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analysis-pipeline

appls

Applied Python Programming for Life Scientists

bedops

:microscope: BEDOPS: high-performance genomic feature operations

bioinformatics-with-python-cookbook-second-edition

Bioinformatics with Python Cookbook Second Edition, published by Packt

brassica_oleracea_rapa_napus_code

Code for the Brassica oleracea/rapa/napus genomic comparison

centromere_repeat_paper

Code used to generate data for our analysis of centromeric repeats

cnn-rnn-yield-prediction

This repository contains codes for the paper entitled "A CNN-RNN Framework for Crop Yield Prediction"

data-science-from-scratch_book

code for Data Science From Scratch book

dataviz-r

A book covering the fundamentals of data visualization

deepgp

A tool to implement Genomic Prediction Experiments using Deep Learning

deepsignal-plant

Detecting methylation using signal-level features from Nanopore sequencing reads of plants

dgenies

Dotplot large Genomes in an Interactive, Efficient and Simple way

dlpipeline

Practical Deep Learning for Genomic Prediction: A Keras based guide to implement deep learning

docs

Documentation of the Snakemake-Workflows project

dupgen_finder

A pipeline used to identify different modes of duplicated gene pairs

epiteome

Simultaneous Detection of Transposable Element Insertion Sites and their DNA Methylation Levels from Plant Genomes

evachan.org-rscripts

Handy genetics-related R scripts

gbs_snakemake_pipeline

a pipeline based on the utility of snakemake to generate a vcf file from paired end sequencing data obtained from Illumina platforms

genomic-selection

ggpubfigs

colorblind friendly color palettes and ggplot2 graphic system extensions for publication-quality scientific figures

ggtext

Improved text rendering support for ggplot2

gwaspoly

GWAS software that can handle autopolyploids

hapdup

Pipeline to convert a haploid assembly into diploid

itips

Identification of transposable element insertion polymorphisms (TIPs) based on a pan-genome and large-scale resequencing data

jasmine

Jasmine: SV Merging Across Samples

kaks-calculator

Automatically exported from code.google.com/p/kaks-calculator

kaml

:bicyclist: Kinship Adjusted Multi-Loci Best Linear Unbiased Prediction

learning_vcf_file

Learning the Variant Call Format

maize_v4_te_annotation

scripts and intermediate files used to annotate TEs in Jiao et al.

maizeumn.github.io