huangl07

popgen

Population genetics analyses

vcfR

:exclamation: This is a read-only mirror of the CRAN R package repository. vcfR — Manipulate and Visualize VCF Data. Homepage: https://github.com/knausb/vcfR, https://knausb.github.io/vcfR_documentation/

cambodiaWGS

Workflows and analyses related to my Cambodian WGS project.

poppr

🌶 An R package for genetic analysis of populations with mixed (clonal/sexual) reproduction

whtstbk_geno

An analysis of genomic differences between two species of stickleback

workshop-popgenome

Tutorial about R package PopGenome

RpairwiseFST

Pairwise FST by population. From VCF to Table & Plot.

GppFst

GppFst: Genomic Posterior Predictive Simulations of Fst and Dxy

rvtests

Rare variant test software for next generation sequencing data

CNVnator

a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads

discoal

discoal is a coalescent simulation program capable of simulating models with recombination, selective sweeps, and demographic changes including population splits, admixture events, and ancient samples

vt

A tool set for short variant discovery in genetic sequence data.

SO-Ontologies

Collect of SO Ontologies

vcftools

A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project.

VCF-kit

VCF-kit: Assorted utilities for the variant call format

ggman

R package for plotting a manhattan plot using ggplot2.

gg.ldplot

Plot a pairwise LD matrix from vcftools with ggplot2.

ngsutils

Tools for next-generation sequencing analysis

smcpp

SMC++ infers population history from whole-genome sequence data.

angsd

Program for analysing NGS data.

LEP-Map_Pipe

Pipeline for generating a linkage map and supporting files for QTL analysis

RgeneticMap

Draw genetic map (linkage map) in R

lepmap2_workflow

Pipeline for linkage map construction from NGS data

brassica_genetic_map_paper