_structure
Simple nextflow pipeline for running NGSadmix starting with a VCF
silastittes/panandbib
Annotated bibliography for RILAB panand project
silastittes/parv_local
silastittes/penta_channel
silastittes/pyslim
Tools for dealing with tree sequences coming to and from SLiM.
silastittes/ReLERNN
Recombination Landscape Estimation using Recurrent Neural Networks
silastittes/SLiM
SLiM is a genetically explicit forward simulation software package for population genetics and evolutionary biology. It is highly flexible, with a built-in scripting language, and has a cross-platform graphical modeling environment called SLiMgui.
silastittes/slim_bgs
Simple SLiM code to think about background selection and sweeps.
silastittes/stdpopsim
A library of standard population genetic models
silastittes/sweep_regions
command line tool to define outliers and merge them into regions
silastittes/tidy-tour
Departmental Brown bag presentation on some tools from the tidyverse
silastittes/tribolium_pipeline