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nsaba's Introduction

Nsaba (NeuroSynth, Allen Brain Atlas)

Methods to analyze genome-scale gene expression data from the Allen Human Brain Atlas in conjunction with fMRI activation maps from Neurosynth

Local Setup Instructions

  • Download the H0351.2001 file from http://human.brain-map.org/static/download and save the file in a place that you will remember (/Users/User/Documents/Nsaba_analysis/). This file is genome-scale gene expression at ~900 sites on one human brain.

  • Download current_data.tar.gz from https://github.com/neurosynth/neurosynth-data This is a bank of thousands of fMRI studies where a significant region of activation was found. These activated regions are matched with how often certain terms were used in these papers (i.e 'aging', 'schizophrenia', 'fear') Save the decompressed output of this file to somewhere you will remember (/Users/User/Documents/Nsaba_analysis/).

Example Usage:

See for this notebook for a full demonstration.

Futures

  • A pip package is currently under development as well as a hosted binder.

  • Multi-brain analysis.

  • Full suite of demonstration and example notebooks.

nsaba's People

Contributors

avicennax avatar torbenator avatar parenthetical-e avatar

Stargazers

Saurabh Ranjan avatar Jenny Hamer avatar

Watchers

Tal Yarkoni avatar Torsten Betz avatar James Cloos avatar Natalie avatar Cognitive Axon Laboratory avatar Roemer van der Meij avatar Scott Cole avatar  avatar tom avatar Richard Gao avatar  avatar Erin avatar  avatar Scott avatar Christian Cazares avatar  avatar Tunmise Olayinka avatar  avatar  avatar

nsaba's Issues

selenium

Do we want this to be a necessary dependency for just using NSABA locally?

sphere

generalize estimation methods

Validation module.validate(method = '?', term = '?', genes = '?')

Different methods produce p values to say how well our estimates were:
methods:
term_to_genes(one_term, some_genes,alpha)
returns how many genes were in the alpha quartile

gene_to_terms(one_gene, some_terms,alpha)
returns how many terms were in the alpha quartile

...more coming

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