From d7af53957ec5624d32307c7695fba3a8c62713a4 Mon Sep 17 00:00:00 2001 From: DrCodeZ Date: Wed, 17 Jun 2020 09:37:29 +0100 Subject: [PATCH 1/3] Added a page on extracting data from allen atlas as well as resources on PLS on statistics page --- docs/allen_software.md | 26 ++++++++++++++++++++++++++ docs/statistics.md | 10 ++++++++++ 2 files changed, 36 insertions(+) create mode 100644 docs/allen_software.md diff --git a/docs/allen_software.md b/docs/allen_software.md new file mode 100644 index 0000000..912d796 --- /dev/null +++ b/docs/allen_software.md @@ -0,0 +1,26 @@ +# 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](aurina.arnatkeviciute@monash.edu) \ No newline at end of file diff --git a/docs/statistics.md b/docs/statistics.md index a4e860f..f76aace 100644 --- 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) \ No newline at end of file From 7997197f9ea63cf46449c977af658e151a4ab5ec Mon Sep 17 00:00:00 2001 From: DrCodeZ Date: Wed, 17 Jun 2020 11:23:42 +0100 Subject: [PATCH 2/3] Updated nav file Signed-off-by: DrCodeZ --- mkdocs.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/mkdocs.yml b/mkdocs.yml index 6173320..dd29360 100644 --- 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" + - The Allen atlas (postmortem gene expression data): "allen_software.md" - Quality control: - About: "06-quality-control.md" - Reporting methods and results: From c44bf88466b6d834e13a3e9ca0251999b381b7c4 Mon Sep 17 00:00:00 2001 From: DrCodeZ Date: Thu, 18 Jun 2020 09:45:24 +0100 Subject: [PATCH 3/3] Updated names and referencing of genetic pages --- docs/{allen_software.md => genetic_software.md} | 4 +++- docs/open_science.md | 2 +- docs/programming.md | 5 ++--- mkdocs.yml | 2 +- 4 files changed, 7 insertions(+), 6 deletions(-) rename docs/{allen_software.md => genetic_software.md} (96%) diff --git a/docs/allen_software.md b/docs/genetic_software.md similarity index 96% rename from docs/allen_software.md rename to docs/genetic_software.md index 912d796..289cf4b 100644 --- a/docs/allen_software.md +++ b/docs/genetic_software.md @@ -1,4 +1,6 @@ -# Extracting data from the Allen atlas +# 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! diff --git a/docs/open_science.md b/docs/open_science.md index 98d1bca..bd9e7ea 100644 --- 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 index 3e48b52..38898f8 100644 --- 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/mkdocs.yml b/mkdocs.yml index dd29360..24ca469 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -36,7 +36,7 @@ nav: - About: "05-analysis.md" - Statistics: "statistics.md" - Machine learning and Deep learning: "machine_and_deep_learning.md" - - The Allen atlas (postmortem gene expression data): "allen_software.md" + - Integrating genetics: "genetic_software.md" - Quality control: - About: "06-quality-control.md" - Reporting methods and results: