ShadeLab / ConditionallyRareTaxa
R scripts and tutorial datasets to detect conditionally rare taxa in time series of microbial communities
☆20Updated 4 years ago
Related projects ⓘ
Alternatives and complementary repositories for ConditionallyRareTaxa
- Speedy versions of phyloseq functions☆46Updated 7 months ago
- The is mostly a wrapper tool using phyloseq and microbiome R packages.☆33Updated 2 years ago
- functions for analyzing phyloseq data☆26Updated 3 months ago
- The Microbiome Explorer provides methods to analyze and visualize microbial community sequencing data either from the R command line or t…☆69Updated 2 years ago
- Miscellaneous functions for metagenomic analysis.☆46Updated 5 months ago
- AMPtk: Amplicon ToolKit for NGS data (formally UFITS)☆38Updated last year
- diversity estimation under ecological networks☆83Updated last year
- A set of R scripts for the analysis of microbial profiles☆40Updated 6 months ago
- Various customs functions written to enhance the base functions of phyloseq. Most of them are used in the formation "Métagénomique 16S" p…☆33Updated last year
- An R package for analysis of microbiome relative abundance data using zero inflated beta GAMLSS and meta-analysis across microbiome studi…☆33Updated 4 years ago
- An R package for microbial community analysis in an environmental context☆66Updated 4 years ago
- A robust and fast clustering method for amplicon-based studies☆31Updated last year
- QIIME 2 plugin wrapping DADA2☆19Updated last month
- Barcode demultiplex for Illumina I1, R1, R2 fastq.gz files☆31Updated 7 years 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☆31Updated 4 years ago
- power estimation for microbiome studies analyzed with pairwise distances and PERMANOVA☆35Updated 9 years ago
- Tools for visualising microbial community amplicon data☆67Updated 6 months ago
- Protocol for finding informative protein families and then using them to score metagenomic sets.☆9Updated 3 years ago
- ☆69Updated 11 months ago
- ☆50Updated this week
- Phylogenetic Organization of Metagenomic Signals (POMS)☆19Updated last year
- Sparse Cooccurence Network Investigation for Compositional data☆23Updated 3 weeks ago
- Compare different differential abundance and expression methods☆50Updated 2 years ago
- Growth Rate Index (GRiD) measures bacterial growth rate from reference genomes (including draft quality genomes) and metagenomic bins at …☆31Updated 4 years ago
- Experimental pipeline to perform de novo PICRUSt on de-noised amplicon sequence variants (ASV)☆19Updated 6 years ago
- Various functions for analysis of microbial community data☆42Updated 2 years ago
- R scripts for performing co-occurrence analyses☆34Updated 9 years ago
- Visualize microbiome data with black magic ggtree☆68Updated 4 years ago
- Amplicon sequencing pipelines suitable for SSU (16S, 18S), LSU (23S, 28S) and ITS.☆53Updated 2 months ago