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allhic

Genome scaffolding based on HiC data in heterozygous and high ploidy genomes

cuscuta_hgt_ms_code

Stolen genes in parasitic plants: convergent horizontal transfer and crosstalk of mobile nucleic acids

deeplearning-500-questions

深度学习500问，以问答形式对常用的概率知识、线性代数、机器学习、深度学习、计算机视觉等热点问题进行阐述，以帮助自己及有需要的读者。 全书分为17个章节，20多万字。由于水平有限，书中不妥之处恳请广大读者批评指正。 未完待续............ 如有意合作，联系[email protected] 版权所有，违权必究 Tan 2018.06

dip-c

Tools to analyze Dip-C (or other 3C/Hi-C) data

dupgen_finder

A pipeline used to identify different modes of duplicated gene pairs

edge

EDGE is a highly adaptable bioinformatics platform that allows laboratories to quickly analyze and interpret genomic sequence data.

fastp

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

free-photos

Places to find CC0 photos and the like

github-bioinformatics

Code for Russell et al. "A large-scale analysis of bioinformatics code on GitHub"

hickit

TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C

idgrm

IDGRM-Inferring Duplicated Gene Retention Mechanism

iterm2-with-oh-my-zsh

iTerm2 + Oh My Zsh 打造舒适终端体验

jcvi

Python utility libraries on genome assembly, annotation and comparative genomics

kallisto

Near-optimal RNA-Seq quantification

lastz

Program for aligning DNA sequences, a pairwise aligner.

lqhhhhh

ltr_finder_parallel

A parallel wrapper for LTR_FINDER

maize-fractionation

Repository hosts the code used in the manuscript titled "Limited role of differential fractionation in genome content variation and function in maize (Zea mays L.) inbred lines."

mcscanx

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

nano-snakemake

A snakemake pipeline for SV analysis from nanopore genome sequencing

nd1_pacbio

scripts associated with the Nd-1 genome assembly based on PacBio data

nextsv

orthofinder

Accurate inference of orthologous gene groups made easy. "OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthologous gene group inference accuracy"

perl_modules

poplddecay

PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format(VCF) files

python

Python scripts

rpkm_rnaseq_count

RPKM for RNASeq counts

scripts

scripts_for_gb

The code used in the manuscript titled "Gene duplication and evolution in recurring polyploidization-diploidization cycles in plants".

sleuth

Differential analysis of RNA-Seq