Embedded Files
Exploring microbial diversity using Ranacapa
Exploring microbial diversity using Ranacapa
Overview
Overview
Ranacapa is a web hosted R app maintained by Gaurav Kandlikar, in collaboration with the CALeDNA program. CALeDNA developed and performs the Anacapa eDNA Processing Toolkit. Ranacapa is designed to help explore biodiversity using results from environmental DNA (eDNA) analyses.
We recommend ranacapa as an initial exploration and visualization of the data to help in generation of hypotheses to test using STAMP statistical analyses. Plots produced in ranacapa can be manipulated and saved by hovering over the plots. In addition, ranacapa calculates a number of alpha and beta diversity metrics for making comparisons between samples.
Ranacapa is available at https://gauravsk.shinyapps.io/ranacapa/
Instructions are available in the PUMAA Manual: Activity 2
Concept slides available below.
Learning Objectives
Learning Objectives
Define various parameters of diversity (e.g. richness, evenness).
Compare various indices of diversity (e.g. alpha-diversity and beta-diversity).
Analyze microbial diversity data about samples from different environments.
Hypothesize about the relationship of diversity to other parameters (functional diversity, abiotic factors, plants present, etc.).
Sample/Demo Data
Sample/Demo Data
OTU or ASV table from PUMAA or Anacapa output: 16S_ASV_raw_taxonomy_70_Skirball-example.txt
Metadata: Metadata_anacapa_skirball-example.txt
Page updated
Report abuse