ksamuk
Evolutionary biologist at The University of California, Riverside.
University of California, RiversideRiverside, CA
Pinned Repositories
dplyr_magrittr_demo
A demo of the capabilities of the R libraries dplyr and magrittr
inversion_constraint
Swiss/North America team exploring inversion constraints
LD_recomb
Code and data for a scientific manuscript focused on assessing the effect of gene flow on LD-based estimates of recombination rate
pixy
Software for painlessly estimating average nucleotide diversity within and between populations
pixy_analysis
Analysis scripts used in the academic manuscript accompanying the pixy software
rehh_helper
Convenience scripts for preparing vcf files for input into rehh
samuk_et_al_curr_biol_2020
Code and data for Samuk et al. (2020)
syntR
R package for the reproducible detection of synteny blocks using genetic map data
whtstbk_geno
An analysis of genomic differences between two species of stickleback
ksamuk's Repositories
ksamuk/pixy
Software for painlessly estimating average nucleotide diversity within and between populations
ksamuk/pixy_analysis
Analysis scripts used in the academic manuscript accompanying the pixy software
ksamuk/inversion_constraint
Swiss/North America team exploring inversion constraints
ksamuk/syntR
R package for the reproducible detection of synteny blocks using genetic map data
ksamuk/LD_recomb
Code and data for a scientific manuscript focused on assessing the effect of gene flow on LD-based estimates of recombination rate
ksamuk/samuk_et_al_curr_biol_2020
Code and data for Samuk et al. (2020)
ksamuk/whtstbk_geno
An analysis of genomic differences between two species of stickleback
ksamuk/gene_flow_linkage
Tools for analyzing the relationship between recombination rate and divergence.
ksamuk/website
My personal (academic) website
ksamuk/2016-12-01-miskatonic
ksamuk/academic-kickstart
ksamuk/conda-forge-pinning-feedstock
A conda-smithy repository for conda-forge-pinning.
ksamuk/dpse_gbs
Design and analysis of a reduced genomic representation dataset
ksamuk/genome_meta_scripts
Precursor to the "gene_flow_linkage" repo
ksamuk/grenepipe
A flexible, scalable, and reproducible pipeline to automate variant calling from sequence reads.
ksamuk/hugo_website
ksamuk/ksamuk
ksamuk/ksamuk.github.io
The Samuk Lab Website
ksamuk/pixy-feedstock
A conda-smithy repository for pixy.
ksamuk/R-ecology-lesson
Data Carpentry R lessons on ecology
ksamuk/r-novice-gapminder
Introduction to R for non-programmers using gapminder data.
ksamuk/samuk_et_al_2020
Code and data associated with Samuk et al. 2020 (Current Biology)
ksamuk/stacks_sex_linked
Analysis of sex-linked genetic markers generated by STACKS
ksamuk/sticklebrains
An analysis of brain size in experimental populations of threespine stickleback
ksamuk/sv-meta
Pipeline for structural variant identification
ksamuk/tidypop
An optimistic vision of population genetics in the tidyverse
ksamuk/training-prep-2015-09
Instructor training preparation, September 2015
ksamuk/VCFSimulator-SamukLab
Script for generating simulated VCF's (variant call format files for encoding genetic data) leveraging a coalescent simulating backend. Provided an interface from Msprime coalescent simulating package to pandas. Output can be used to benchmark any population genetic software.
ksamuk/weighted_pi
ksamuk/whtstbk_morpho
Analysis of morphometric and differences between two species of stickleback