tleonardi

#!/bin/bash
# Wrapper script to run Vim-R-plugin R sessions as interactive jobs on LSF platforms.
# To use it, edit ~/.vimrc and add 'let vimrplugin_r_path = <path_to_script>'

# lets you deicde 
echo What version of R do you want?
echo "1) R vX.X.X"
echo "2) R vZ.Z.Z"
echo "3) R vY.Y.Y"
read -t 60 -p '>' answer

tleonardi

bjobs -r -u all | tail -n +2 | awk '{print $2}' | sort | uniq -c | sed 's/^*//' | sort -k1,1nr | head -30 | /usr/bin/gnuplot -persist -e "set boxwidth 0.1;set style fill solid 0.5 border -1; set logscale y;plot '-' using 1:xtic(2) with boxes"

tleonardi

library(reshape2)
library(ggplot2)

tasks <- c("M1.1: Text \n here", 
"M1.2: Text \n here", 
"M1.3: Text \n here",
"M2.1: Text \n here",
"M2.2: Text \n here",
"M2.3: Text \n here"
)

tleonardi

```{r set-options}
  my_hook <- function(x, options) {
    if (options$fig.show == 'animate') return(hook_plot_html(x, options))
    "%n%" <- knitr:::"%n%"
    base = opts_knit$get('base.url') %n% ''
    cap = knitr:::.img.cap(options)

    if (is.null(w <- options$out.width) & is.null(h <- options$out.height) &
      is.null(s <- options$out.extra) & options$fig.align == 'default') {
      return(sprintf('![%s](%s%s){#fig:%s} ', cap, base, knitr:::.upload.url(x), options$label))

tleonardi

Keybase proof

I hereby claim:

• I am tleonardi on github.
• I am tleonardi (https://keybase.io/tleonardi) on keybase.
• I have a public key whose fingerprint is E6BA BA6A 0F8A 5B99 24B9 25E0 5FB4 E671 D50A 5A4E

To claim this, I am signing this object:

tleonardi

#Flags and scores in Tophat output

Tophat version 2.1.1

There are two functions 'bool rewrite_sam_record()', with different sets of parameters.

The first one is used for singletons the second for paired alignements:

tleonardi

# Tunnel Display
# This function sets up an ssh tunnel that forwards a local display port
# back to the login node's display port. The tunnel is controlled by the
# socket in $HOME/tmp/ssh-${LSB_SUB_HOST}-${HOSTNAME}-${DISPLAY_NUMBER}.
# The ssh tunnel is in the background and keeps running even after the
# interactive shell is closed, thus preventing completion of the LSF job.
# To avoid this, we setup a trap on SIGINT SIGTERM EXIT that uses the ssh
# control socket to signal the tunnel to exit.
tund(){
if [[ -n $LSB_JOBID ]]; then

tleonardi

#!/bin/awk -f
function logfactorial(n,    f, i){
  f=0
  for(i=1;i<=n;i++){
    f+=log(i)
   }
  return f
}

# m: Mean

tleonardi

# Converts a tab-separated file containing
# DAVID's functional annotation results to
# Markdown format
# It reports: KEGG and GO terms along with
# the gene symbol and name

FILE=
cut -f 1,2,5,6,7,9 $FILE | awk '
BEGIN{OFS=FS="\t"}NR>1{
print "#"$1

tleonardi

plotDispEsts2 <- function(dds){
        require(dplyr)
        require(reshape2)
        require(ggplot2)
        as.data.frame(mcols(dds)) %>% 
        select(baseMean, dispGeneEst, dispFit, dispersion) %>% 
                melt(id.vars="baseMean") %>% 
                filter(baseMean>0) %>% 
                ggplot(aes(x=baseMean, y=value, colour=variable)) + 
                        geom_point(size=0.1) +