Archive

2024

Using AI to find heterogeneous scientific speakers | Nov 4

The many ways to calculate Moran's I for identifying spatially variable genes in spatial transcriptomics data | Aug 29

Characterizing spatial heterogeneity using spatial bootstrapping with SEraster | Jul 23

I use R to (try to) figure out which hospital I should go to for shoppable medical services by comparing costs through analyzing Hospital Price Transparency data | Apr 22

Cross modality image alignment at single cell resolution with STalign | Apr 11

Spatial Transcriptomics Analysis Of Xenium Lymph Node | Mar 24

Querying Google Scholar with Rvest | Mar 18

2023

Alignment of Xenium and Visium spatial transcriptomics data using STalign | Dec 27

Aligning 10X Visium spatial transcriptomics datasets using STalign with Reticulate in R | Nov 5

Aligning single-cell spatial transcriptomics datasets simulated with non-linear disortions | Aug 20

10x Visium spatial transcriptomics data analysis with STdeconvolve in R | May 29

Impact of normalizing spatial transcriptomics data in dimensionality reduction and clustering versus deconvolution analysis with STdeconvolve | May 4

Aligning Spatial Transcriptomics Data With Stalign | Apr 16

2022

3D animation of the brain in R | Nov 8

Ethical Challenges in Biomedical Engineering - Data Collection, Analysis, and Interpretation | Oct 15

I use R to (try to) figure out the cost of medical procedures by analyzing insurance data from the Transparency in Coverage Final Rule | Sep 12

Annotating STdeconvolve Cell-Types with ASCT+B Tables | Aug 30

Deconvolution vs Clustering Analysis: An exploration via simulation | Jul 11

Coloring SVGs in R | Jun 17

Deconvolution vs Clustering Analysis for Multi-cellular Pixel-Resolution Spatially Resolved Transcriptomics Data | May 3

Exploring UMAP parameters in visualizing single-cell spatially resolved transcriptomics data | Jan 19

2021

Animating RNA velocity with moving arrows | Oct 15

A tale of two cell populations: integrating RNA velocity information in single cell transcriptomic data visualization with VeloViz | Oct 6

Story-telling with Data Visualization | Aug 12

Complementing single-cell clustering analysis with MERINGUE spatial analysis | Jun 21

Randomly Generating Music with R | Apr 19

2020

Animating the Cell Cycle | Dec 28

Using R To Find The Missing Faculty | Nov 30

Using scVelo in R using Reticulate | Aug 25

A Guide to Responding to Scientific Peer Review | Jun 17

Quickly Creating Pseudobulks | Apr 6

A Guide to Scientific Peer Review | Mar 23

Ten PhD Transition Tips for the Biological Sciences | Jan 23

RNA Velocity Analysis (In Situ) - Tutorial and Tips | Jan 14

2019

How to write an abstract | Sep 24

Figure style faux pas | Jul 19

Single-Cell RNA-seq Dimensionality Reduction with Deep Learning in R using Keras | May 17

Automate testing of your R package using Travis CI, Codecov, and testthat | Feb 17

Online bargain-hunting in R with rvest | Jan 12

2018

Interactive Exploration Of The Gender Pay Gap | Dec 15

Nih F99 K00 Grant Tips Example And Personal Experience | Oct 31

Single Cell Clustering Comparison | Jun 28

Get your R package on CRAN in 10 steps | Jun 18

Top 10 Must Use Terms To Get Your Next Nih Grant Funded | Jun 11

Data Driven Faculty Job Search | Jun 7

Visually Summarizing Differential Gene Expression | Apr 25

Interactive Honeybadger Laf Profiles | Apr 15

Interactive Tsne | Apr 10

Setting Up New Server | Mar 10

Stability Testing | Feb 28

Phd Program Interview And Application Tips And Advice | Feb 26

Biomedical Analogies | Feb 16

Interactive Visualizations With Highcharter | Feb 10

Fun With Word2vec | Feb 6

Simpsons Paradox | Jan 5

2017

Barcode Doublets | Dec 14

Nih F Series Grant Tips And Example | Oct 19

Nsf Grfp Application Tips And Example | Oct 15

Connected Barplot For Series Data Visualization | Sep 21

Graph Based Community Detection For Clustering Analysis | Sep 13

Machine Learning Feature Selection For Diffexp Analysis | Aug 31

5 Useful Bash Aliases And Functions | Aug 13

A Practical Introduction To Finite Mixture Models | Aug 5

5 Must Dos For Efficient Bioinformatics | Aug 3

Custom Sequencing Library Bioinformatics | Jun 9

Multiclass Diffential Expression Analysis | May 31

How To Be A Research Parasite | Apr 28

Cigar Strings For Dummies | Mar 28

Practical Machine Learning For Everyday Life | Mar 19

Lsf For Dummies | Jan 25

2016

Mapping Snps And Peaks To Genes In R | Dec 6

Identifying And Characterizing Heterogeneity In Single Cell Rnaseq Data | Nov 24

Signaling Network Reconstruction Using Bayesian Networks In R | Sep 30