BioTuring's Blog

BioTuring Cellpedia, Single Cell Analysis, Single-cell RNA-seq tutorials

How to explore “Characterizing smoking-induced transcriptional heterogeneity in the human bronchial epithelium at single-cell resolution” (Duclos et. al 2019) | BioTuring Cellpedia

by biomembers • December 25, 2019

Multiple studies have shown smoking’s effects on the human bronchi. However, few have characterized its precise impact at cellular resolution. Published recently on Science Advances, a study by Duclos and colleagues has employed single-cell RNA sequencing into exploring the cellular changes in the human bronchial epithelium between current and never […]

BioTuring Cellpedia, Single Cell Analysis

Exploring “Dysfunctional CD8 T Cells Form a Proliferative, Dynamically Regulated Compartment within Human Melanoma” (Li et al., 2018) | BioTuring Cellpedia

by biomembers • December 18, 2019

Welcome to our new BioTuring Cellpedia series! We are excited to introduce a new blog series that provides you with an overview of some interesting datasets indexed in BioTuring Browser public repository, a platform for instant access and reanalysis of published single-cell RNA-seq data. Details on their experimental designs and […]

Single Cell Analysis, Single-cell RNA-seq tutorials

A sub-clustering tutorial: explore T cell subsets with BioTuring Single-cell Browser

by biomembers • October 25, 2019

Single-cell RNA sequencing technologies have enabled many exciting discoveries of novel cell types and sub-types, such as the rosehip neurons (Boldog et al., 2018), disease-associated microglia (Keren-Shaul et al., 2017) and lipid-associated macrophages (Jaitin, Adlung, Thaiss, Weiner and Li et al., 2019). While sub-clustering cell populations is essential to find […]

Single Cell Analysis, Single-cell RNA-seq tutorials

A new tool to interactively visualize single-cell objects (Seurat, Scanpy, SingleCellExperiments, …)

by biomembers • September 26, 2019

Seurat (Butler et. al 2018) and Scanpy (Wolf et. al 2018) are two great analytics tools for single-cell RNA-seq data due to their straightforward and simple workflow. However, for those who want to interact with their data, and flexibly select a cell population outside a cluster for analysis, it is […]

Single Cell Analysis

5,500,000 cells will be indexed into BioTuring Single-cell Data Repository this September

by biomembers • August 30, 2019

We are glad to announce that we will upsize the current single-cell database in BioTuring Single-cell Browser to 5,500,000 cells this September. With this release, we will double the current number of publications indexed in BioTuring Single-cell Browser, and cross the number of cells hosted on available public single-cell data […]

Single Cell Analysis, Single-cell RNA-seq tutorials

4 simple steps to perform differential expression analysis in single-cell data using BioTuring Browser

by biomembers • July 2, 2019

In single-cell data analysis, it is critical to understand how gene expression varies among different cell types, tissue compartments, conditions, or different patients. Although many tools and methods have been developed to support single-cell differential expression analysis, they all require some basic coding skills. In this blog, we show you […]

Single Cell Analysis

Venice: a non-parametric test for finding marker genes in single-cell RNA-seq data

by biomembers • June 24, 2019

In this blog, we introduce Venice a non-parametric approach for finding marker genes in single-cell RNA-seq data. Using a widely adopted benchmarking approach (Wang et al. 2019), Venice obtains the best accuracy among 14 other tools. Venice is also the fastest tool among all the benchmarked methods. Venice is open-source, […]

Single Cell Analysis

BioTuring Single-cell Browser: a modern interactive single-cell database with 3D visualizations and downstream analyses

by biomembers • June 18, 2019

Single-cell sequencing technologies have brought up an unprecedented level of resolution to omics studies with extremely detailed views into individual cells’ expression patterns. With the emergence of drop-based sequencing methods, the resolution now even comes with scale and efficiency. In a single experiment, scientists can now profile hundreds of thousands […]

Single Cell Analysis

Exploring the single-cell atlas of mouse retinal development (Clark et al., 2019): interesting stories revealed

by biomembers • June 3, 2019

Tiny as they are, retinal cells are extremely abundant and complex. The total population of about 100 million rod photoreceptors is among the most numerous neuron populations in the human body, second to cerebellar granule cells (Masland et al., 2012). Forming a sheet of tissue that is only ~200 μm […]

Single Cell Analysis

Single-cell News and Views: March 2019

by biomembers • April 2, 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 […]

Single Cell Analysis

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

by biomembers • January 4, 2019

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 […]

RNA-seq data analysis, Single Cell Analysis

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

by biomembers • December 5, 2018

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 […]

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How to explore “Characterizing smoking-induced transcriptional heterogeneity in the human bronchial epithelium at single-cell resolution” (Duclos et. al 2019) | BioTuring Cellpedia

Exploring “Dysfunctional CD8 T Cells Form a Proliferative, Dynamically Regulated Compartment within Human Melanoma” (Li et al., 2018) | BioTuring Cellpedia

A sub-clustering tutorial: explore T cell subsets with BioTuring Single-cell Browser

A new tool to interactively visualize single-cell objects (Seurat, Scanpy, SingleCellExperiments, …)

5,500,000 cells will be indexed into BioTuring Single-cell Data Repository this September

4 simple steps to perform differential expression analysis in single-cell data using BioTuring Browser

Venice: a non-parametric test for finding marker genes in single-cell RNA-seq data

BioTuring Single-cell Browser: a modern interactive single-cell database with 3D visualizations and downstream analyses

Exploring the single-cell atlas of mouse retinal development (Clark et al., 2019): interesting stories revealed

Single-cell News and Views: March 2019

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

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