waldronlab / lefser
R implementation of the LEfSe method
☆56Updated last month
Alternatives and similar repositories for lefser:
Users that are interested in lefser are comparing it to the libraries listed below
- Archive: R functions for Analysis of Composition of Microbiomes (ANCOM). Please check our ANCOMBC R package for the most up-to-date ANCOM…☆61Updated 2 years ago
- ☆55Updated last year
- Transform files to the microtable object with microeco package☆25Updated 3 months ago
- Compare different differential abundance and expression methods☆51Updated 3 years ago
- Statistical analysis for sparse high-throughput sequencing☆69Updated 3 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
- Amplicon sequencing pipelines suitable for SSU (16S, 18S), LSU (23S, 28S) and ITS.☆54Updated 2 months ago
- Visualize microbiome data with black magic ggtree☆67Updated 4 years ago
- Scripts for stat and plot figures in rice microbiome paper☆31Updated 5 months ago
- Microbiome Analysis Using R Workshop originally organized for the 2018 ASM General Meeting in Atlanta, GA, but regularly updated since.☆27Updated 2 years ago
- Reproducible Analyses accompanying DADA2 + PacBio Manuscript☆32Updated 4 years ago
- Rice (Oryza Sative) root microbiome time-course analysis. (Zhang2018SCLS)☆32Updated 5 years ago
- A set of R scripts for the analysis of microbial profiles☆41Updated 10 months ago
- Fantaxtic - Nested Bar Plots for Phyloseq Data☆29Updated 8 months ago
- Scripts for stat and plot figures in rice microbiome paper☆19Updated 5 years ago
- Analysis of metagenomic shotgun sequences including assembly, speciation, ARG discovery and more☆27Updated last year
- A microbiome analysis toolkit for R☆22Updated last year
- Statistics and visualization for amplicon data☆71Updated last year
- Course material for the metagenomics course☆43Updated 3 years ago
- Differential abundance (DA) and correlation analyses for microbial absolute abundance data☆120Updated this week
- Parse NCBI taxonomy and accessions to find taxonomic assignments☆73Updated last week
- R package for microbiome data visualization and statistics. Uses phyloseq, vegan and the tidyverse. Docker image available.☆114Updated 2 months ago
- Track, Analyze, Visualize: Unravel Your Microbiome's Temporal Pattern with MicrobiomeStat☆39Updated last month
- gutSMASH☆53Updated 3 months ago
- Batch effects removal for microbiome data via conditional quantile regression☆27Updated 2 years ago
- The dysbiosisR package implements tools for calculating some common microbiome dysbiosis measures☆14Updated 2 years ago
- Archive: Data, scripts, and outputs for the Nat. Comm. paper "Analysis of Composition of Microbiomes with Bias Correction". Please check …☆30Updated 4 years ago
- Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing☆115Updated 10 months 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
- Collection of notebooks describing the basic analysis workflow for a 16S rRNA gene amplicon sequencing project☆11Updated 2 years ago