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alignmentprocessor

Prepares CDS fasta Alignments for use with several programs

anole_expression

Understanding variation in squamate sex determination and sex chromosome evolution

aseofbases

Allele Specific Expression method and pipeline for analysis

bioinformaticsintroduction

coverage_bsp

How does reduced coverage affect demographic inference in Bayesian Skyline Plots

diversity_simulations

eqtl

mmb_apes

Codes related to studying male mutation bias across apes

mmb_flies

myeloma

This repository contains the code used in the myeloma/selection project.

nasonia

Wasp parent of origin effects

neoepitope_prediction

pardiversity

pctf_differential_expression

Code for analyzing RNAseq data from cell lines expressing PcTF, and code for making figures

placenta1

Reanalysis of preexisting placenta RNAseq data

popinf

Method to infer the major population (or populations) ancestry of a sample or set of samples.

sexdiffexpression

RNAseq analysis code, specifically focusing on sex differences in expression

teaching_geneticdrift

tumorheterogeneity

turkanaselection

useful_code

xy_rnaseq

Alignment and filtering effects on RNAseq analysis on the X and Y chromosomes

xyalign

Identifying, understanding, and correcting technical biases on the sex chromosomes in next-generation sequencing data

y_diversity

Scripts for modeling and empirically calculating diversity on Y and mtDNA. Potentially to expand at a later date.