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Genealogies

# Ivan Krukovivan-krukov

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Genealogies
Last active Apr 27, 2016
Get ENSEMBL IDs for a given KEGG pathway

# 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:

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
Created Apr 21, 2016
Generating multinomial random variates via the binomial conditional method
View multinomial.cpp
 #include #include #include using namespace std; template T sum(vector v) { return accumulate(v.begin(), v.end(), 0.0); }
Created Apr 19, 2016
Print vectors in C++, easy as `cout << vector << endl`
View print_vector.cpp
 template ostream &operator<<(ostream &os, const vector &v) { os << "["; typename vector::const_iterator it; for (it = v.begin(); it != v.end() - 1; ++it) { os << *it << ", "; } os << *(it) << "]"; return os; }
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)
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
Created Aug 24, 2015
Multiple file suffixes in makefile rules
View hello.fa
 >sequence 1 ACTG
Last active Aug 29, 2015
Shuffle and relabel observations in a csv file

#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>
``````
Last active Aug 29, 2015
My favourite keymap

#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.

Last active Aug 29, 2015
Chords
``````git clone https://gist.github.com/ivan-kryukov/c265c9df6bfeda28abc8