A set of R codes for the analysis of network, statistics and demonstrations in general

Characterizing associations between genetic elements with convergent phenotypes.

Inference of ploidy and heterozygosity structure using whole genome sequencing data

An all-in-one R/Bioconductor package for gene list enrichment analysis and pathway visualization

The analytical pipeline of the AL4 strain genome

Scripts that were used in "Divergent genome evolution caused by regional variation in DNA gain and loss between human and mouse"

Long-range promoter-enhancer contacts are conserved during evolution and contribute to gene expression robustness

Scripts to run permutation analysis of methylation levels in apes.

Workflow for analysis of Z-linked and autosomal genomic variation in barn swallows

Additional test cases of branch support rearrangements after tree re-rooting inspired by http://biorxiv.org/content/early/2015/12/25/035360 (APE, dendropy, biopython, ete3, newick-utilities, bioperl)

Understanding variation in squamate sex determination and sex chromosome evolution

Workflow and scripts used in rattlesnake male mutation bias analyses

ExprX - an R package to streamline interspecies differential expression analysis

Contains scripts used in Edsall et al., 2019

Naked mole rat data analysis for submitting to Gigascience

Functional modules for analysing single cell omics data.

Sex chromosome dosage compensation across vertebrates

Whole genome alignments using LastZ software in vertebrate species. Code (1) drives embarrassingly parallel execution of commands, (2) merge output into sensible formats and (3) provides ways to dr…

assign orthologs and test for molecular convergence in coral transcriptomes

Single Nucleus Analysis Pipeline for ATAC-seq

analysis of rhodopsin locus in Atlantic herring

Scripts for calculating kurtosis based conservation