Bioinformatics and Computational Biology Solutions Using R and Bioconductor

Part I. Preprocessing data from genomic experiments

1. Preprocessing Overview
W. Huber, R. A. Irizarry, R. Gentleman

2. Preprocessing High-density Oligonucleotide Arrays
B. M. Bolstad, R. A. Irizarry, L. Gautier, Z. Wu

3. Quality Assessment of Affymetrix GeneChip Data
B. M. Bolstad, F. Collin, J. Brettschneider, K. Simpson, L. Cope, R. A. Irizarry, T.P. Speed

4. Preprocessing Two-Color Spotted Arrays
Y. H. Yang, A. C. Paquet

5. Cell-Based Assays
W. Huber, F. Hahne

6. SELDI-TOF Mass Spectrometry Protein Data
X. Li, R. Gentleman, X. Lu, Q. Shi, J.D. Iglehart, L. Harris, A. Miron

Part II. Meta-data: biological annotation and visualization

7. Meta-data Resources and Tools in Bioconductor
R. Gentleman, V. J. Carey, J. Zhang

8. Querying On-line Resources
V. J. Carey, D. Temple Lang, J. Gentry, J. Zhang, R. Gentleman

9. Interactive Outputs
C. A. Smith, W. Huber, R. Gentleman

10. Visualizing Data
W. Huber, X. Li, R. Gentleman

Part III. Statistical analysis for genomic experiments

11. Analysis Overview
V. J. Carey, R. Gentleman

12. Distance Measures in DNA Microarray Data Analysis
R. Gentleman, B. Ding, S. Dudoit, J. Ibrahim

13. Cluster Analysis of Genomic Data
K. S. Pollard, M. J. Laan

14. Analysis of Differential Gene Expression Studies
D. Scholtens, A. Heydebreck

15. Multiple Testing Procedures: the multtest Package and Applications to Genomics
K. S. Pollard, S. Dudoit, M. J. Laan

16. Machine Learning Concepts and Tools for Statistical Genomics
V. J. Carey

17. Ensemble Methods of Computational Inference
T. Hothorn, M. Dettling, P. Bühlmann

18. Browser-based Affymetrix Analysis and Annotation
C. A. Smith

Part IV. Graphs and networks

19. Introduction and Motivating Examples
R. Gentleman, W. Huber, V. J. Carey

20. Graphs
W. Huber, R. Gentleman, V. J. Carey

21. Bioconductor Software for Graphs
V. J. Carey, R. Gentleman, W. Huber, J. Gentry

22. Case Studies Using Graphs on Biological Data
R. Gentleman, D. Scholtens, B. Ding, V. J. Carey, W. Huber

Part V. Case studies

23. limma: Linear Models for Microarray Data
G. K. Smyth

24. Classification with Gene Expression Data
M. Dettling

25. From CEL Files to Annotated Lists of Interesting Genes
R. A. Irizarry

DRM-restrictions

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Nyckelord: COMPUTERS / Computer Science COM014000