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Stelios Sfakianakis sgsfak

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@sgsfak
sgsfak / vph_cats.json
Last active December 14, 2015 21:28
Extract the VPH-Toolkit tools from their web page
[
{
"self": "http://toolkit.vph-noe.eu/home/tools/data-conversion-tools.html",
"name": "Data Conversion Tools"
},
{
"self": "http://toolkit.vph-noe.eu/home/tools/data-fusion.html",
"name": "Data Fusion"
},
{
@sgsfak
sgsfak / Kaggle Amazon employee competition
Created June 17, 2013 22:20
training = read.csv("train.csv")
testing = read.csv("test.csv")
training$ACTION = as.factor(training$ACTION)
libs = c("caret", "randomForest", "rpart", "kernlab", "glmnet", "gbm",
"doMC")
for (l in libs) {
@sgsfak
sgsfak / august5.sh
Last active August 29, 2015 13:56
Find Years with August with 5 Fridays, Saturdays , and Sundays
for j in `seq 2014 2050`; do
i=8
ncal $i $j | tail -3 | (echo -n "$j," ; awk 'BEGIN{ORS=","} {print NF-1}';echo)
done | egrep "5,5,5,$" |cut -f1 -d,
@sgsfak
sgsfak / parse_scpecg.js
Created February 11, 2014 13:01
Parses an SCP-ECG file and prints the demographics/data acquisition information (in Section 1)
var fs = require('fs')
var DEBUG = true;
var log = console.log;
if (!DEBUG)
log = function() {};
function parse_scp_time(fval) {
var hour = fval.readInt8(0);
@sgsfak
sgsfak / heatmap3.R
Created June 9, 2014 10:09 — forked from nachocab/heatmap3.R
# EXAMPLE USAGE
# example of colsidecolors rowsidecolors (single column, single row)
mat <- matrix(1:100, byrow=T, nrow=10)
column_annotation <- sample(c("red", "blue", "green"), 10, replace=T)
column_annotation <- as.matrix(column_annotation)
colnames(column_annotation) <- c("Variable X")
row_annotation <- sample(c("red", "blue", "green"), 10, replace=T)
row_annotation <- as.matrix(t(row_annotation))
@sgsfak
sgsfak / 1000genomes_reprod_align.md
Last active August 29, 2015 14:03

Reproducing (some of) the sequence alignment processes of 1000genomes project

Download the 100genomes samples

First I download the sequence.index file from the 1000genomes EBI FRP site:




  


  




    


          
    

      

        
        

          

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                sgsfak
                / gist:98a5ca34bffe41958f88
            
            

              Last active
              September 18, 2017 07:59
            

              
                Adding a `git hub` alias
              
          

        

      

        

  

    
    


        



  


  

        

          
          git config --global alias.hub '!open $(git config --get remote.origin.url | sed -e "s|git@github\.com:|https://github.com/|" -e "s|git@bitbucket\.org:|https://bitbucket.org/|" -e "s|\.git$||")'
        

  





    


  




    


          
    

      

        
        

          

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                sgsfak
                / jq producing CSV
            
            

              Last active
              August 29, 2015 14:10
            

              
                For the background see http://doublebyteblog.wordpress.com/2014/11/25/piping-an-api-into-r-a-data-science-workflow/
              
          

        

      

        

  

    
    


        



  


  

        

          
          <out.json jq -r '.Root.ResultSet.Entity[] | [.color, .width, .average, .reference, .Time]|@csv' > out.csv
        

  





    


  




    


          
    

      

        
        

          

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                sgsfak
                / exiv2date
            
            

              Created
              January 7, 2015 20:28
            

              
                Given a set of JPEG images in a single directory, it prints the Exif based date time information
              
          

        

      

        

  

    
    


        



  


  

        

          
          exiv2  -Pv -g Exif.Image.DateTime *.JPG | awk '{gsub(/:/,"/", $2); print $1,$2}'
        

  





    


  




    


          
    

      

        
        

          

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                sgsfak
                / single tree classifiers
            
            

              Last active
              August 29, 2015 14:13
                — forked from chrishwiggins/single tree classifiers
            

          

        

      

        

  

    
    


        



  


  

        

          
          Q: what are "single tree-based" (as opposed to forest-based) supervised learning methods?
        

        

          
          

        

        

          
          A: some of my favorites:
        

        

          
          

        

        

          
          - ADT
        

        

          
              + wiki: http://en.wikipedia.org/wiki/Alternating_decision_tree
        

        

          
              + ref: http://perun.pmf.uns.ac.rs/radovanovic/dmsem/cd/install/Weka/doc/classifiers-papers/trees/ADTree/atrees.pdf
        

        

          
          

        

        

          
          - rpart in R
        

        

          
              + http://cran.r-project.org/web/packages/rpart/vignettes/longintro.pdf