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Introduction
NGS Workflow Overview
1. Introduction
2. Getting Started
3. Workflow overview
4. Workflow templates
5. Version information
6. References
RNA-Seq Workflow
1. Introduction
2. Samples and environment settings
3. Read preprocessing
4. Alignments
5. Read quantification
6. Analysis of DEGs
7. GO term enrichment analysis
8. Clustering and heat maps
9. Version Information
10. Funding
11. References
ChIP-Seq Workflow
1. Introduction
2. Workflow environment
3. Read preprocessing
4. Alignments
5. Utilities for coverage data
6. Peak calling with MACS2
7. Annotate peaks with genomic context
8. Count reads overlapping peaks
9. Differential binding analysis
10. GO term enrichment analysis
11. Motif analysis
12. Version Information
13. Funding
14. References
VAR-Seq Workflow
1. Introduction
2. Workflow environment
3. Read preprocessing
4. Alignments
5. Variant calling
6. Filter variants
7. Annotate filtered variants
8. Combine annotation results among samples
9. Summary statistics of variants
10. Venn diagram of variants
11. Plot variants programmatically
12. Version Information
13. Funding
14. References
RIBO-Seq Workflow
1. Introduction
2. Load workflow template
3. Read preprocessing
4. Alignments
5. Read distribution across genomic features
6. Adding custom features to workflow
7. Genomic read coverage along transripts or CDSs
8. Read quantification per annotation range
9. Analysis of differentially expressed genes with edgeR
10. GO term enrichment analysis of DEGs
11. Differential ribosome loading analysis (translational efficiency)
12. Clustering and heat maps
13. Render report in HTML and PDF format
14. Version Information
15. Funding
16. References
Training Events
Training Events
Publications
Publications
Acknowledgement
Acknowledgement
Contacts
Contacts
Acknowledgement
Acknowledgement
This project is funded by NSF award
ABI-1661152
.