A tool for designing HCR (Hybridization Chain Reaction) v3 probes
Project description
Pybridizer is a python repository to generate HCR v3.0 probes for in situ hybridization visualization of mRNA. The module allows for quick and easy design of probe pairs for the Hybridization Chain Reaction approach with visualization (Choi et al. Development 2018.)
You can install the Pybridizer HCR probe design tool by first creating a virtual environment using conda:
conda create --name pyrbidize python conda activate pybridize
You can then use pip to install the HCR probe design tool:
pip install pybridizer
Dependencies: BLAST+ Install BLAST+ by downloading executable from https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/
To build a BLAST database, use the BLAST+ 'makeblastdb' command. Detailed instructions are available on the NIH website at https://www.ncbi.nlm.nih.gov/books/NBK569841/
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