Microbiome Data Analysis Workshops by Institute for Environmental Genomics @ OU
Time: Friday 10:00 to 12:00 am on Dec 13 and from Jan 10 to Mar 20.
Location: SRTC board room (room 1020), 101 David L Boren Blvd, Norman. * On Dec 13, we will use the SRTC core room.
Topics: The workshops are mainly about microbial community data analysis. Each workshop has introduction and hands-on practice (you need to bring your own laptop). Current schedule is as below. Further changes will be announced via email list and on http://ccl.oucreate.com/. Please contact daliang (email@example.com) to be included in the email list if you are interested.
(1) Dec 13, Opening & Sequencing data analysis
Overview of data analysis methods and tools in workshops.
Amplicon sequencing data pre-processing: web-based pipeline.
(2) Jan 10, Sequencing & Diversity
Amplicon sequencing data pre-processing: DADA2
Alpha and beta diversity, taxonomic and phylogenetic diversity
Estimation of coverage and species pool
IEG statistical analysis pipeline (new)
(3) Jan 17, Comparison
Dimension reduction: PCA DCA NMDS PCoA PCNM
Comparison: dissimilarity test, dispersion, specificity, response ratio, effect size, etc.
Show difference on large tree
(4) Jan 24, Linkage-1
Vector-based: Correlation test, partial correlation, linear model, GLM, HLM, etc.
Matrix-based: Mantel, partial mantel, MRM, CCA/RDA, distance-based RDA, VPA, etc.
Adjusted and cross validated R squared
(5) Jan 31, Linkage-2
SEM: structural equation modeling
Random forest (machine learning)
(6) Feb 7, Linkage-3
Network analysis pipeline
(7) Feb 14, Mechanisms
Spatial and temporal patterns: taxa area relationship, distance decay, time decay, etc.
Community assembly mechanisms: stochasticity, ecological processes, etc.
(8) Feb 21, Metagenomics
Assembly-based analysis (TBD)
Eco-Fun Map pipeline
(9) Feb 28, Function
GeoChip data analysis
Infer function from sequencing data
(10) Mar 6, Modeling (new)
Ecosystem modeling and MEND model
(11) Mar 13, Programing (new)
Build your own R function
Build your own R package
Introduction of Python
(12) Mar 20, Closing
Future plan for tools/pipelines development