Code, analyses, and other resources accompanying the RADAR manuscript.

radar.py contains functions to generate new sensor designs, and to analyze whole genomes based on Biomart transcript exports.

You can access Biomart exports for mouse and human transcriptomes at https://rnasensing.bio/biomart-files

You additionally need blast-indexed, Fasta-formatted genome files. E.g., for mouse, download GCF_000001635.27_GRCm39_genomic.fna.gz from https://www.ncbi.nlm.nih.gov/assembly/GCF_000001635.27/, uncompress and index it for blast:

zcat GCF_000001635.27_GRCm39_genomic.fna.gz > GRCm39.fa
makeblastdb -in GRCm39.fa -dbtype nucl

RADAR human transcripts.ipynb and RADAR mouse transcripts.ipynb contain analysis of transcriptomes. The generated files are available at https://rnasensing.bio/

python radar.py design_based_on_mart_export \
    --gene Bdnf --variant CCA \
    --mart-export musmusculus_3UTR_mart_export.txt.gz --fa-genome GRCm39.fa \
    --verbose 5 \
    > Bdnf_designs
less Bdnf_designs

The --verbose flag can be omitted for less output.