adham90

SPC s c remove highlight

**** Files manipulations key bindings
Files manipulation commands (start with ~f~):

| Key Binding | Description                                                    |
|-------------+----------------------------------------------------------------|
| ~SPC f c~   | copy current file to a different location                      |
| ~SPC f C d~ | convert file from unix to dos encoding                         |
| ~SPC f C u~ | convert file from dos to unix encoding                         |

jwcarr

# Variation of information (VI)
#
# Meila, M. (2007). Comparing clusterings-an information
#   based distance. Journal of Multivariate Analysis, 98,
#   873-895. doi:10.1016/j.jmva.2006.11.013
#
# https://en.wikipedia.org/wiki/Variation_of_information

from math import log

rasmusab

# Prior to the tutorial make sure that the script below runs without error on your R installation.
# What you need is a working installation of Stan: http://mc-stan.org/ .
# For installation instructions, see here: 
# https://github.com/stan-dev/rstan/wiki/RStan-Getting-Started

# After installation you should be able to run this script which should output
# some summary statistics and some pretty plots, :)

# Generating some fake data
set.seed(123)

k3yavi

import sys

##########################################################
#requires snakemake, python3, pyfasta to be installed
#save this file and provide all the binaries and their path
#in variables below.
#to run flux pipeline:
#snakemake run_flux_pipeline
#to run rsem pipeline:
#snakemake run_rsem_pipeline

stephenturner

## RNA-seq analysis with DESeq2
## Stephen Turner, @genetics_blog

# RNA-seq data from GSE52202
# http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gse52202. All patients with
# ALS, 4 with C9 expansion ("exp"), 4 controls without expansion ("ctl")

# Import & pre-process ----------------------------------------------------

# Import data from featureCounts

bsweger

Useful Pandas Snippets

A personal diary of DataFrame munging over the years.

Data Types and Conversion

Convert Series datatype to numeric (will error if column has non-numeric values)
(h/t @makmanalp)

davfre

SAM and BAM filtering one-liners

@author: David Fredman, david.fredmanAAAAAA@gmail.com (sans poly-A tail)
@dependencies: http://sourceforge.net/projects/bamtools/ and http://samtools.sourceforge.net/

Please extend with additional/faster/better solutions via a pull request!

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

nathanhaigh

#!/bin/bash
# Usage: interleave_fastq.sh f.fastq r.fastq > interleaved.fastq
# 
# Interleaves the reads of two FASTQ files specified on the
# command line and outputs a single FASTQ file of STDOUT.
# 
# Can interleave 100 million paired reads (200 million total
# reads; a 2 x 22Gbyte files), in memory (/dev/shm), in 6m54s (414s)
# 
# Latest code: https://gist.github.com/4544979

joaopizani

# the following two lines give a two-line status, with the current window highlighted
hardstatus alwayslastline
hardstatus string '%{= kG}[%{G}%H%? %1`%?%{g}][%= %{= kw}%-w%{+b yk} %n*%t%?(%u)%? %{-}%+w %=%{g}][%{B}%m/%d %{W}%C%A%{g}]'

# huge scrollback buffer
defscrollback 5000

# no welcome message
startup_message off