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    BioTuring's Blog

    Data analysis made easy. For biologists, especially.

    6,000,000 cells
    at ease with
    BioTuring Browser
    Explore now
    Single Cell Analysis, Single-cell RNA-seq tutorials, Visium Spatial Transcriptomics Analysis
    Explore 10X Visium Spatial Transcriptomics data at ease with BioTuring Browser
    by biomembers • November 9, 2020 November 9, 2020

    Cells don’t function independently. They belong to a complex and interconnected network. This makes gene expression profiling of individual cells not enough for understanding their activities and crosstalk in the tissue context.  Like a marriage between imaging and RNA sequencing, Spatial Transcriptomics is a revolutionized method to map gene activity […]

    Single Cell Analysis, Single-cell RNA-seq tutorials
    A tiny world inside non-small cell lung cancer revealed by single-cell omics: 35 cell types, and their marker genes
    by biomembers • October 20, 2020 October 29, 2020

    Take a non-small cell lung tumor. What do we see? To answer this challenging question, a lot of single-cell omics experiments have been conducted, yielding significant insights into the heterogeneity of non-small cell lung cancer (NSCLC) microenvironment. While each successfully characterizes a facet of this ecosystem, until now no work […]

    Data visualization and analysis, Principal component analysis
    The Why, When and How of 3D PCA
    by Tien • October 12, 2020 October 20, 2020

    Principal component analysis (PCA) is one of the most popular dimension reduction methods. It works by converting the information in a complex dataset into principal components (PC), a few of which can describe most of the variation in the original dataset. The data can then be plotted with just the […]

    Box plots, Data visualization and analysis
    6 best box and whisker plot makers
    by biomembers • September 18, 2020 September 27, 2020

    A box and whisker plot, or just box plot, is a graph that visualizes how spread-out a dataset is. A box plot displays 5 values: minimum, first quartile, median, third quartile, and maximum.  How to read a box plot: The box is drawn from the first quartile to the third […]

    Single Cell Analysis, Single-cell RNA-seq tutorials
    Immunoglobulin genes up-regulated in lung adenocarcinoma infiltrating T cells: A report from BioTuring lung cancer single cell database
    by biomembers • September 8, 2020 September 9, 2020

    Highlights: In every biology textbook, expression of the B cell receptor (BCR) defines B cells, and the T cell receptor (TCR) defines T cells. However, in 2019, Ahmed et al. discovered a strange cell population in Type I Diabetes that coexpresses the BCR and TCR, and key lineage markers of […]

    Single Cell Analysis
    Is Survivin (BIRC5) linked to tumor resistance at single-cell resolution?
    by biomembers • July 27, 2020 July 30, 2020

    BIRC5, known as Survivin, is one member of the Inhibitor of apoptosis protein family and plays an important role in preventing cell death (Jaiswal et al., 2015) and poor survival in cancers (Supplementary). For this reason, BIRC5 can be hypothesized to be associated with tumor resistance to cancer treatments. With […]

    Single Cell Analysis
    Revisiting AML single-cell datasets in BBrowser to learn how monocytic AML survives Venetoclax
    by biomembers • July 7, 2020 July 10, 2020

    Acute myeloid leukemia (AML) happens when the myeloid precursor cells in the bone marrow grow abnormally (making up  myeloblasts). A common treatment for AML is Venetoclax. This drug inhibits BCL2, an oncoprotein that prevents cell death and is often overexpressed in the majority of blasts from AML patients (Bensi et […]

    Single Cell Analysis
    BioTuring Big Data Portal: Exploring huge public single-cell data sets without limits
    by biomembers • May 4, 2020 May 6, 2020

    Single-cell data sets are exploding in size. From a few thousand cells, we now see more than 1 million data points being generated (Cao et. al., 2019). Large single-cell atlases are valuable resources for exploration and insights, but also pose a great challenge to anyone who wants to view and […]

    Box plots, Data visualization and analysis, Heatmap, Principal component analysis, Venn diagrams, Violin plots
    BioVinci: high-dimensional data visualization made easy for biologists
    by biomembers • April 24, 2020 September 21, 2020

    “How to extract the biology behind this huge matrix of thousands of rows and columns?”  Large numbers of data points hold valuable biological stories yet are tricky to graph and analyze. Imagine you had the data for 1000 features and observations, your mind would be full of questions, wondering how […]

    Single Cell Analysis
    Single-cell analysis of CD8+ T cells in immune checkpoint blockade: some reproducible insights from BioTuring Database
    by biomembers • March 30, 2020 March 30, 2020

    Cancer treatment, as challenging as it sounds, has been revolutionized by recent advances in immune checkpoint blockade (ICB) therapies, which use monoclonal antibodies (mAb) to block the suppressive immune checkpoints, helping the patient’s immune system to kill cancer cells. However, despite several clinical case studies of success, some patients still […]

    Single Cell Analysis
    Interactive CITE-Seq data analysis with BioTuring Browser
    by biomembers • March 2, 2020 March 2, 2020

    Nominated as Method of the year by Nature in 2019, single-cell multimodal omics has enabled scientists to uncover many facets of the cells by simultaneously measuring multiple modalities in one single-cell experiment. One candidate for multimodal analysis is CITE-Seq, a technique that layers cell surface protein information on top of […]

    Single Cell Analysis
    BioTuring Cell Search: a new tool to search for similar populations in public single-cell data sets
    by biomembers • January 15, 2020 January 22, 2020

    A machine learning model for cell type classification? When analyzing single-cell transcriptomic data, scientists often perform cell type annotations by checking individual marker genes. However, marker genes are not even consistent among different literature sources. Six months ago, armed with the largest curated single-cell transcriptomic data, BioTuring single-cell team naively […]

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    Recent Posts
    • Explore 10X Visium Spatial Transcriptomics data at ease with BioTuring Browser November 9, 2020
    • A tiny world inside non-small cell lung cancer revealed by single-cell omics: 35 cell types, and their marker genes October 20, 2020
    • The Why, When and How of 3D PCA October 12, 2020
    • 6 best box and whisker plot makers September 18, 2020
    • Immunoglobulin genes up-regulated in lung adenocarcinoma infiltrating T cells: A report from BioTuring lung cancer single cell database September 8, 2020
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      • Principal component analysis
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    • RNA-seq data analysis
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    • Single-cell RNA-seq tutorials
    • Visium Spatial Transcriptomics Analysis
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