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SNU Bioinformatics and Practice 2 - Week 2

Contains the notebooks for the practice sessions.

@hyeshik
hyeshik / KNUE-20190510-Slides.pdf
Last active May 15, 2020
파이썬으로 하는 데이터 분석: 일상에서 배우기
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@hyeshik
hyeshik / WASET abstract database processing.ipynb
Last active May 10, 2019
Processes the downloaded WASET database to generate tables of Korean authors and abstracts
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@hyeshik
hyeshik / download-waset.py
Last active Jul 31, 2018
Download WASET conference abstracts
View download-waset.py
#!/usr/bin/env python3
#
# Copyright (c) 2018 Hyeshik Chang
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
View 0524 Bamtori NIPT Interpretation.ipynb
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View 0609 Mad Scienctist Generator.ipynb
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@hyeshik
hyeshik / 1226 Burger Index.ipynb.json
Last active May 24, 2019
An IPython notebook for analysis of the distributions of fast-food hamburger shops.
View 1226 Burger Index.ipynb.json
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{
"metadata": {
"name": "",
"signature": "sha256:f99925a6f73a1e36bc91415d84266705e3bdf72304d8dba7bcfb6c94ca7b270a"
},
"nbformat": 3,
"nbformat_minor": 0,
"worksheets": [
{
@hyeshik
hyeshik / Citation trends 2013.ipynb.json
Created Aug 1, 2014
a notebook to plot citation trends from JCR 2004-2013
View Citation trends 2013.ipynb.json
View jobscript.sh
#!/bin/sh
#rule: {job}
#input: {job.input}
#output: {job.output}
#threads: {job.threads}
{self.workflow.snakemakepath} --snakefile {self.workflow.snakefile} \
--force -j{self.cores} \
--directory {workdir} --nocolor --notemp --quiet --nolock {job.output} \
> /dev/null && touch "{jobfinished}" || touch "{jobfailed}"
exit 0
View sgesnake.sh
#!/bin/sh
#
# Adopts and submit a snakemake cluster job script to SGE queue
#
# by Hyeshik Chang
#
JOBSCRIPT_SNAKEMAKE=$1
JOBSCRIPT_SGE="`dirname $1`/sge`basename $1`"
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