research

Lessons Learned Applying Tangram on Visium Data

By Nick Eagles We’ve recently been interested in exploring the (largely python-based) tools others have published to process spatial transcriptomics data for various end goals. A common goal is to integrate data from platforms like Visium, which provides some information about how gene expression is spatially organized, with other approaches with potentially better spatial resolution or gene throughput. In particular, we came across a paper by Biancalani, Scalia et al.

Using tidymodels to Predict Health Insurance Cost

By Arta Seyedian Medical Cost Personal Datasets Insurance Forecast by using Linear Regression Link to Kaggle Page Link to GitHub Source Around the end of October 2020, I attended the Open Data Science Conference primarily for the workshops and training sessions that were offered. The first workshop I attended was a demonstration by Jared Lander on how to implement machine learning methods in R using a new package named tidymodels.

Using VisiumExperiment at spatialLIBD package

By Brenda Pardo A month ago, I started an enriching adventure by joining Leonardo Collado-Torres’ team at Lieber Institute for Brain Development. Since then, I have been working on modifying spatialLIBD, a package to interactively visualize the LIBD human dorsolateral pre-frontal cortex (DLPFC) spatial transcriptomics data (Maynard, Collado-Torres, Weber, Uytingco, et al., 2020). The performed modifications allow spatialLIBD to use objects of the VisiumExperiment class, which is designed to specifically store spatial transcriptomics data (Righelli and Risso, 2020).

Using Space Ranger at JHPCE

By Nick Eagles As part of recent LIBD work with spatial gene expression, I recently was recommended the tool Space Ranger, which provides software pipelines walking Visium spatial RNA-seq samples through the steps we ultimately need to explore gene expression coupled with spatial information. In this blog post, I’ll explain how to start using Space Ranger at JHPCE, focusing heavily on the set-up details relevant to this cluster in particular.

Quality Surrogate Variable Analysis

By Amy Peterson Studying genetic differential expression using postmortem human brain tissue requires an understanding of the effect brain tissue degradation has on genetic expression. Particularly when brain tissue degradation confounds1 the differences in gene expression levels between subject groups. This problem of confounding necessitates measures from a control dataset of postmortem tissue from individuals who do not have the outcome of interest. Doing so provides a comparative measure of the impact of tissue degradation on expression that can then be used in a case-control study to examine the impact of the outcome of interest on genetic expression.