RaiaN

#!/bin/bash

gffs=`ls -1 | grep -E "*.gff" | sort`
RNA_SUFFIX=".rnaseqs.gff" 
mkdir 16s

echo "Cleaning..."
rm *rnaseq*
rm *16s*
rm *.fai

roblanf

source("http://bioconductor.org/biocLite.R")
biocLite("genomes")

library(genomes)
library(ggplot2)

valid <- c("released", "created", "submitted")

data(proks)
update(proks)

sckott

to get similar results for GBIF search and download APIs

Load rgbif

library("rgbif")

occ_search() method

jrherr

SAM and BAM filtering one-liners

@author: David Fredman, [email protected] (sans poly-A tail)
@dependencies: http://sourceforge.net/projects/bamtools/ and http://samtools.sourceforge.net/

Please comment or extend with additional/faster/better solutions.

BWA mapping (using piping for minimal disk I/O)

0x0dea

def Process.gsub pat, sub
  mem  = File.open('/proc/self/mem', 'r+')
  maps = File.open('/proc/self/maps')

  maps.each do |map|
    from, to, perms, offset = map.scan(/(\h+)-(\h+) (\S+) (\h+)/)[0]

    if perms['rw']
      from, to = [from, to].map { |addr| addr.hex + offset.hex }
      data = mem.tap { |m| m.seek from }.read(to - from) rescue next

ttscoff

# Voices available to `say` on OS X
# "*" indicates new additions since 10.8

 Agnes                (en_US)
 Albert               (en_US)
 Alex                 (en_US)
*Alice                (it_IT)
*Alva                 (sv_SE)
*Amelie               (fr_CA)
*Anna                 (de_DE)

jooolia

## Quick attempt to ggplot-i-fy the heatmap post seen here:  https://biomickwatson.wordpress.com/2015/04/09/recreating-a-famous-visualisation/
measles_cases <- read.csv("../data/MEASLES_Cases_1909-2001_20150409092603.csv", skip=2, stringsAsFactors=FALSE)

## From blog post
measles_cases[measles_cases=="-"] <- 0

## not sure what is happening in the last col
measles_cases <- measles_cases[,-62]

for (i in 2:61) {

lindenb

$ (find ./ -name "*final.bam"  | while read F; do samtools view -c ${F} 22 ; done ) | sort -n | gnuplot -e "set terminal dumb 130 40 ; set title 'Reads chr22'; plot '-' with lines notitle;"

                                                                Reads chr22

    1.6e+06 ++------------+--------------+-------------+--------------+-------------+-------------+--------------+------------++
            +             +              +             +              +             +             +              +             +
            |                                                                                                                  *
    1.5e+06 ++                                                                                                                *+
            |                                                                                                                * |
            |                                                                                                  

dwinter

#Finding the number of sequence records by taxonomic group

Ricardo wants to know how to find the number of sequence records associated with sub-groups within a given taxon . This example grew a bit too big to make into a comment, so here it is in gist form.

So, let's find out how many DNA sequences are present in genbank for each

stephenturner

[include]
	# For user/credentials/token/etc
	path = ~/.gitconfig.local
[core]
	editor = vim
	excludesfile = ~/.gitignore
[color]
	branch = auto
	diff = auto
	status = auto