Genomic Data Analysis for Plant Research
( 24 Modules )

Module #1
Introduction to Genomic Data Analysis
Overview of genomics and its applications in plant research

Module #2
Plant Genomics and Genome Assembly
Introduction to plant genomes, genome assembly, and annotation

Module #3
Sequencing Technologies and Data Generation
Overview of sequencing technologies and data generation for plant genomics

Module #4
Quality Control and Preprocessing of Sequencing Data
Quality control, trimming, and filtering of sequencing data

Module #5
Genome Assembly and Scaffolding
Genome assembly and scaffolding using popular tools and methods

Module #6
Gene Prediction and Annotation
Gene prediction and annotation using ab initio, evidence-based, and hybrid approaches

Module #7
Functional Annotation and Gene Ontology
Functional annotation of genes using Gene Ontology (GO) and other resources

Module #8
Variant Detection and Genotyping
Variant detection and genotyping using SNPs, indels, and structural variations

Module #9
Association Mapping and GWAS
Association mapping and genome-wide association studies (GWAS) for trait mapping

Module #10
RNA-Seq Data Analysis
RNA-Seq data analysis for gene expression, differential expression, and isoform detection

Module #11
ChIP-Seq Data Analysis
ChIP-Seq data analysis for chromatin immunoprecipitation and histone modification profiling

Module #12
Epigenomics and DNA Methylation Analysis
Epigenomics and DNA methylation analysis using bisulfite sequencing and other methods

Module #13
Transcriptome Assembly and Quantification
Transcriptome assembly and quantification using RNA-Seq and other data

Module #14
Differential Expression Analysis
Differential expression analysis using DESeq2, edgeR, and other popular tools

Module #15
Gene Regulatory Network Inference
Gene regulatory network inference using co-expression analysis and other methods

Module #16
Pathway Analysis and Gene Set Enrichment
Pathway analysis and gene set enrichment using tools like KEGG, Reactome, and MSigDB

Module #17
Comparative Genomics and Phylogenetics
Comparative genomics and phylogenetics using whole-genome alignment and tree reconstruction methods

Module #18
Plant Genome Databases and Resources
Overview of popular plant genome databases and resources, including Ensembl Plants and Phytozome

Module #19
Command-Line Interfaces and Scripting for Genomic Data Analysis
Introduction to command-line interfaces and scripting for genomic data analysis

Module #20
R and Bioconductor for Genomic Data Analysis
Using R and Bioconductor for genomic data analysis and visualization

Module #21
Visualizing Genomic Data with Circos and Other Tools
Visualizing genomic data using Circos, IGV, and other popular visualization tools

Module #22
Big Data and Cloud Computing for Genomic Data Analysis
Using big data and cloud computing for large-scale genomic data analysis

Module #23
Best Practices and Collaborative Research in Genomic Data Analysis
Best practices, collaborative research, and publishing genomic data analysis results

Module #24
Course Wrap-Up & Conclusion
Planning next steps in Genomic Data Analysis for Plant Research career

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Genomic Data Analysis for Plant Research ( 24 Modules )

Genomic Data Analysis for Plant Research
( 24 Modules )