ivan-krukov

Problem

For a given KEGG pathway, we want to get a list of all the genes. Ensembl IDs are convenient here.

KEGG provides a REST API for some tasks, but is far from complete. For example, it is possible to map from KEGG to NCBI IDs, but not to Ensembl IDs.

The implementation peforms the following steps:

ivan-krukov

import cv2
import urllib.request

# Will use matplotlib for showing the image
from matplotlib import pyplot as plt

# Plot inline
%matplotlib inline

# For local images, read as usual

ivan-krukov

#include <vector>
#include <numeric>
#include <random>

using namespace std;

template <typename T>
T sum(vector<T> v) {
  return accumulate(v.begin(), v.end(), 0.0);
}

ivan-krukov

template <typename T>
ostream &operator<<(ostream &os, const vector<T> &v) {
  os << "[";
  typename vector<T>::const_iterator it;
  for (it = v.begin(); it != v.end() - 1; ++it) {
    os << *it << ", ";
  }
  os << *(it) << "]";
  return os;
}

ivan-krukov

# Use dots (.) instead of ($)
R_ify <- function(expr) eval(parse(text=
                                      gsub("\\.","$",substitute(expr))))
                                      

R_ify(mtcars.mpg)

ivan-krukov

#Get repo list, filter git urls
GITHUB_NAME=octocat
curl https://api.github.com/users/$GITHUB_NAME/repos > github_response

for repo in `cat github_response | jq -r '.[] | .git_url'`; do; 
  git clone $repo; 
done

ivan-krukov

>sequence 1
ACTG

ivan-krukov

#Randomization script

The idea is to do bootstrap resampling on the control dataset to make sure it is appropriate as a control dataset.

#Usage

python randomize.py <input.csv> <resample_times>

ivan-krukov

#Custom Keymap (Lenovo T430)

This will apply settings for both system console and Xorg server.

• CapsLock will become an extra Esc
• Home will be switched with PageUp
• End will be switched with PageDown

This makes sense for the Lenovo T430, where PageUp and PageDown are right next to the arrow keys.

ivan-krukov

#20 chords A simple chord diagram for amino-acid relationships ##Usage

The input data should be a 20x20 table with tabs as separators.

To run the thing, do this (uses firefox)

git clone https://gist.github.com/ivan-kryukov/c265c9df6bfeda28abc8