jun3234

MetaPhlAn

MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data

voronoiTreemap

R package for voronoi treemaps with added interactivity by shiny

WeightedTreemaps

Create Voronoi and Sunburst Treemaps from Hierarchical data

bubble-treemaps

Implementation of Bubble Treemaps for Uncertainty Visualization.

treemap

R package for treemap visualisation

treemap-chart

A treemap interactive chart web component for visualizing hierarchical data

GLnexus

Scalable gVCF merging and joint variant calling for population sequencing projects

smudgeplot

Inference of ploidy and heterozygosity structure using whole genome sequencing data

merqury

k-mer based assembly evaluation

genometools

GenomeTools genome analysis system.

KMC

Fast and frugal disk based k-mer counter

yahs

Yet another Hi-C scaffolding tool

cactus

Official home of genome aligner based upon notion of Cactus graphs

minigraph

Sequence-to-graph mapper and graph generator

zotero-pdf-translate

Translate PDF, EPub, webpage, metadata, annotations, notes to the target language. Support 20+ translate services.

Clair3

Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling

ngmlr

NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on reads that span structural variations

SVision

Detecting genome structural variants with deep learning in single molecule sequencing

pyGenomeViz

A genome visualization python package for comparative genomics

lumpy-sv

lumpy: a general probabilistic framework for structural variant discovery

delly

DELLY2: Structural variant discovery by integrated paired-end and split-read analysis

microeco

An R package for data analysis in microbial community ecology

lefser

R implementation of the LEfSe method

TRF

Tandem Repeats Finder: a program to analyze DNA sequences

Waifu2x-Extension-GUI

Video, Image and GIF upscale/enlarge(Super-Resolution) and Video frame interpolation. Achieved with Waifu2x, Real-ESRGAN, Real-CUGAN, RTX Video Super Resolution VSR, SRMD, RealSR, Anime4K, RIFE, IFRNet, CAIN, DAIN, and ACNet.

Squirrel-RIFE

效果更好的补帧软件，显存占用更小，是DAIN速度的10-25倍，包含抽帧处理，去除动漫卡顿感

singularity

SingularityCE is the Community Edition of Singularity, an open source container platform designed to be simple, fast, and secure.

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。

phased-assembly-check

v2rayN

A GUI client for Windows, support Xray core and v2fly core and others