https://github.com/yhoogstrate/gsam
gsam
https://github.com/yhoogstrate/gsam
Last synced: 5 months ago
JSON representation
gsam
- Host: GitHub
- URL: https://github.com/yhoogstrate/gsam
- Owner: yhoogstrate
- License: mit
- Created: 2019-08-23T10:07:07.000Z (almost 6 years ago)
- Default Branch: master
- Last Pushed: 2023-09-12T09:56:23.000Z (almost 2 years ago)
- Last Synced: 2023-12-19T18:59:32.460Z (over 1 year ago)
- Language: Shell
- Size: 1.74 MB
- Stars: 3
- Watchers: 4
- Forks: 2
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
___
_____
_.'_____`._
.'.-' 12 `-.`.
/,' 11 1 `.\
// 10 / 2 \\
;; / ::
|| 9 ----O 3 ||
:: ;;
\\ 8 4 //
\`. 7 5 ,'/
'.`-.__6__.-'.'
((-._____.-))
_)) ((_
'--' '--'
-. .-. .-. .-. .-. .-. .-. .-. .-. .
\ / \ / \ / \ / \ / \ / \ / \ / \ /
\ / \ / \ / \ / \ / \ / \ / \ / \ /
`-~ `-~ `-~ `-~ `-~ `-~ `-~ `-~ `-~
██████╗ ██████╗ █████╗ ███╗ ███╗
██╔════╝ ██╔════╝██╔══██╗████╗ ████║
██║ ██╗ █████╗╚█████╗ ███████║██╔████╔██║
██║ ╚██╗╚════╝ ╚═══██╗██╔══██║██║╚██╔╝██║
╚██████╔╝ ██████╔╝██║ ██║██║ ╚═╝ ██║
╚═════╝ ╚═════╝ ╚═╝ ╚═╝╚═╝ ╚═╝
-. .-. .-. .-. .-. .-. .-. .-. .-. .
\ / \ / \ / \ / \ / \ / \ / \ / \ /
\ / \ / \ / \ / \ / \ / \ / \ / \ /
`-~ `-~ `-~ `-~ `-~ `-~ `-~ `-~ `-~
___
# G-SAM RNA pipe-line and analysis code #
Dr. Youri Hoogstrate, 2019 - 2023
---
# Citing recursiveCorPlot
Please cite this paper ([10.1016/j.ccell.2023.02.019](https://doi.org/10.1016/j.ccell.2023.02.019)) when using *recursiveCorPlot* for your
publications:
```
Youri Hoogstrate, Kaspar Draaisma, Santoesha A. Ghisai, Levi van Hijfte, Nastaran Barin, Iris de Heer,
Wouter Coppieters, Thierry P.P. van den Bosch, Anne Bolleboom, Zhenyu Gao, Arnaud J.P.E. Vincent,
Latifa Karim, Manon Deckers, Martin J.B. Taphoorn, Melissa Kerkhof, Astrid Weyerbrock, Marc Sanson,
Ann Hoeben, Slávka Lukacova, Giuseppe Lombardi, Sieger Leenstra, Monique Hanse,
Ruth E.M. Fleischeuer, Colin Watts, Nicos Angelopoulos, Thierry Gorlia, Vassilis Golfinopoulos,
Vincent Bours, Martin J. van den Bent, Pierre A. Robe, Pim J. French
Transcriptome analysis reveals tumor microenvironment changes in glioblastoma,
Cancer Cell, 2023, ISSN 1535-6108, https://doi.org/10.1016/j.ccell.2023.02.019
```
---
Directory structure:
```
# main R data analyses:
./scripts/load_*.R [loading of data]
- data is typically structured at 3 levels:
* per gene
* per patient
* per resection/sample
./scripts/analysis_*.R [analysis of data, typically exporting results to ./cache]
./scripts/vis_*.R [visualisation of data]
./if/*.ijm [ImageJ IF analysis scripts]
LICENSE [copy of MIT license]
```