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3krg-hap

Haplotype marker based on 3,000 Rice Genomes for subpopulation inference

abc-enhancer-gene-prediction

Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)

bioinformatics-one-liners

Bioinformatics one liners from Ming Tang

cisdecoding_cistrome

cistransregulation

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

daligner

Find all significant local alignments between reads

fastq_phred_convert

Converts 33 offset to 64 and vice versa

gff2gtf

AWK script for conversion of GFF files to GTF.

gffread

GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more

ggnet

Network visualization with ggplot2

ggomics

Visualization tools for genomics analysis based on ggplot2

giraffe-sv-paper

graph_peak_caller

ChIP-seq peak caller for reads mapped to a graph-based reference genome

hdgene

HDGENE: High Dimensional Genetic Association Analysis Package

hetpi

Nucleotide diversity estimation using VCF input with special treatment for heterozygous genotypes

hfi

Haplotype Fixation Index for crop populations with homozygous nature, such as rice

html_test

huffman

Huffman Encoding & Decoding in 27 lines of Perl

invcheck

keggdecoder-binder

metabolic heatmap

ksnp-k-mer-based-haplotype-assembly

mcclintock

Meta-pipeline to identify transposable element insertions using next generation sequencing data

mcscanx

MCScanX: Multiple Collinearity Scan toolkit X version. The most popular synteny analysis tool in the world!

minigraph

Proof-of-concept seq-to-graph mapper and graph generator

mummer2indel

Detect large insertions/deletions from mummer alignment results

netcontig

nquire

A statistical framework for ploidy estimation using NGS short-read data

nsr-nwad029

Codes used in NSR nwad029.

plant-trait-ontology

Explore the Plant Trait Ontology on the Planteome site.

plantgrns

Integration of genome-wide TF binding and expression data to characterize plant gene regulatory networks