learn-neuroimaging · AngelikaZa · Jun 17, 2020 · Jun 17, 2020 · Jun 18, 2020
diff --git a/docs/genetic_software.md b/docs/genetic_software.md
@@ -0,0 +1,28 @@
+# Integrating genetics
+
+## Extracting data from the Allen atlas
+
+The Allen atlas is an amazing resource of regional gene expression in the human brain. It contains a database of expression levels of 20,737 genes represented by 58,692 probes across the complete cortical mantle and is constructed postmortem from the brains of 6 human donors with no history of psychiatric or neuropathological disorders. The donor brains also underwent MRI postmortem and the probe locations mapped into each donor's MRI data in MNI space, providing a great opportunity to correlate regional gene expression with imaging findings!
+
+Data is freely available to download from AIBS [AIBS](http://human.brain-map.org/static/download). 
+Extracting appropriate gene expression data from the Allen Atlas has many caveats, detailed in the excellent paper [here] (https://doi.org/10.1016/j.neuroimage.2019.01.011) but tools have now been developed to make gene extraction easier. 
+
+The following list includes software/packages and useful resources that can be used to extract gene expression data in imaging space. 
+
+## Abagen
+
+-   Open-source Python software for extracting gene expression data from the ALlen atlas.
+-   repository URL: [Github](https://github.com/rmarkello/abagen/)
+-   website URL: [http://martinos.org/mne/stable/index.html](http://martinos.org/mne/stable/index.html)
+-   tutorial URL: 
+-   documentation: [https://abagen.readthedocs.io/en/stable/index.html](https://abagen.readthedocs.io/en/stable/index.html)
+-   programming language: {python}
+-   paper DOI: [https://doi.org/10.5281/zenodo.3726257.](https://doi.org/10.5281/zenodo.3726257.)
+
+## Matlab repository from Aurina Arnatkeviciute
+
+-   Repository from the Aurina's paper describing best practice when extracting data from the Allen atlas.
+-   repository URL: [Github](https://github.com/BMHLab/AHBAprocessing)
+-   programming language: {matlab}
+-   paper DOI: [https://doi.org/10.1016/j.neuroimage.2019.01.011](https://doi.org/10.1016/j.neuroimage.2019.01.011)
+-   contact: [Aurina Arnatkeviciute]([email protected])
diff --git a/docs/open_science.md b/docs/open_science.md
@@ -13,4 +13,4 @@
 -   MRC Cognition and Brain Sciences Unit Open Science Day 2018
 [Here](https://www.youtube.com/watch?list=PLp67eqWCj2f-SsbYZFQVb-ecjxqr1CpRu&v=jKmv3-Nk8iE)
 
--   Orthogonal Research and Education Laboratory's [Open Science Database] (https://orthogonal-research.weebly.com/open-science-and-data.html)
+-   Orthogonal Research and Education Laboratory's [Open Science Database](https://orthogonal-research.weebly.com/open-science-and-data.html)
diff --git a/docs/programming.md b/docs/programming.md
@@ -5,8 +5,7 @@
 -   [Documenting Python Code: A Complete Guide](https://realpython.com/documenting-python-code/)
 
 ## GitHub
--   [A Quick Introduction to Version Control with
-Git and GitHub](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004668) by Bilschak et al. (2016)
+-   [A Quick Introduction to Version Control with Git and GitHub](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004668) by Bilschak et al. (2016)
 -   [Introduction to git and GitHub](https://www.youtube.com/watch?v=XyMCsEGPcjM&list=PLNt4AJV1JZbfq0vdD4vcITV7x3OqGxLKp) by Chris Gorgolewski within Brainhack Americas (45 min)
 -   [Git and GitHub 1 & 2](https://neurohackademy.org/course/git-and-github/) by Bernease Herman within Neurohackweek 2016
 -   [Git tutorial](https://www.youtube.com/watch?v=0DGCnBZBoc0&index=2&t=5s&list=PLEE6ggCEJ0H0KOlMKx_PUVB_16VoCfGj9) by Eshin Jolly within MIND 2018 (36 min)
@@ -64,4 +63,4 @@ Git and GitHub](https://journals.plos.org/ploscompbiol/article?id=10.1371/journa
 -   [Introduction to Neurohacking in R](https://www.coursera.org/learn/neurohacking) MOOC on coursera
 
 ## Introduction & Basics
--   [Khan Academy] (https://www.khanacademy.org/): Beginners' coursework on programming, algorithms, and more.
+-   [Khan Academy](https://www.khanacademy.org/): Beginners' coursework on programming, algorithms, and more.
diff --git a/docs/statistics.md b/docs/statistics.md
@@ -17,3 +17,13 @@ A list of R based web based apps from [shiny apps](http://shinyapps.org/) and [R
 -   [null hypothesis significance testing](http://rpsychologist.com/d3/NHST/)
 -   [p hacking](https://www.shinyapps.org/apps/p-hacker/)
 -   [positive predictive values](http://shinyapps.org/showapp.php?app=https://tellmi.psy.lmu.de/felix/PPV&by=Michael%20Zehetleitner%20and%20Felix%20Sch%C3%B6nbrodt&title=When%20does%20a%20significant%20p-value%20indicate%20a%20true%20effect?&shorttitle=When%20does%20a%20significant%20p-value%20indicate%20a%20true%20effect?)
+
+Partial least squares regression:
+
+This is particularly useful for highdimensional neuroimaging data (particularly when correlating with genetic/transcriptome data). It finds a linear regression model by projecting the predicted variables and the observable variables to a new space. 
+Useful resources if you are new to PLS-R:
+
+- [A beginner's guide to PLS](https://www.researchgate.net/publication/228861711_A_Beginner's_Guide_to_Partial_Least_Squares_Analysis)
+- [python package](https://hoggorm.readthedocs.io/en/latest/)
+- [r package](https://cran.r-project.org/web/packages/pls/)
+- [matlab](https://uk.mathworks.com/help/stats/examples/partial-least-squares-regression-and-principal-components-regression.html)
diff --git a/mkdocs.yml b/mkdocs.yml
@@ -36,6 +36,7 @@ nav:
     - About: "05-analysis.md"
     - Statistics: "statistics.md"
     - Machine learning and Deep learning: "machine_and_deep_learning.md"
+    - Integrating genetics: "genetic_software.md"
   - Quality control:
       - About: "06-quality-control.md"
   - Reporting methods and results: