JingminCheng

ReporterScore

Generalized Reporter Score-based Functional Enrichment Method for Omics Data

gt-pro

VIRGO

PTB

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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。

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DAS_Tool

DAS Tool

mOTUs

motus - a tool for marker gene-based OTU (mOTU) profiling

randomcoloR

An R package for generating attractive and distinctive colors.

KrakenTools

KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files

kraken2

The second version of the Kraken taxonomic sequence classification system

microbiome

microbiome R package

DESeq2

Differential expression of RNA-seq data using the Negative Binomial

parsnp

Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can be both draft assemblies and finished genomes, and output includes variant (SNP) calls, core genome phylogeny and multi-alignments. Parsnp leverages contextual information provided by multi-alignments surrounding SNP sites for filtration/cleaning, in addition to existing tools for recombination detection/filtration and phylogenetic reconstruction.

MicrobiotaProcess

:microbe: A comprehensive R package for deep mining microbiome

Rarefaction

Rarefaction scripts

PathoScope

Pathoscope: Species identification and strain attribution with unassembled sequencing data

biobakery_workflows

bioBakery workflows is a collection of workflows and tasks for executing common microbial community analyses using standardized, validated tools and parameters.

export2graphlan

Conversion software tool for producing both annotation and tree files for GraPhlAn

seqtk

Toolkit for processing sequences in FASTA/Q formats

MetaPhlAn

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

Demovir

Taxonomic classification of viruses at Order and Family level

singularity

Singularity has been renamed to Apptainer as part of us moving the project to the Linux Foundation. This repo has been persisted as a snapshot right before the changes.

VirFinder

VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data

VirSorter2

customizable pipeline to identify viral sequences from (meta)genomic data

graphlan

High-quality circular representations of taxonomic and phylogenetic trees

Bracken

Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.

parquet-cli

Command line (CLI) tool to inspect Apache Parquet files on the go

emg-viral-pipeline

VIRify: detection of phages and eukaryotic viruses from metagenomic and metatranscriptomic assemblies