Explore projects

Files from the Advanced Concepts of Deep Learning Nanocourse

Transcript Analyzer is a module that aids in looking at and identifying target phrases in transcripts. There are two main files ProbTimeSeries.py and TranscriptAnalyzer.py the latter of which uses Streamlit to create an app

Source codes to perform simulations of microtubule growth. McCormick and Cleary et al. 2023 (in preparation), "Interface-acting nucleotide controls polymerization dynamics at microtubule plus- and minus-ends".

Gearification of Sybil Lung Cancer Risk Prediction (https://github.com/reginabarzilaygroup/Sybil)

Move Flywheel data to box.com

An Astrocyte workflow to run cellranger count on droplet-based single cell RNA data generated by 10x Genomics.

AI segmentation for axial T2W MR Autosomal Dominant Polycystic Kidney Disease (https://github.com/aksg87/adpkd-segmentation-pytorch)

Three variants of regression models based on deep neural networks, random forest, and gradient boosting to predict chromatin interaction strength.

An Astrocyte workflow to clean single cell or single nucleus RNA data of technical artifacts using the tool CellBender.

This is the conversion of the BICF RNASeq pipeline into the nextflow framework.

An example workflow package for the BioHPC Astrocyte workflow engine.

Tools for processing droplet microfluidics data in R.