https://github.com/dgrtwo/barseqg3
Reproduction information for "Design and Analysis of Bar-Seq Experiments"
https://github.com/dgrtwo/barseqg3
Last synced: about 1 year ago
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Reproduction information for "Design and Analysis of Bar-Seq Experiments"
- Host: GitHub
- URL: https://github.com/dgrtwo/barseqg3
- Owner: dgrtwo
- License: mit
- Created: 2014-10-03T02:08:21.000Z (over 11 years ago)
- Default Branch: master
- Last Pushed: 2014-10-03T02:08:59.000Z (over 11 years ago)
- Last Synced: 2025-02-10T13:12:17.606Z (over 1 year ago)
- Language: R
- Size: 7.25 MB
- Stars: 2
- Watchers: 3
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
Design and Analysis of Bar-seq Experiments
==========================================
This repository contains instructions for reproducing the manuscript:
[David G. Robinson, Wei Chen, John D. Storey and David Gresham. "Design and
Analysis of Bar-seq Experiments." G3. 10.1534/g3.113.008565](http://www.g3journal.org/content/4/1/11.long)
We use [knitr](http://yihui.name/knitr/) to generate the manuscript from the
input data, and compile the manuscript with LaTeX.
This was originally provided as [File S1 with the original manuscript](http://www.g3journal.org/content/4/1/11/suppl/DC1)- providing it as a GitHub repository is an attempt to make it easier to keep it working, whether with bugs in the original or with changing R packages.
### SETUP
This manuscript requires R at least version 2.15 (recommended 3.0) to reproduce,
as well as pdflatex to compile. You'll also need to install the
following packages from CRAN and BioConductor:
install.packages(c("plyr", "data.table", "reshape", "ggplot2", "gplots",
"colorRamps", "gridExtra", "xtable"))
source("http://bioconductor.org/biocLite.R")
biocLite(c("GSEABase", "org.Sc.sgd.db", "GO.db", "edgeR", "DESeq",
"qvalue"))
You also have to install the eigenR2 package from [here](http://www.genomine.org/eigenr2/)
### REPRODUCTION
To reproduce the manuscript, run the following lines on your terminal:
Rscript -e "library(knitr); knit('Robinson_2013.Rnw')" # reproduce manuscript
pdflatex Robinson_2013.tex # compile LaTeX
In a few minutes it should generate the full PDF of the manuscript, along with
all figures except 1A and all tables except Tables 1 and 2.
### SESSION
The manuscript was originally compiled with the following sessionInfo():
R version 3.0.1 (2013-05-16)
Platform: x86_64-apple-darwin10.8.0 (64-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] grid parallel stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] qvalue_1.34.0 gridExtra_0.9.1 scales_0.2.3
[4] colorRamps_2.3 gplots_2.11.3 MASS_7.3-28
[7] KernSmooth_2.23-10 caTools_1.14 gdata_2.13.2
[10] gtools_3.0.0 eigenR2_1.0 xtable_1.7-1
[13] reshape_0.8.4 plyr_1.8 ggplot2_0.9.3.1.99
[16] GO.db_2.9.0 org.Sc.sgd.db_2.9.1 RSQLite_0.11.4
[19] DBI_0.2-7 GSEABase_1.22.0 graph_1.38.3
[22] annotate_1.38.0 AnnotationDbi_1.22.6 DESeq_1.12.1
[25] lattice_0.20-23 locfit_1.5-9.1 Biobase_2.20.1
[28] BiocGenerics_0.6.0 edgeR_3.2.4 limma_3.16.7
[31] data.table_1.8.8 knitr_1.4.1
loaded via a namespace (and not attached):
[1] bitops_1.0-6 colorspace_1.2-2 dichromat_2.0-0 digest_0.6.3
[5] evaluate_0.4.7 formatR_0.9 genefilter_1.42.0 geneplotter_1.38.0
[9] gtable_0.1.2 IRanges_1.18.3 labeling_0.2 munsell_0.4.2
[13] proto_0.3-10 RColorBrewer_1.0-5 reshape2_1.2.2 splines_3.0.1
[17] stats4_3.0.1 stringr_0.6.2 survival_2.37-4 tcltk_3.0.1
[21] tools_3.0.1 XML_3.95-0.2