Dave Bridges davebridges

davebridges / mousedb_access.R

Last active June 13, 2019 17:09

Code for extracting data from mousedb

	#To use this you must supply:
	#a cohort_id number
	#an output datafile ('something.csv')
	#the api_key to access the database

	#for example:

	#raw_data_file <- "Raw MRI Data.csv"
	#cohort_id <- 35
	#api_key <- 'SEE SLACK FOR THE API KEY'

davebridges / sample mapping code

Last active August 29, 2015 14:11

Sample mapping code

	library(biomaRt)
	ensembl=useMart("ensembl")
	#show possible datasets
	listDatasets(ensembl)

	#your results are listed here
	dataset <- read.csv('Hits_PvsM_HighinMimic_filt.csv')
	#you have several different ensembl results
	unique(substr(dataset$Gene, 1,7))

davebridges / counts_table.R

Created November 21, 2012 14:15

Generate Exon and Transcript Counts Table

	require(GenomicFeatures)
	require(biomaRt)
	#set this to where your tophat_out directory is.
	working_directory = "/some_directory/"
	setwd(working_directory)
	#make a database of transcripts from the ensembl assembly
	#first get the current release 69 from ensembl, change this to your species if not using mice
	txdb <- makeTranscriptDbFromBiomart(biomart="ensembl",dataset = 'mmusculus_gene_ensembl')
	#make exon and transcript annotation objects
	save(txdb, file="txdb.Robject")

davebridges / django-model-tests.py

Created September 23, 2012 13:40

Sample ModelTests for a Django App

	"""
	This package contains the unit tests for the :mod:`app` app.


	There are tests for each model in this app.
	"""

	from django.test import TestCase
	from django.test.client import Client
	from django.contrib.auth.models import User

davebridges / django-view-tests.py

Created September 7, 2012 13:48

Sample View Tests for a Django App

	"""This file contains tests for views."""

	import datetime

	from django.test import TestCase
	from django.test.client import Client
	from django.contrib.auth.models import User

	from app.models import SampleModel