JingminCheng's Stars
binary-husky/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。
getaurora/download
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apptainer/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.
lh3/seqtk
Toolkit for processing sequences in FASTA/Q formats
DerrickWood/kraken2
The second version of the Kraken taxonomic sequence classification system
thelovelab/DESeq2
Differential expression of RNA-seq data using the Negative Binomial
jenniferlu717/KrakenTools
KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files
biobakery/MetaPhlAn
MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data
jenniferlu717/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.
microbiome/microbiome
microbiome R package
jiarong/VirSorter2
customizable pipeline to identify viral sequences from (meta)genomic data
YuLab-SMU/MicrobiotaProcess
:microbe: A comprehensive R package for deep mining microbiome
chhantyal/parquet-cli
Command line (CLI) tool to inspect Apache Parquet files on the go
motu-tool/mOTUs
motus - a tool for marker gene-based OTU (mOTU) profiling
cmks/DAS_Tool
DAS Tool
jessieren/VirFinder
VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data
marbl/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.
EBI-Metagenomics/emg-viral-pipeline
VIRify: detection of phages and eukaryotic viruses from metagenomic and metatranscriptomic assemblies
biobakery/biobakery_workflows
bioBakery workflows is a collection of workflows and tasks for executing common microbial community analyses using standardized, validated tools and parameters.
biobakery/graphlan
High-quality circular representations of taxonomic and phylogenetic trees
ronammar/randomcoloR
An R package for generating attractive and distinctive colors.
Asa12138/ReporterScore
Generalized Reporter Score-based Functional Enrichment Method for Omics Data
PathoScope/PathoScope
Pathoscope: Species identification and strain attribution with unassembled sequencing data
zjshi/gt-pro
feargalr/Demovir
Taxonomic classification of viruses at Order and Family level
hildebra/Rarefaction
Rarefaction scripts
ravel-lab/VIRGO
SegataLab/export2graphlan
Conversion software tool for producing both annotation and tree files for GraPhlAn
Vaginal-Microbiome-Consortium/PTB
gaoyifeng1987/download
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