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Avinash R gatoravi

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gatoravi / tomasetti-vogelstein-table-s1.tsv
Created April 29, 2016 21:27 — forked from lmmx/tomasetti-vogelstein-table-s1.tsv
Tomasetti & Vogelstein (2015) Science 'bad luck of cancer' paper supplementary table S1. Finalised via Yaniv Erlich & Aaron Quinlan's draft clean-ups of the PDF supplement
Cancer_type Lifetime_cancer_incidence Total_cells_tissue Total_Stem_Cells Stem_cell_divisions_per_year Stem_cell_divisions_per_lifetime LSCD
ALL 0.0041 3000000000000 135000000 12 960 129900000000
BCC 0.3 180000000000 5820000000 7.6 608 3550000000000
CLL 0.0052 3000000000000 135000000 12 960 129900000000
Colorectal 0.048 30000000000 200000000 73 5840 1168000000000
Colorectal_FAP 1 30000000000 200000000 73 5840 1168000000000
Colorectal_Lynch 0.5 30000000000 200000000 73 5840 1168000000000
Duodenum_adenocarcinoma 0.0003 680000000 4000000 24 1947 7796000000
Duodenum_adenocarcinoma_with_FAP 0.035 680000000 4000000 24 1947 7796000000
Esophageal_squamous_cell_carcinoma 0.001938 3240000000 846000 17.4 1390 1203000000
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gatoravi / get_count_with_sufficient_coverage.cc
Last active November 4, 2015 15:47 — forked from anonymous/get_count_with_sufficient_coverage.cc
Parse 'samtools depth' and obtain lines with sufficient coverage. Assumes two samples in the output. Same as, awk '$3 >= cutoff && $4 >= cutoff'
#include <stdint.h>
#include <cstdlib>
#include <iostream>
#include <fstream>
#include <sstream>
using namespace std;
void usage() {
cerr << "Usage: ./get_count_with_sufficient_coverage samtools_depth_file cutoff[INT]";
cerr << "Assumes 2 samples.";
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gatoravi / cs_programming_resources.md
Last active August 29, 2015 14:26 — forked from anonymous/cs_programming_resources.md
Programming/Computer Science books.
  1. The Practice of programming - Brian W. Kernighan
  2. The Unix Programming Environment - Brian W. Kernighan and Rob Pike
  3. Numerical Recipes in C: The Art of Scientific Computing
  4. Structure and Interpretation of Computer Programs.
  5. Higher-Order Perl: Transforming Programs with Programs - Mark Jason Dominus
  6. Reverse Engineering for Beginners - Dennis Yurichev
  7. The Pragmatic Programmer: From Journeyman to Master
  8. The Mythical Man-Month
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gatoravi / .gitignore
Last active August 29, 2015 14:24 — forked from octocat/.gitignore
# Compiled source #
###################
*.com
*.class
*.dll
*.exe
*.o
*.so
# Packages #
@gatoravi
gatoravi / nationalParksArea.R
Last active August 29, 2015 14:04 — forked from mollietaylor/nationalParksArea.R
# load up area shape file:
library(maptools)
area <- readShapePoly("ne_10m_parks_and_protected_lands_area.shp")
# # or file.choose:
# area <- readShapePoly(file.choose())
library(RColorBrewer)
colors <- brewer.pal(9, "BuGn")