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BioMart
http://www.biomart.org/

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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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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

Posted from Diigo. The rest of my favorite links are here.

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## Great explanation about many apply funct …

Great explanation about many apply functions in R

A brief introduction to “apply” 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

nx[]

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.

```