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bioi

An R package containing a collection of cell biology image processing tools

cell-sheet-abm

An agent based model of collective cell migration

cell-sheet-piv

Analysis of Image cross correlation velocimetry/Particle image velocimetry performed on time lapse microscopy of cell sheets

collectivecellmigration

Analyze scratch assays

evolution

Model genetic changes over time using a Monte Carlo-based approach

lab-report-corrector_shiny-app

An R Shiny Web App for providing students real-time feedback on their lab reports https://tinyurl.com/lab-report-corrector

mouse_rnaseq_timecourse

Analysis of RNA-Seq using counts data generated by the Johns Hopkins ReCount project for the paper "Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation." by Trapnell et. al., 2010.

phase-microscopy-computer-vision

A machine learning model to classify regions of phase microscopy images as containing or lacking cells. This was made to classify the cell sheet, wound edge, and wound regions in scratch assays.

programming-news_android

An Android application for reading news and troubleshooting information for various programming languages

random-walk-cluster-analysis

Using a distance matrix as input, perform random walks between neighbors to analyze the clustering of cells.

screenplayanalysis

simple-colocalization-analysis

A simple analysis of the colocalization of fluorophores in two channel fluorescent microscopy data

simplifystats

An R package consisting of a set of functions that simplify hypothesis testing