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ggrepel

GitHub Slides

ggrepel is an R package that provides geoms for ggplot2 to repel overlapping text labels:

• geom_text_repel()
• geom_label_repel()

Text labels repel away from each other, away from data points, and away from edges of the plotting area.

library(ggrepel)
ggplot(mtcars, aes(wt, mpg, label = rownames(mtcars))) +
 geom_text_repel() +
 geom_point(color = 'red') +
 theme_classic(base_size = 16)

SNPSEA

GitHub

SNPSEA is a SNP Set Enrichment Algorithm to identify which cell types preferentially express the genes that are associated with a trait.

1. A list of genome-wide significant SNP identifiers (e.g. rs42) from a genome-wide association study (GWAS) on your preferred trait.
2. A (NxM) matrix of gene expression values for all genes (N) across a large number (M) of cell types.

SNPSEA compares the trait-associated single-nucleotide polymorphisms (SNPs) to randomly sampled SNPs while accounting for linkage disequilibrium (LD). It's implemented in C++ with executables available for macOS or Linux.

Immunogenomics.io

View

View the primary genomics data from several biomedical research studies. I developed all of the data visualizations on this site with R and Javascript. You can view bulk RNA-seq, single-cell RNA-seq, and mass cytometry data.

Quickgene.net

View

Quickly turn a messy list of genes or SNPs into a tidy table with symbols, links, and identifiers.

CuSTEMized

CuSTEMized.org

At CuSTEMized, we make one-of-a-kind personalized children's books about scientific careers. CuSTEMized is a 501c3 non-profit created by Jean Fan.

I help develop the website and maintain the server. Do you want to help out? Let us know.

snpbook

GitHub View

Find proxies for your favorite single nucleotide polymorphism (SNP). This is a simple HTML and Javascript page that uses some tricks to query the variants in the 1000 Genomes Project and compute linkage disequilibrium (LD) in the web browser.