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Genealogies

Ivan Krukov ivan-krukov

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Genealogies
  • Canada
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@ivan-krukov
ivan-krukov / README.md
Last active Apr 27, 2016
Get ENSEMBL IDs for a given KEGG pathway
View README.md

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
ivan-krukov / jupyter-imshow.py
Last active May 12, 2020
Show opencv image in ipython notebook
View jupyter-imshow.py
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
ivan-krukov / multinomial.cpp
Created Apr 21, 2016
Generating multinomial random variates via the binomial conditional method
View multinomial.cpp
#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
ivan-krukov / print_vector.cpp
Created Apr 19, 2016
Print vectors in C++, easy as `cout << vector << endl`
View print_vector.cpp
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
ivan-krukov / R_ify.R
Created Mar 30, 2016
Use dots instead of dollar signs in R
View R_ify.R
# Use dots (.) instead of ($)
R_ify <- function(expr) eval(parse(text=
gsub("\\.","$",substitute(expr))))
R_ify(mtcars.mpg)
@ivan-krukov
ivan-krukov / clone_all.sh
Last active Mar 17, 2016
Clone all repos for a given user
View clone_all.sh
#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
ivan-krukov / hello.fa
Created Aug 24, 2015
Multiple file suffixes in makefile rules
View hello.fa
>sequence 1
ACTG
@ivan-krukov
ivan-krukov / README.md
Last active Aug 29, 2015
Shuffle and relabel observations in a csv file
View README.md

#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
ivan-krukov / README.md
Last active Aug 29, 2015
My favourite keymap
View README.md

#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.

View README.md

#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
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