davebridges

#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

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

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

"""
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

"""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