Skip to content

Commit af803e2

Browse files
committed
Add support/contribute section and references to README.md
1 parent 91105e0 commit af803e2

File tree

1 file changed

+8
-4
lines changed

1 file changed

+8
-4
lines changed

README.md

Lines changed: 8 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -117,9 +117,9 @@ Outputs are placed in a directory called `test_output`.
117117

118118
Sources of data used in these tests are:
119119

120-
* The [Bottomly dataset](http://bowtie-bio.sourceforge.net/recount/ExpressionSets/bottomly_eset.RData) from [ReCount](http://bowtie-bio.sourceforge.net/recount/).
120+
* 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).
121121

122-
* The "arab" dataset provided in the [NBPSeq package](https://cran.rstudio.com/web/packages/NBPSeq/index.html).
122+
* The "arab" dataset provided in the [NBPSeq package](https://cran.rstudio.com/web/packages/NBPSeq/index.html) (Di et al, 2011).
123123

124124
* Simulated data following negative binomial distributions.
125125

@@ -128,9 +128,9 @@ Dispersion estimates are compared to those calculated by the [edgeR biocnoductor
128128

129129
## Supporting/contributing
130130

131-
Please email questions about using this software to the author [[email protected]](email:[email protected]).
131+
Please email questions about using this software to the author, <[email protected]>.
132132

133-
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]).
133+
Please file bug reports and feature requests by [filing a bug report](https://github.com/MonashBioinformaticsPlatform/varistran/issues), or by contacting the author.
134134

135135
Pull requests gratefully considered.
136136

@@ -146,6 +146,10 @@ Pull requests gratefully considered.
146146

147147
Anscombe, Francis J. 1948. "The Transformation of Poisson, Binomial and Negative-Binomial Data." *Biometrika* 35 (3/4): 246–54.
148148

149+
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
150+
151+
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
152+
149153
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
150154

151155
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

0 commit comments

Comments
 (0)