chilampoon

Upgrade RStudio Server (Version:1.1.463 Released:2018-10-29) in Ubuntu

sudo /usr/sbin/rstudio-server stop #stop the current version
# Download
sudo apt-get install gdebi-core
wget https://download2.rstudio.org/rstudio-server-1.1.463-amd64.deb
sudo gdebi rstudio-server-1.1.463-amd64.deb

chilampoon

Download AWS s3 bucket objects

• Install AWS CLI

pip3 install awscli --upgrade --user
# export PATH=~/.local/bin:$PATH (add into ~/.bashrc)
# source ~/.bashrc

• Configure the CLI

chilampoon

GSoC 2020 Final Report

This Gist summarizes my work for the Reactome project "Query Reactome Data in R" during the Google Summer of Code 2020.

I would first like to begin by thanking my mentors Justin Cook, Joel Weiser, and Solomon Shorser for their guidance and support this summer. It was a privilege to learn from such a talented and experienced team.

Main objective

The main objective was to create an interface in R to query data from the Reactome knowledgebase.

chilampoon

chilampoon

# setup
gcloud auth list
gcloud config set compute/zone us-east1-b
gcloud config set compute/region us-east1

# create an instance template
cat << EOF > startup.sh
#! /bin/bash
apt-get update
apt-get install -y nginx

chilampoon

# ------ a python cell ------
%load_ext rpy2.ipython

pd_df = pd_df.T

# ------ an R cell ------
%%R -i pd_df
# `-i pd_df` means access to the global variable pd_df

r_df = do.something(pd_df)

chilampoon

#!/usr/bin/env python

# fix t2t gff3 error
# now the problem is ids for some start&stop condons/exons are not unique
# 11/20/2022

import sys,gzip
from collections import defaultdict

def sep_info(info):