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3d-dna

3D de novo assembly (3D DNA) pipeline

ampir

antimicrobial peptide prediction in R

apollo

Genome annotation editor with a Java Server backend and a Javascript client that runs in a web browser as a JBrowse plugin.

asmhighlighter

fork of http://asmhighlighter.codeplex.com/

assembly-annotation-pipeline

Plant genome assembly and annotation pipeline using snakemake

baiduyun

一个免费开源的网盘下载助手

bamdeal

BamDeal: a comprehensive toolkit for bam manipulation

bash-oneliner

A collection of handy Bash One-Liners and terminal tricks for data processing and Linux system maintenance.

bcbio-nextgen

Validated, scalable, community developed variant calling and RNA-seq analysis

biocode

Bioinformatics code libraries and scripts

bioconda-recipes

Conda recipes for the bioconda channel.

biome

An experimental Moose-based BioPerl implementation

bioperl6

reimplementation of BioPerl classes in Perl6

biopython

Official git repository for Biopython (converted from CVS)

book-r1

R的极客理想-工篇篇

braker

BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes

breedr

Statistical methods for forest genetic resources analysts

cafe_fig

A tool to extract and visualize the results of CAFE (Computational Analysis of gene Family Evolution)

cafeplotter

A tool for plotting CAFE5 gene family expansion/contraction result

ccgpworkflow

Snakemake workflow for highly parallel variant calling designed for ease-of-use in non-model organisms.

chatgpt-prompts-for-academic-writing

This list of writing prompts covers a range of topics and tasks, including brainstorming research ideas, improving language and style, conducting literature reviews, and developing research plans.

chatpaper

Use ChatGPT to summarize the arXiv papers. 全流程加速科研，利用chatgpt进行论文全文总结+专业翻译+润色+审稿+审稿回复

cn

Chinese blog of Yihui Xie

commands-for-hologenomic-analyses

dairry-blup

A high-performance computing approach to genomic prediction

dot

Dot: An interactive dot plot viewer for comparative genomics

easycodeml

easyspeciestree

Easily construct the ML species tree with single-copy gene shared by different species.

edta

Extensive de-novo TE Annotator

en

English blog of Yihui Xie