BioMart
Sequence and feature download tools
http://www.biomart.org/
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Month: January 2011
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RSAT (Regulatory Sequence Analysis Tools …
RSAT (Regulatory Sequence Analysis Tools)
http://rsat.ccb.sickkids.ca/index.html
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E. coli promoter sequences: RegulonDB
E. coli promoter sequences: RegulonDB
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Human TF motifs JASPAR database
Human TF motifs
JASPAR database
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Prodoric database E. coli TF motifs ht …
Prodoric database
E. coli TF motifs
http://prodoric.tu-bs.de/
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GOMO: predicting GO terms from PWM http …
GOMO: predicting GO terms from PWM
http://meme.nbcr.net
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R 01/22/2011
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Great explanation about many apply funct …
Great explanation about many apply functions in R
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Use sapply(), lapply(), vapply() when th …
Use sapply(), lapply(), vapply() when the data is data frame or list and use apply() when the data is matrix. Because matrix does not have the “direction”, e.g., row-wise or column-wise, to apply the function. So it has to be explicitly given.
apply(data, 2, FUN) # for example, column-wise application of the FUN
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Difference between “[” and “[[” in R …
Difference between “[” and “[[” in R
Those are operators for elements in R.
The difference between the two is that “[” slices the data while “[[” extracts the data.
The reason is “[[” iterates to get the data.
The manual says it in this way; “[” keep the name while “[[” drops the name, which is hard for me to understand what it means.
Example,
nx <- c(Abc = 123, pi = pi) nx[1] nx[[1]]The difference between "[" and "[[" is more prominent when they are used with c()
z <- list(a = list(b=9, c= c("helo", "world")), d=1:5) z[[c(1,2)]] returns the first and the second elements of z which are all a and d. On the other hand, z[[c(1,2)]] returns the second element of the first element which is the list c.