caporaso-lab / mockrobiota
A public resource for microbiome bioinformatics benchmarking using artificially constructed (i.e., mock) communities.
☆78Updated 5 years ago
Alternatives and similar repositories for mockrobiota:
Users that are interested in mockrobiota are comparing it to the libraries listed below
- SHallow shOtGUN profiler☆53Updated 2 years ago
- Statistical analysis for sparse high-throughput sequencing☆69Updated 2 months ago
- Scripts and tutorials on how to assemble individual microbial genomes from metagenomes☆80Updated 8 years ago
- Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data☆153Updated last year
- functions to analyse sanger sequencing reads in R☆100Updated 10 months ago
- Snakemake workflow for metagenomic classification with Kraken2☆65Updated last year
- ☆60Updated 5 years ago
- Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWoo…☆52Updated 2 years ago
- treeWAS: A Phylogenetic Tree-Based Tool for Genome-Wide Association Studies in Microbes☆98Updated 3 weeks ago
- Computational workflows for metagenomics tasks, by the Bhatt lab☆46Updated 2 years ago
- All of my various bioinformatic scripts fit for public consumption (loosely defining "fit")☆71Updated 2 years ago
- SAMSA pipeline, version 2.0. An open-source metatranscriptomics pipeline for analyzing microbiome data, built around DIAMOND and customi…☆57Updated 11 months ago
- Automated pipeline for analyses of fungal ITS from the Illumina☆31Updated 6 months ago
- Phylogenetic Investigation of Communities by Reconstruction of Unobserved STates (PICRUST): Official repository for software and unit tes…☆90Updated 2 years ago
- Parse NCBI taxonomy and accessions to find taxonomic assignments☆71Updated this week
- Analysis of metagenomic shotgun sequences including assembly, speciation, ARG discovery and more☆27Updated last year
- Statistical Analysis of Metagenomic Profiles☆93Updated 5 years ago
- Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing☆115Updated 9 months ago
- scripts for estimating bacteria replication rates based on population genome copy number variation☆70Updated 5 years ago
- Rapid and scalable correlation estimation for compositional data☆83Updated 9 months ago
- Sparse Cooccurence Network Investigation for Compositional data☆24Updated 4 months ago
- Course material for the metagenomics course☆43Updated 3 years ago
- Metatranscriptomics Tutorial☆60Updated last year
- Visualize microbiome data with black magic ggtree☆68Updated 4 years ago
- A list of R environment based tools for microbiome data exploration, statistical analysis and visualization☆113Updated last year
- An efficient and objective tool for optimizing microbiome rRNA gene trimming parameters☆86Updated 7 months ago
- r package for post-clustering curation of amplicon next generation sequencing data (metabarcoding)☆63Updated last year
- Genome wide orthology inference and dNdS estimation☆89Updated last year
- DDBJ Fast Annotation and Submission Tool☆79Updated this week
- A set of R scripts for the analysis of microbial profiles☆42Updated 9 months ago