janxkoci

#!/bin/bash

FASTA="$1"
awk 'ORS = $1~/>/ ? RS:FS' $FASTA | sed 's/ >/\n>/g' | sed '2~2s/ //g'

janxkoci

#!/bin/bash

# SCRIPT USAGE:
# bash plink_pruning_prep.sh filtered_snp_file.vcf

# REQUIREMENTS:
# This script uses several software packages, all available from [Bioconda channel](https://bioconda.github.io/).
# They can be installed with simple:
# conda install tabix bcftools plink

janxkoci

janxkoci

#!/bin/bash

# bash awk_vcf_anim_chrom_pos.sh in.vcf sample chrom pos

echo vcf: "$1"
echo sample: "$2"
echo chrom: "$3"
echo pos: "$4"

awk -v sample=$2 -v chrom="$3" -v pos=$4 \

janxkoci

#!/bin/bash

## USAGE:
# bash melt_table.sh INFILE.tsv > OUTPUT.tsv

# set variables
outfile=/dev/stdout
tot_ncol=$(head -1 $1 | wc -w)
nsample=$(head -1 $1 | cut -f 3- | sed 's/\.[A-Z][A-Z]\>//g' | tr "\t" "\n" | uniq | wc -l)
ncol=$(expr $(expr $tot_ncol - 2) / $nsample)

janxkoci

Comments: Jupyter and R for Scientists

This is a place to share comments about the post Jupyter and R for Scientists I published on my blog.

Contributing

If you'd like to improve the post, you can fork it on Github and submit a pull request.

Comments

janxkoci

name: pylab
channels:
  - conda-forge
dependencies:
  - python=3
  - jupyter
  - jupyterthemes
  - scipy
  - numpy
  - pandas

janxkoci

(function() {
    var API_KEY = "YOUR_API_KEY_GOES_HERE";

    // code for IE7+, Firefox, Chrome, Opera, Safari - forget IE6
    var xmlhttp = new XMLHttpRequest();

    xmlhttp.open("POST", "https://api.pushbullet.com/v2/pushes", true);
    xmlhttp.setRequestHeader('Content-Type', 'application/json');
    xmlhttp.setRequestHeader('Authorization', "Bearer " + API_KEY);
    /// @todo needs oauth2 update? ugh.

janxkoci

#!/bin/bash

IN=$1
OUT=$2

# uses ImageMagick convert command
convert $IN \
-sampling-factor 4:2:0 \
-strip \
-quality 85 \

janxkoci

javascript:document.getElementsByTagName("body")[0].appendChild(document.createElement("script")).setAttribute("src","https://static.mendeley.com/bin/extensions/bookmarklet.js");