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package_references.txt
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package_references.txt
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Imported Package References
Alboukadel Kassambara and Fabian Mundt (2017). factoextra: Extract and Visualize the Results of Multivariate Data Analyses. R
package version 1.0.5. https://CRAN.R-project.org/package=factoextra
Andrew McDavid, Greg Finak and Masanao Yajima (2019). MAST: Model-based Analysis of Single Cell Transcriptomics. R package
version 1.10.0. https://github.com/RGLab/MAST/
Baptiste Auguie (2017). gridExtra: Miscellaneous Functions for "Grid" Graphics. R package version 2.3.
https://CRAN.R-project.org/package=gridExtra
Cole Trapnell and Davide Cacchiarelli et al (2014): The dynamics and regulators of cell fate decisions are revealed by
pseudo-temporal ordering of single cells. Nature Biotechnology
Daniel Müllner (2013). fastcluster: Fast Hierarchical, Agglomerative Clustering Routines for R and Python. Journal of
Statistical Software, 53(9), 1-18. URL http://www.jstatsoft.org/v53/i09/.
Dean Attali (2018). shinyjs: Easily Improve the User Experience of Your Shiny Apps in Seconds. R package version 1.0.
https://CRAN.R-project.org/package=shinyjs
Hadley Wickham. ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York, 2016.
Hadley Chen (2018). VennDiagram: Generate High-Resolution Venn and Euler Plots. R package version 1.6.20.
https://CRAN.R-project.org/package=VennDiagram
Hadley Wickham, Romain François, Lionel Henry and Kirill Müller (2019). dplyr: A Grammar of Data Manipulation. R package
version 0.8.3. https://CRAN.R-project.org/package=dplyr
John Coene (2019). waiter: Loading Screen for 'Shiny'. R package version 0.0.1. https://CRAN.R-project.org/package=waiter
Kamil Slowikowski (2019). ggrepel: Automatically Position Non-Overlapping Text Labels with 'ggplot2'. R package version
0.8.1. https://CRAN.R-project.org/package=ggrepel
Love, M.I., Huber, W., Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 Genome
Biology 15(12):550 (2014)
Lun ATL, McCarthy DJ, Marioni JC (2016). “A step-by-step workflow for low-level analysis of single-cell RNA-seq data with
Bioconductor.” _F1000Res._, *5*, 2122. doi: 10.12688/f1000research.9501.2 (URL: https://doi.org/10.12688/f1000research.9501.2).
Marc Carlson (2019). org.Mm.eg.db: Genome wide annotation for Mouse. R package version 3.8.2.
Marc Carlson (2019). org.Hs.eg.db: Genome wide annotation for Human. R package version 3.8.2.
Marc Carlson (2019). GO.db: A set of annotation maps describing the entire Gene Ontology. R package version 3.8.2.
Matthew Young (2019). geneLenDataBase: Lengths of mRNA transcripts for a number of genomes. R package version 1.20.0.
R Core Team (2019). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna,
Austria. URL https://www.R-project.org/.
Ritchie, M.E., Phipson, B., Wu, D., Hu, Y., Law, C.W., Shi, W., and Smyth, G.K. (2015). limma powers differential expression
analyses for RNA-sequencing and microarray studies. Nucleic Acids Research 43(7), e47.
Robinson MD, McCarthy DJ and Smyth GK (2010). edgeR: a Bioconductor package for differential expression analysis of digital
gene expression data. Bioinformatics 26, 139-140
Stuart and Butler et al. Comprehensive integration of single cell data. bioRxiv (2018).
Team BC (2019). GenomeInfoDbData: Species and taxonomy ID look up tables used by GenomeInfoDb. R package version 1.2.1.
Thomas Lin Pedersen, Vincent Nijs, Thomas Schaffner and Eric Nantz (2019). shinyFiles: A Server-Side File System Viewer for
Shiny. R package version 0.7.3. https://CRAN.R-project.org/package=shinyFiles
Victor Perrier, Fanny Meyer and David Granjon (2019). shinyWidgets: Custom Inputs Widgets for Shiny. R package version 0.4.8.
https://CRAN.R-project.org/package=shinyWidgets
Vladimir Yu. Kiselev, et al. (2017): SC3 - consensus clustering of single-cell RNA-Seq data. Nature Methods, URL:
http://dx.doi.org/10.1038/nmeth.4236
Winston Chang, Joe Cheng, JJ Allaire, Yihui Xie and Jonathan McPherson (2019). shiny: Web Application Framework for R. R
package version 1.3.2. https://CRAN.R-project.org/package=shiny
Yihui Xie, Joe Cheng and Xianying Tan (2019). DT: A Wrapper of the JavaScript Library 'DataTables'. R package version 0.7.
https://CRAN.R-project.org/package=DT
Young, M.D., Wakefield, M.J., Smyth, G.K., Oshlack, A., Gene ontology analysis for RNA-seq: accounting for selection bias,
Genome Biology, 11, 2, Feb 2010, R14