R functions for gene selection and analysis of mFISH data
mfishtools includes many functions that are used for analysis of data for the CZI SpaceTx project, and mostly relies on correlation-based analysis with filtering. This library is still in beta testing and may be buggy. Community involvement is encouraged through both issues and pull requests.
Install prerequisites:
install.packages("devtools")
devtools::install_github("AllenInstitute/scrattch.vis")
devtools::install_github("AllenInstitute/tasic2016data")
Note that some people may need to manually install the GO.db
and WGCNA
libraries as well:
install.packages("BiocManager")
BiocManager::install("GO.db")
BiocManager::install("WGCNA")
Install mfishtools
using:
# Quickly, but without the vignettes:
devtools::install_github("AllenInstitute/mfishtools")
# More slowly, but with the vignettes:
install.packages("remotes", repos='http://cran.us.r-project.org')
remotes::install_github("AllenInstitute/mfishtools", build_vignettes = TRUE)
There are two primary use cases for this libary:
Many functions are currently not included in these vignettes; please use the R help ("?") if additional information is needed, or e-mail me at jeremym@alleninstitute.org.
The license for this package is available on Github at: https://github.com/AllenInstitute/mfishtools/blob/master/LICENSE
We are planning on occasional updating this tool with no fixed schedule. Community involvement is encouraged through both issues and pull requests.
If you contribute code to this repository through pull requests or other mechanisms, you are subject to the Allen Institute Contribution Agreement, which is available in full at: https://github.com/AllenInstitute/mfishtools/blob/master/CONTRIBUTION
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.