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## Installing Virtual Environment and Eggifying your source code for OERPub | |
Go to your Repo : cd <repo_name> | |
and then : | |
virtualenv --no-site-packages . | |
./bin/easy_install -U ZopeSkel | |
./bin/paster create --list-templates | |
./bin/paster create -t nested_namespace <repo_name> | |
This will create and empty egg for your repo ! |
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import gdata.docs.data | |
import gdata.docs.client | |
import gdata.docs.service | |
import gdata.client | |
import gdata.docs.client | |
import os | |
import stat | |
import mimetypes | |
from google_api_config import CONSUMER_KEY | |
from google_api_config import CONSUMER_SECRET |
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#!/usr/bin/env python | |
''' | |
Automatically estimate insert size of the paired-end reads for a given SAM/BAM file. | |
Usage: getinsertsize.py <SAM file> or samtools view <BAM file> | getinsertsize.py - | |
Author: Wei Li | |
''' | |
from __future__ import print_function | |
import sys; |
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<tool id="panama1" name="panama" version="1.0.0"> | |
<requirements> | |
<requirement type="package">panama</requirement> | |
</requirements> | |
<description>eQTL Analysis using PANAMA(http://ml.sheffield.ac.uk/qtl/panama/)</description> | |
<command> | |
panama $expression_data $snp_data; mv PANAMA_results.csv output1 | |
</command> | |
<inputs> | |
<param name="expression_data" type="data" format="text" label="Select Expression Data" /> |
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#!/usr/bin/env python | |
""" | |
Run panama on expression and snp data | |
usage: panama_run.py [options] | |
--exp_data: Expression data CSV file | |
--snp_data: SNP data file | |
--output1: Output CSV dataset | |
""" | |
import optparse, os, sys, subprocess, tempfile, shutil |
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<tool id="panama1" name="panama" version="1.0.0"> | |
<requirements> | |
<requirement type="package">panama</requirement> | |
</requirements> | |
<description>eQTL Analysis using PANAMA(http://ml.sheffield.ac.uk/qtl/panama/)</description> | |
<command interpreter="python"> | |
panama_run.py --exp_data=$expression_data --snp_data=$snp_data --output1=$output1 | |
</command> | |
<inputs> | |
<param name="expression_data" type="data" format="text" label="Select Expression Data" /> |
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library(limma) | |
Cy5 <- "F635 Median" | |
Cy5b <- "B635 Mean" | |
targets <- readTargets("Grade2_targets.csv") | |
f <- factor(targets$Condition, levels = unique(targets$Condition)) | |
design <- model.matrix(~0 + f) | |
cont.matrix <- makeContrasts(Grade2vsControl=Grade2-Control, levels=design) | |
colnames(design) <- levels(f) | |
RG <- read.maimages( targets$FileName, |
We can make this file beautiful and searchable if this error is corrected: No commas found in this CSV file in line 0.
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FileName Condition | |
Control_H-02_2000153953.gpr Control | |
Control_H-25_2000153952.gpr Control | |
Control_H-35_2000153943.gpr Control | |
Control_H-58_2000153935.gpr Control | |
Control_HC-25_2000153932.gpr Control | |
Grade II_CF 10729_2000154012.gpr Grade2 | |
Grade II_CF 20468_2000153947.gpr Grade2 | |
Grade II_CF 29538_2000154020.gpr Grade2 | |
Grade II_CF 8551_2000153940.gpr Grade2 |
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// Use Gists to store code you would like to remember later on | |
console.log(window); // log the "window" object to the console |
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name: multiz | |
channels: !!python/object/new:ruamel_yaml.comments.CommentedSeq | |
listitems: | |
- bioconda | |
- r | |
- defaults | |
state: !!python/tuple | |
- _yaml_format: !!python/object:ruamel_yaml.comments.Format | |
_flow_style: false | |
_yaml_line_col: !!python/object:ruamel_yaml.comments.LineCol |