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Add support/contribute section and references to README.md
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@@ -117,9 +117,9 @@ Outputs are placed in a directory called `test_output`. | |
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| Sources of data used in these tests are: | ||
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| * The [Bottomly dataset](http://bowtie-bio.sourceforge.net/recount/ExpressionSets/bottomly_eset.RData) from [ReCount](http://bowtie-bio.sourceforge.net/recount/). | ||
| * The [Bottomly dataset](http://bowtie-bio.sourceforge.net/recount/ExpressionSets/bottomly_eset.RData) from [ReCount](http://bowtie-bio.sourceforge.net/recount/) (Frazee, Langmead and Leek, 2011). | ||
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| * The "arab" dataset provided in the [NBPSeq package](https://cran.rstudio.com/web/packages/NBPSeq/index.html). | ||
| * The "arab" dataset provided in the [NBPSeq package](https://cran.rstudio.com/web/packages/NBPSeq/index.html) (Di et al, 2011). | ||
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| * Simulated data following negative binomial distributions. | ||
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@@ -128,9 +128,9 @@ Dispersion estimates are compared to those calculated by the [edgeR biocnoductor | |
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| ## Supporting/contributing | ||
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| Please email questions about using this software to the author [[email protected]](email:[email protected]). | ||
| Please email questions about using this software to the author, <[email protected]>. | ||
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| Please file bug reports and feature requests by [filing a bug report](https://github.com/MonashBioinformaticsPlatform/varistran/issues), or by [contacting the author](email:[email protected]). | ||
| Please file bug reports and feature requests by [filing a bug report](https://github.com/MonashBioinformaticsPlatform/varistran/issues), or by contacting the author. | ||
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| Pull requests gratefully considered. | ||
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| Anscombe, Francis J. 1948. "The Transformation of Poisson, Binomial and Negative-Binomial Data." *Biometrika* 35 (3/4): 246–54. | ||
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| Di, Yamming, Daniel W. Schafer, Jason S. Cumbie and Jeff H. Chang. 2011. "The NBP Negative Binomial Model for Assessing Differential Gene Expression from RNA-Seq" *Statistical Applications in Genetics and Molecular Biology* 10 (1). doi:10.2202/1544-6115.1637 | ||
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| Frazee, Alyssa C., Ben Langmead and Jeffrey T. Leek. 2011. "ReCount: A multi-experiment resource of analysis-ready RNA-seq gene count datasets." *BMC Bioinformatics* 12: 449. doi:10.1186/1471-2105-12-449 | ||
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| Love, Michael I., Wolfgang Huber and Simon Anders. 2014. "Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2." *Genome Biology* 15 (12): 550. doi:10.1186/s13059-014-0550-8 | ||
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| McCarthy, Davis J., Yunshun Chen and Gordon K. Smyth. 2012. "Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation." *Nucleic Acids Research* 40 (10): 4288-4297. doi:10.1093/nar/gks042 | ||
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