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1001crosses

2022_bisulphite_protocol

Quality control for a tagementation-based bisulphite sequencing protocol using dNTPS with methylated cytosines

amajus_dispersal_ms

Code to support the manuscript "Joint estimation of paternity, sibships and pollen dispersal in a snapdragon hybrid zone"

amajus_mating

Analysis of assortative mating in a snapdragon hybrid zone, and in experimental arrays

ammiad-1

arghqtl

Tools for plotting and downstream analysis of R/QTL objects in R

bs_seq_with_typing_errors

curriculum_vitae

A repo for tracking my CV

dogging_expt

ellisztamas.github.io

:triangular_ruler: Jekyll theme for building a personal site, blog, project documentation, or portfolio.

evolvienna

Poster presentation

faps

Inference of paternity and sibling relationships accounting for uncertainty in genealogy

fecundity_components

Analysis of fitness components, including seed size and number, in *A. thaliana*

gwastoolbox

Set of scripts to run different types of GWAS

hdydi_shiny

Shiny example apps

hmm_ancestry_and_methylation

Developing a Hidden-Markov model to infer ancestry and DNA methylation status in a cross

hyde

A brazen two-column theme for Jekyll.

ibdpainting

Identify parents of a crossed individual by comparing identity in windows across their genomes

mc_inheritance_outside

An experiment invesitgating the effect of spending one generation outside on methylation patterns

meth_pedigree

methlab

Python tools to automate common tasks for the epiclines ERC project in the Nordborg group at the Gregor Mendel Institute.

methylation-common-garden

methylpy

WGBS/NOMe-seq Data Processing & Differential Methylation Analysis

methylseq

Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel

nextflow_pipelines

The set of NGS processing pipelines used at Babraham

nf-haplocaller

Nextflow pipeline for GATK best practices (HaplotypeCaller)

nf-snpmatch

Nextflow pipeline for SNPmatch (https://github.com/Gregor-Mendel-Institute/SNPmatch.git)

qgglmm

Compute various quantitative genetics parameters from a Generalised Linear Mixed Model (GLMM) estimates. Especially, it yields the observed phenotypic mean, phenotypic variance and additive genetic variance.

qtltools

Extentions to r/qtl for importing and plotting QTL

quantifying_pleiotropy_ms

A repo to store code and manuscript details for the paper "A quantitative framework for pleiotropic mechanims