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Saket Choudhary saketkc

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View limma_analysis.R
library(limma)
library(statmod)
library(scatterplot3d)
library(made4)
library(arrayQualityMetrics)
library(Biobase)
## We want to read ony Read channels, the way to do it is to pass custom
## names to read.maimages() function specifying the green.only=TRUE option
## with source="genepix.custom" and G,Gb=Cy5,Cy5b respectively.
## Cy5 => RED Channel Forground
View methpipe.rb
require "formula"
class Methpipe < Formula
head "https://github.com/smithlabcode/methpipe.git"
homepage "http://smithlabresearch.org/software/methpipe/"
url "http://smithlabresearch.org/downloads/methpipe-3.3.1.tar.gz"
sha1 "00dea4a51e7b8ed5e7020bba89db63a91d86a70f"
depends_on "gsl" => :build
View compare_hg19_to_grch37.py
from Bio import SeqIO
import pickle
from pprint import pprint
import sys
hg19_location = "/usr/local/share/bcbio/genomes/Hsapiens/hg19/hg19.fa"
grch37_location = "/usr/local/share/bcbio/genomes/Hsapiens/GRCh37/bowtie/GRCh37.fa"
try:
pickled = pickle.load(open('comparison_pickled.p', 'rb'))
print (pickled)
sys.exit(0)
@saketkc
saketkc / .gitignore
Created Oct 25, 2014
.gitignore for latex/beamer projects
View .gitignore
*.aux
*.glo
*.idx
*.log
*.toc
*.ist
*.acn
*.acr
*.alg
*.bbl
View samblaster.patch
diff --git a/samblaster.cpp b/samblaster.cpp
index 14a2a40..2c33508 100644
--- a/samblaster.cpp
+++ b/samblaster.cpp
@@ -26,6 +26,14 @@
#include <map>
#include "sbhash.h"
+// Define mempcpy for Mac OS
+#ifdef __APPLE__
@saketkc
saketkc / CharScanner.patch
Created Jan 7, 2015
Patch for compiling antlr2 on linux
View CharScanner.patch
--- lib/cpp/antlr/CharScanner.hpp 2015-01-07 00:09:51.747913036 -0800
+++ lib/cpp/antlr/CharScanner.hpp 2015-01-07 00:10:31.883913806 -0800
@@ -11,6 +11,8 @@
#include <antlr/config.hpp>
#include <map>
+#include <cstring>
+#include <stdio.h>
#ifdef HAS_NOT_CCTYPE_H
View Makefile.patch
diff --git libs/kxml/Makefile libs/kxml/Makefile
index 3635fa3..ff19f5b 100644
--- libs/kxml/Makefile
+++ libs/kxml/Makefile
@@ -42,9 +42,7 @@ include $(TOP)/build/Makefile.env
#
ifeq (1,$(HAVE_XML2))
-ifneq (,$(XML2_INCDIR))
INCDIRS += $(addprefix -I,$(XML2_INCDIR))
@saketkc
saketkc / MixedLM_compare_lr_test-Converging.ipynb
Created Jun 13, 2015
MixedLM LR Test[Converging Examples]
View MixedLM_compare_lr_test-Converging.ipynb
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View Vonmises Multidimensional Demo.ipynb
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View MixedLMProfile
Line # Hits Time Per Hit % Time Line Contents
==============================================================
356 @profile
357 def _smw_solver(s, A, AtA, B, BI):
358 """
359 Solves the system (s*I + A*B*A') * x = rhs for an arbitrary rhs.
360
361 Parameters
362 ----------
363 s : scalar