HCBravoLab / metagenomeSeq
Statistical analysis for sparse high-throughput sequencing
☆69Updated 3 months ago
Alternatives and similar repositories for metagenomeSeq:
Users that are interested in metagenomeSeq are comparing it to the libraries listed below
- Reproducible Analyses accompanying DADA2 + PacBio Manuscript☆33Updated 4 years ago
- Scripts and tutorials on how to assemble individual microbial genomes from metagenomes☆80Updated 8 years ago
- SAMSA pipeline, version 2.0. An open-source metatranscriptomics pipeline for analyzing microbiome data, built around DIAMOND and customi…☆57Updated last year
- SHallow shOtGUN profiler☆53Updated 3 years ago
- Analysis of metagenomic shotgun sequences including assembly, speciation, ARG discovery and more☆29Updated last year
- Snakemake workflow for metagenomic classification with Kraken2☆65Updated last year
- Compare different differential abundance and expression methods☆51Updated 3 years ago
- Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWoo…☆53Updated 3 years ago
- Course material for the metagenomics course☆43Updated 3 years ago
- ☆23Updated 6 years ago
- A set of R scripts for the analysis of microbial profiles☆41Updated 10 months ago
- R implementation of the LEfSe method☆58Updated last month
- Computational workflows for metagenomics tasks, by the Bhatt lab☆46Updated 2 years ago
- Rapid and scalable correlation estimation for compositional data☆86Updated 11 months ago
- Amplicon sequencing pipelines suitable for SSU (16S, 18S), LSU (23S, 28S) and ITS.☆53Updated 3 months ago
- Statistical Analysis of Metagenomic Profiles☆93Updated 5 years ago
- Parse NCBI taxonomy and accessions to find taxonomic assignments☆74Updated last month
- Archive: R functions for Analysis of Composition of Microbiomes (ANCOM). Please check our ANCOMBC R package for the most up-to-date ANCOM…☆62Updated 2 years ago
- Visualize microbiome data with black magic ggtree☆67Updated 4 years ago
- All of my various bioinformatic scripts fit for public consumption (loosely defining "fit")☆72Updated 2 years ago
- Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing☆115Updated 11 months ago
- The Microbiome Explorer provides methods to analyze and visualize microbial community sequencing data either from the R command line or t…☆70Updated 2 years ago
- Track, Analyze, Visualize: Unravel Your Microbiome's Temporal Pattern with MicrobiomeStat☆40Updated last week
- Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data☆153Updated 2 years ago
- Metatranscriptomics Tutorial☆62Updated last year
- ☆56Updated last year
- gutSMASH☆53Updated 3 months ago
- Bash pipeline for analysis of ONT full-length 16S sequences in QIIME2☆29Updated 5 years ago
- Sparse Cooccurence Network Investigation for Compositional data☆24Updated 5 months ago
- scripts for estimating bacteria replication rates based on population genome copy number variation☆71Updated 5 years ago