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Batch effect correction
- Leek, J. T. & Storey, J. D. Capturing Heterogeneity in Gene Expression Studies by Surrogate Variable Analysis. PLoS Genet 3, e161 (2007). [TAKEN: Gloria and Marea]
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RNA-seq
- Anders, S., Reyes, A. & Huber, W. Detecting differential usage of exons from RNA-seq data. Genome Res. 22, 2008-2017 (2012).
- Frazee, A. C., Sabunciyan, S., Hansen, K. D., Irizarry, R. A. & Leek, J. T. Differential expression analysis of RNA-seq data at single-base resolution. Biostatistics kxt053 (2014). doi:10.1093/biostatistics/kxt053. [TAKEN: Yatong, Xiaowen and Kelsey]
- Risso, D., Ngai, J., Speed, T. P. & Dudoit, S. Normalization of RNA-seq data using factor analysis of control genes or samples. Nature Biotechnology 32, 896–902 (2014). [TAKEN: Ben and Aaron]
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Single-cell gene-expression
- McDavid, A. et al. Data exploration, quality control and testing in single-cell qPCR-based gene expression experiments. Bioinformatics 29, 461-467 (2013).
- Shalek, A. K. et al. Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells. Nature 498, 236-240 (2013).
- Trapnell, C. et al. The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells. Nature Biotechnology 32, 381–386 (2014).
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Gene expression deconvolution
- Shen-Orr, S. S. et al. Cell type-specific gene expression differences in complex tissues. Nat. Methods 7, 287-289 (2010).
- Zhong, Y. & Liu, Z. Gene expression deconvolution in linear space. Nat. Methods 9, 8–9– author reply 9 (2012). [TAKEN: Benjamin & Sara]
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Methylation
- Hansen, K. D., Langmead, B. & Irizarry, R. A. BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions. Genome Biol. (2012).
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Flow cytometry
- Finak, G. et al. OpenCyto: an open source infrastructure for scalable, robust, reproducible, and automated, end-to-end flow cytometry data analysis. PLoS Comput. Biol. 10, e1003806 (2014).
- Amir, E.-A. D. et al. viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia. Nature Biotechnology 31, 545–552 (2013).
- Read and understand the paper
- Reproduce some of the analysis
- Summarize the paper with the analysis in reproducible presentation (a .Rmd file)
- Present your work to the rest of the class