Hep_Ploidy_protocol

This is the ploidy identification workflow from the article "Stereo-cell Deciphers the Spatial and Functional Heterogeneity of Polyploid Hepatocytes". The method employs deep learning techniques: Cellpose & StarDist to accurately identify DAPI fluorescence-stained images and brightfield images, respectively. It acquires detailed information on the morphological characteristics and spatial localization of nuclei and cells, which serves as the core process for hepatocyte ...

SMIntegration : Spatial Multi-omics Integration Platform

Introduction

SMIntegration is an innovative open-source platform for integrated analysis of spatial transcriptomics and metabolomics data. It integrates spatial pattern recognition, differential comparison, network construction, and functional annotation into a unified workflow. Designed to address key challenges in spatial multi-omics correlation analysis, SMIntegration enables researchers to explore gene-metabolite co-regulation ...

Petrisnake: A secondary analysis pipeline for PETRI-seq data.

This is a Snakemake pipeline for the secondary computational analysis of single cell RNA-seq data from the PETRI-seq protocol (https://www.nature.com/articles/s41564-020-0729-6 and https://www.nature.com/articles/s41586-024-08124-2), this is: From the input FASTQ files, this workflow constructs a gene count table showing the expression of each gene in each cell.

Dependencies

This pipeline ...

ARG-Sniper

A Nextflow pipeline for antibiotic resistance gene detection from paired-end sequencing reads.

Introduction

ARG-Sniper is a Nextflow DSL-2 pipeline designed for metagenomic analysis that processes paired-end FASTQ files to detect antibiotic resistance genes using multiple bioinformatics tools. The pipeline runs five different analysis tools in parallel: GROOT, ARIBA, KMA (adopted from ARGprofiler), KARGA, and SRST2, each requiring their respective databases. Users can selectively ...

SMIntegration : Spatial Multi-omics Integration Platform

Introduction

SMIntegration is an innovative open-source platform for integrated analysis of spatial transcriptomics and metabolomics data. It integrates spatial pattern recognition, differential comparison, network construction, and functional annotation into a unified workflow. Designed to address key challenges in spatial multi-omics correlation analysis, SMIntegration enables researchers to explore gene-metabolite co-regulation ...

SMIntegration : Spatial Multi-omics Integration Platform

Introduction

SMIntegration is an innovative open-source platform for integrated analysis of spatial transcriptomics and metabolomics data. It integrates spatial pattern recognition, differential comparison, network construction, and functional annotation into a unified workflow. Designed to address key challenges in spatial multi-omics correlation analysis, SMIntegration enables researchers to explore gene-metabolite co-regulation ...

SMIntegration : Spatial Multi-omics Integration Platform

Introduction

SMIntegration is an innovative open-source platform for integrated analysis of spatial transcriptomics and metabolomics data. It integrates spatial pattern recognition, differential comparison, network construction, and functional annotation into a unified workflow. Designed to address key challenges in spatial multi-omics correlation analysis, SMIntegration enables researchers to explore gene-metabolite co-regulation ...