This repository contains computer codes for main analyses of the manuscript titled 'Multi-omic Landscape of Airway Microbe-Host Interaction in Chronic Obstructive Pulmonary Disease'.
☆33Aug 16, 2022Updated 3 years ago
Alternatives and similar repositories for COPD_multiomics
Users that are interested in COPD_multiomics are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- This repository contains original codes for major analyses in the manuscript 'The multi-kingdom airway microbiome mediates the interactio…☆13Apr 27, 2024Updated last year
- ☆21Feb 13, 2020Updated 6 years ago
- Repo for a Microbiome Protocol☆10Apr 26, 2018Updated 7 years ago
- The construction of reference gene catalog and metagenome-assembled genomes of pig gut microbiome.☆29Jul 21, 2022Updated 3 years ago
- MTD: a unique pipeline for host and meta-transcriptome joint and integrative analyses of RNA-seq data☆17Jul 15, 2025Updated 8 months ago
- bioBakery workflows is a collection of workflows and tasks for executing common microbial community analyses using standardized, validate…☆130Oct 20, 2025Updated 5 months ago
- A 'time'-like utility for Unix that measures peak memory usage☆18Jun 5, 2024Updated last year
- MicrobiomeReview☆11Jun 6, 2023Updated 2 years ago
- ☆29Jan 16, 2024Updated 2 years ago
- Scripts to quality control for metagenomic raw data, including removing the adapters, low quality reads, bases or PCR duplicates☆18Aug 13, 2020Updated 5 years ago
- Predictive models and analysis of cancer prognosis and drug response using primary tumor microbial abundances derived from WGS and RNA-se…☆18Nov 13, 2024Updated last year
- Comprehensive analysis of single cell RNAseq and spatial transcriptomics in human acute and chronic wounds☆14Mar 19, 2025Updated last year
- Microbial ecological network visualization clustering☆144Nov 20, 2025Updated 4 months ago
- Nature Communications | BASALT (Binning Across a Series of Assemblies Toolkit) for binning and refinement of short- and long-read sequenc…☆128Feb 8, 2026Updated last month
- Metagenomics Taxonomic Reads Assembly Single-Species☆16May 25, 2023Updated 2 years ago
- EasyMultiOmics: An R package for comprehensive multi-omics data mining in systematic microbiome research☆102Dec 17, 2025Updated 3 months ago
- ☆11Feb 9, 2024Updated 2 years ago
- Code for de novo discovery of viral families in virome data☆16Jun 20, 2024Updated last year
- Scripts for calculating features and regression of prokaryote OGT☆25Feb 13, 2024Updated 2 years ago
- FOR my learing☆12Feb 19, 2026Updated last month
- Strain resolved metagenome simulator☆13Aug 11, 2018Updated 7 years ago
- Recovery of prokaryotic genomes from shotgun metagenomic sequencing data☆62Apr 18, 2021Updated 4 years ago
- ☆18Oct 13, 2023Updated 2 years ago
- a novel encoding method for viral identification in metagenomics☆15Sep 20, 2023Updated 2 years ago
- R package for microbiome biomarker discovery☆194Feb 19, 2025Updated last year
- Phage virion protein classifier☆14Nov 6, 2024Updated last year
- ☆24Dec 5, 2018Updated 7 years ago
- Codebase for the paper Zucha et al. titled "Spatiotemporal transcriptomic map of glial cell response in mouse model of acute brain ischem…☆13Oct 23, 2024Updated last year
- phyloseq R☆12Sep 18, 2019Updated 6 years ago
- Analysis framework for integrating gut microbiome and host gene expression data☆36Apr 25, 2022Updated 3 years ago
- SourceTracker2☆86Jul 10, 2024Updated last year
- strain-level analysis tools☆39Oct 21, 2024Updated last year
- ☆18Nov 19, 2022Updated 3 years ago
- SynTracker is a pipeline, designated to determine the biological relatedness of conspecific strains (microbial strains of the same specie…☆40Sep 17, 2025Updated 6 months ago
- Source code of the VirSorter tool, also available as an App on CyVerse/iVirus (https://de.iplantcollaborative.org/de/)☆101Oct 3, 2020Updated 5 years ago
- A selection of short scripts for analyzing microbial genomes☆14Jun 26, 2018Updated 7 years ago
- Reproducible scripts and notebooks for 2019 paper on population genetics in metagenomes☆16Feb 26, 2020Updated 6 years ago
- Spatial transcriptomics of heart tissue☆28Jun 16, 2022Updated 3 years ago
- Antibiotic resistance genes (ARGs) have accelerated microbial threats to human health during the last decade. Here we determined the risk…☆19Apr 8, 2022Updated 3 years ago