mandyzhang6 Goto Github PK

2018_ecological_genomics

The Spring 2018 Ecological Genomics course at the University of Vermont

abc_inferences

allele-specific-expression

Pipeline to perform the allele-specific expression analysis (based on the work by Skelly et al. 2011)

atac-seq

atacseq

ATAC-seq peak-calling, QC and differential analysis pipeline

bio_tools

Useful bioinformatic scripts

bioinformatics_scripts

Just a bunch of scripts I use for bioinformatics -- feel free to use, reuse, and improve

book

brassica-napus-genomes

brassica_oleracea_rapa_napus_code

Code for the Brassica oleracea/rapa/napus genomic comparison

circrna

circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data

cistransregulation

Project description and analytic scripts for cis/trans regulation of fiber development in G. hirsutum

cleaveland4

CleaveLand4: Analysis of degradome data to find sliced miRNA and siRNA targets

demographicinference

Scripts to compare models of divergence using diffusion approximation (dadi)

docs

Documentation of the Snakemake-Workflows project

eqtl

fibernetwork

WGCNA analysis using Fiber RNA seq data

gatk_haplotype

genomebiology-2018-photoperiodlocaladaptation

Scripts for Wang et al. (2018) "A major locus controls local adaptation and adaptive life history variation in a perennial plant". Genome Biology, 19, 72.

genomicprediction_2018

Influence of algorithms, parameter choice, and feature selection on genomic prediction accuracy

getting-started-with-genomics-tools-and-resources

Unix, R and python tools for genomics and data science

gwas

UNDER CONSTRUCTION: A pipeline for Genome Wide Association Studies

haploblocks

Scripts and resources for the haploblocks manuscript

heterosis-gwas

hic

Analysis of Chromosome Conformation Capture data (Hi-C)

homoeologgeneexpression-coexpression

Challenges and pitfall in the use of partitioned gene counts for homoeologous gene expression and co-expression network analyses

jarad.github.com

Github userpage

ldhat_workflow

learn-bioinformatics

linked-selection