This page is being updated. (November 2018)
Articles
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Stably expressed genes in single-cell RNA-sequencing
Julie Deeke and J. A. Gagnon-Bartsch -
scMerge: Integration of multiple single-cell transcriptomics datasets leveraging stable expression and pseudo-replication
Y. Lin, S. Ghazanfar, K. Wang, J. A. Gagnon-Bartsch, K. K. Lo, X. S. Su, Z.-G. Han, J. T. Ormerod, T. P. Speed, P. Yang, and J. Y. H. Yang -
A new normalization for the Nanostring nCounter gene expression assay
Ramyar Molania, J. A. Gagnon-Bartsch, A. Dobrovic, and T. P. Speed -
Correcting gene expression data when neither the unwanted variation nor the factor of interest are observed
Laurent Jacob, Johann A Gagnon-Bartsch, and Terence P Speed -
Statistical methods for handling unwanted variation in metabolomics data
Alysha M De Livera, Marko Sysi-Aho, Laurent Jacob, Johann A Gagnon-Bartsch, Sandra Castillo, Julie A Simpson, and Terence P Speed -
Systematic noise degrades gene co-expression signals but can be corrected
Saskia Freytag, Johann A Gagnon-Bartsch, Terence P Speed, and Melanie Bahlo -
Using control genes to correct for unwanted variation in microarray data
Johann A Gagnon-Bartsch and Terence P Speed -
Removing unwanted variation in a differential methylation analysis of illumina humanmethylation450 array data
Jovana Maksimovic, Johann A Gagnon-Bartsch, Terence P Speed, and Alicia Oshlack -
Removing Unwanted Variation from High Dimensional Data with Negative Controls
J. A. Gagnon-Bartsch, L. Jacob, T. P. Speed
Software
Datasets
- gender.sm.rda "Not preprocessed." Summarized (sm) by RMA, but without background or quantile normalization.
- gender.bgnmsm.rda "Preprocessed." Background correction (bg), quantile normalization (nm) and summarization (sm) by RMA.
- gender.bgnmsmls.rda "Fully preprocessed." Background correction (bg), quantile normalization (nm) and summarization (sm) by RMA, followed by a location-scale adjustment to account for different chip versions.
- alzheimers.sm.rda "Not preprocessed." Summarized (sm) by RMA, but without background or quantile normalization.
- alzheimers.bgnmsm.rda "Preprocessed." Background correction (bg), quantile normalization (nm) and summarization (sm) by RMA.
Lists of Stably Expressed Genes
- List of housekeeping genes from Eisenberg and Levanon (2003).
- List of single cell housekeeping genes from Lin, et al. (2017)
- Gene annotations from Deeke and Gagnon-Bartsch. The cytosolic ribosomal genes seem to be especially stable. See manuscript and supplementary information.
Additional Resources
- useR 2018 RUV tutorial on github
- Docker image on Docker Hub. Includes shiny app and tutorial.
Old
- A how-to for the old ruv_starter_analysis script.