Author Archives: biomembers

Single-cell News and Views: March 2019

1. An atlas of acute myeloid leukemia at single-cell resolution Adapted from Galan et. al., 2019 Acute myeloid leukemia (AML) is a cancer characterized by the accumulation of white blood cells in the bone marrow and blood. The disease has been notoriously challenging to study because of its extreme intratumoral… Read more »

A review of Haining Lab’s work: Loss of ADAR1 in tumors overcomes resistance to immune checkpoint blockade

Ever questioned why the immune system does not attack our own double-stranded RNA? Speaking of this, we should not ignore the role of ADAR, the gene that encodes Double-stranded RNA-specific adenosine deaminase enzyme, responsible for converting adenosines to inosines (A -> I editing) in double-stranded RNA (dsRNA) substrates. ADAR was… Read more »

BBrowser: the software to resolve major challenges in single-cell RNA-seq data analysis

Single-cell RNA-seq technologies have opened up a completely new era for transcriptomic studies. For the first time ever, scientists can look at individual transcriptomic profiles of millions of cells, and better understand how each cell functions in a tissue. Yet science is confronting bigger challenges analyzing these massive amounts of… Read more »

k-means clustering algorithm and example

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“I’m clueless” You say, looking at an ocean of unlabeled data, waving in front of you. It is true that the lack of labels can sometimes freak us out, leaving us wondering how to group the data together. But luckily, k-means clustering algorithm is here to rescue, one of the… Read more »

Cell Ranger Problems and Hera-T

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Today we finished the first version of Hera-T, a new single-cell RNA-seq quantification algorithm. We developed Hera-T by improving challenging alignment errors that Cell Ranger has. As a result, Hera-T is more accurate than Cell Ranger. Hera-T is more than 10 times faster than Cell Ranger, while consuming just a small amount of… Read more »

Dos and don’ts for a heatmap color scale

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Heatmaps. We see them all over the scientific journals — the shading matrices that convey meaningful stories. Wanna interpret gene expressions? Draw a heatmap. Gotta examine the correlation among variables? Get it done with a heatmap. It seems that the shading has breathed such life into those cheerless matrices of… Read more »

Proportional Venn diagram in 1 minute with BioVinci

Venn diagram is an excellent tool to visualize the relationship among sets. Ideally, the sizes of the circles and their overlapping area should be proportional to the relationship they convey. It is, however, quite a challenge to create a proportional Venn diagram. No worries: With BioVinci, you can get this job done… Read more »

How to build a hierarchical clustering heatmap with BioVinci?

Heatmap, heatmap everywhere. They are an intuitive way to visualize information from complex data. You see them showing gene expression, phylogenetic distance, metabolomic profiles, and a whole lot more. In this tutorial, we will show you how to perform hierarchical clustering and produce a heatmap with your data using BioVinci. It’s… Read more »

BioVinci: a drag-and-drop tool for data visualization

Massive amounts of biological data are emerging everyday, waiting to be deciphered. There is almost no way to analyze and visualize them without writing complex code. As a biologist, you may not find it an optimal use of your time to develop such code from scratch. That is why we… Read more »