Soymethylation

GMStool

bwa

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

ActivePathways

Integrative pathway enrichment analysis of multivariate omics data

clusterProfiler

:bar_chart: A universal enrichment tool for interpreting omics data

gatk4-germline-snps-indels

Workflows for germline short variant discovery with GATK4

deepvariant

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

crossmap-workflow

Workflow and script for converting genomic coordinates using MUMmer output and CrossMap

rna-seq-pipeline

HiTE

High-precision TE Annotator

rtg-tools

RTG Tools: Utilities for accurate VCF comparison and manipulation

PopLDdecay

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

IIIVmrMLM

The R tool associated with 3VmrMLM, a comprehensive GWAS method for identifying QTNs, QTN-by-environment interactions, and QTN-by-QTN interactions for quantitative traits.

OrthoFinder

Phylogenetic orthology inference for comparative genomics

GenomeSyn

samplot

Plot structural variant signals from many BAMs and CRAMs

ppsPCP

A Plant Presence/absence Variants Scanner and Pan-genome Construction Pipeline

GeneSelectR

GeneSelectR_benchmarking

breed4biomass

Multi-omics data of forage grass hybrids.

bsalign

Banded Striped DNA Sequence Alignment

rTASSEL

R front-end for TASSEL

CWGCNA

CWGCNA is an R package to perform causal inference from the WGCNA framework.

ilus

A handy variant calling pipeline generator for whole-genome sequencing (WGS) and whole exom sequencing data (WES) analysis. 一个简易且全面的 WGS/WES 分析流程生成器.

popgen-notes

Population genetics notes

SpliceAI

A deep learning-based tool to identify splice variants

gpt_academic

为GPT/GLM等LLM大语言模型提供实用化交互接口，特别优化论文阅读/润色/写作体验，模块化设计，支持自定义快捷按钮&函数插件，支持Python和C++等项目剖析&自译解功能，PDF/LaTex论文翻译&总结功能，支持并行问询多种LLM模型，支持chatglm3等本地模型。接入通义千问, deepseekcoder, 讯飞星火, 文心一言, llama2, rwkv, claude2, moss等。

farmvibes-ai

FarmVibes.AI: Multi-Modal GeoSpatial ML Models for Agriculture and Sustainability

SoyDNGPNext

A deeplearning driving bioinformatic toolkit.

CoGPT

Hmm Copilot or GPT? Who knows. Get access to gpt-4 via copilot.

DISCVRSeq

A collection of command line tools for working with sequencing data