Spatial MOtif REcognition (SMORE)
SMORE is a computational method we have developed for identifying overrepresented arrangements of cells in spatial transcriptomics data. Here you can find the code, test examples, and everything you need to apply it on your data.
MATLAB STREME
We have reimplemented the popular motif discovery algorithm STREME in MATLAB. You can find the code and documentation here. This is especially convenient for Windows users who might have difficulty installing the MEME Suite.
Protocol for making libraries
Here is a simplified protocol for cloning libraries, including combinatorial libraries, that uses liquid culture instead of commonly used large plates.
Designing image readable barcode libraries
Information about design of combinatorial barcode libraries can be found here. This repository also includes a set of 20bp barcode sequences that we have verified in our screening experiments. Limited amount of these lentiviral libraries as well as some piggyBac based DNA libraries are available for collaborative projects. Please contact us, if you are interested in learning more or using these in your projects.
Protocol for imaging barcodes in adherent cells
Here is an updated version of our Zombie protocol for reading out barcodes in cultured cells (e.g. mES or HEK293 cells) using fluorescence microscopy.
Protocol for imaging barcodes in tissue sections
Here is an updated version of our Zombie protocol for reading out barcodes in cryosections using fluorescence microscopy.