sahilseth

a<-1:5

fn<-lapply(a, function(i) {
    force(i)
    function(x) {
        x * i
    }
})

sahilseth

# clone
git clone source

# add changes to be committed
git add .

git commit -m "my message"

git push

sahilseth

dbNSFP version 3.0b2a

Release:
	April 12, 2015
	
Major sources:
	Variant determination:
		Gencode release 22/Ensembl 79, released March, 2015 (hg38)
	Functional predictions:
		SIFT ensembl 66, released Jan, 2015 http://provean.jcvi.org/index.php

sahilseth

# http://www.r-bloggers.com/r-function-of-the-day-foodweb/

#install.packages("mvbutils")
library(mvbutils)

foodweb()

sahilseth

#!/bin/bash
#set -x 

# Shows you the largest objects in your repo's pack file.
# Written for osx.
#
# @see http://stubbisms.wordpress.com/2009/07/10/git-script-to-show-largest-pack-objects-and-trim-your-waist-line/
# @author Antony Stubbs

# set the internal field spereator to line break, so that we can iterate easily over the verify-pack output

sahilseth

Rscript wrangl_00_run_htseq.R | tee wrangl_00_run_htseq.Rout

sahilseth

awk '{ if($1 !~ /^#/){print "chr"$0} else{print $0} }'  Homo_sapiens.GRCh37.75.gtf

sahilseth

# idea is to, first filter based on a condition, and then display the results
Rscript -e 'library(dplyr);params::read_sheet("flow_details.txt") %>% filter(exit_code>0)' | less

# we add select, to show only a few columns:
Rscript -e 'library(dplyr);params::read_sheet("flow_details.txt") %>% filter(exit_code>0) %>% select(jobname, jobnm, num, exit_code, cmd)' | less

# add kable, to show results in a markdown format:
Rscript -e 'library(dplyr);library(params);read_sheet("flow_details.txt") %>% filter(exit_code>0) %>% select(jobname, jobnm, num, exit_code, cmd)%>% kable()' | less

sahilseth

log2(as.numeric(select(clust, PATC53.377)[1,]) / as.numeric(select(clust, one_of(newrefs))[1,]))


VS

as.numeric(select(clust, PATC53.377)[1,]) / as.numeric(select(clust, one_of(newrefs))[1,]) %>% log2()

sahilseth

# http://stackoverflow.com/questions/14113427/brew-update-failed
cd $(brew --prefix)
git reset --hard HEAD

# cellar on hpcc cluster
# --prefix=~/.linuxbrew/Cellar

git clean -df

brew update