Sweave Engine for TeXShop
cameron.bracken.bz » Sweave Engine for TeXShop. An alternative to Emacs org-mode (though highlighting is still LaTeX-specific, not R).
View Articlencbi_decrypt
I’m tired of writing little shell script “one liners” to decrypt files we get from dbGaP, and I’m tired of having to keep a terminal window open while they finish (with many BAM files, this can take...
View Articlecontrasts and factorial designs in limma
I thought this was a pretty cute trick: > Pop Trt Time contrasts(Pop) contrasts(Trt) contrasts(Time) design rownames(design) solve(crossprod(design),t(design)) BMA.c.0 BMA.c.1 BMA.e.0 BMA.e.1...
View ArticleR reference card(s)
This is pretty extensive, while still being compact: Short-refcard.pdf. Actually, there’s lots of good reference material here.
View Article5-way venn diagrams
library(gplots) w1 = (100*runif(100)) %/% 1 w2 = (100*runif(100)) %/% 1 w3 = (100*runif(100)) %/% 1 w4 = (100*runif(100)) %/% 1 w5 = (100*runif(100)) %/% 1 VennList<-list(A=w1, B = w2, C = w3, D =...
View Articleggplot legend positioning
I found this cute trick here: https://github.com/hadley/ggplot2/wiki/Legend-Attributes plot + opts(legend.position = c(0.5, 0.5)) you can adjust the values between 0 and 1 for x- and y- relative...
View Articleheatmaps of significant gene expression
Thought I’d share this little ditty, which starts out assuming you have a matrix of gene expression results, significant for some contrast of interest. In this particular case, the matrix variable...
View ArticleModel-based gene set analysis for Bioconductor
Model-based gene set analysis for Bioconductor. We should give this a try for our various GO enrichment tests …
View Articlecqn paper
REMOVING TECHNICAL VARIABILITY IN RNA-SEQ DATA USING CONDITIONAL QUANTILE NORMALIZATION.
View Articleimproved gene selection for heatmaps
In a previous post I demonstrated a heatmap analysis. Here I’ll make some significant improvements to that code: 1) blue-white-red instead of green-black-red color gradients (friendly to the color...
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