IEG Data Analysis Workshop 2019-2020 is coming

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 (ningdaliang@ou.edu) 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

P adjustment

 

(5) Jan 31, Linkage-2

SEM: structural equation modeling

Random forest (machine learning)

 

(6) Feb 7, Linkage-3

Network analysis pipeline

Network visualization

 

(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

Read-based analysis

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

Questions

 

Daliang Ning
About Daliang Ning 3 Articles
Research Scientist at CCL OU.

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