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    BioTuring's Blog

    Data analysis made easy. For biologists, especially.

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    Single Cell Analysis
    Cell Ranger Problems and Hera-T
    by biomembers • October 12, 2018 November 8, 2018

    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 […]

    Data visualization and analysis, Heatmap
    Dos and don’ts for a heatmap color scale
    by biomembers • September 24, 2018 September 21, 2020

    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 […]

    Data visualization and analysis, Principal component analysis, RNA-seq data analysis
    How to read PCA biplots and scree plots
    by Linh Ngo • June 18, 2018 September 21, 2020

    Principal component analysis (PCA) has been gaining popularity as a tool to bring out strong patterns from complex biological datasets. We have answered the question “What is a PCA?” in this jargon-free blog post — check it out for a simple explanation of how PCA works. In a nutshell, PCA capture […]

    Data visualization and analysis, Principal component analysis, RNA-seq data analysis, Single Cell Analysis
    Principal component analysis explained simply
    by Linh Ngo • June 14, 2018 December 5, 2018

    As we are entering the era of Big Data, everyone and their moms seem to be talking about PCA. All the papers you read mention PCA (with lots of jargon, of course). Half of the seminars you’ve been to this month touch on PCA. Your boss/collaborators suggest trying PCA on your data. “What […]

    Box plots, Data visualization and analysis
    More on how to compare box plots
    by Linh Ngo • May 22, 2018 December 5, 2018

    We showed a quick and easy way to compare box plots in previous post. Let’s dig deeper into what information you can use to compare two box plots. Overlapping boxes and medians It gets tricky when the boxes overlap and their median lines are inside the overlap range. As always, math comes to […]

    Box plots, Data visualization and analysis
    How to compare box plots
    by Linh Ngo • May 22, 2018 September 27, 2020

    Box plots, a.k.a. box-and-whiskers plots, are an excellent way to visualize differences among groups. They manage to carry a lot of statistical details — medians, ranges, outliers — without looking intimidating. But box plots are not always intuitive to read. How do you compare two box plots? The key information […]

    Data visualization and analysis, Violin plots
    5 reasons you should use a violin graph
    by Linh Ngo • May 16, 2018 December 5, 2018

    1. Violin graph is like box plot, but better Box-and-whisker plots are great. They show medians, ranges and variabilities effectively. They allow comparing groups of different sizes. They are super simple to create and read, so naturally, they are all over the place. But box plots can be misleading. They are not […]

    Box plots, Data visualization and analysis
    How to draw a modified box plot
    by Linh Ngo • May 13, 2018 December 5, 2018

    Box plots, a.k.a box-and-whisker plots, are an excellent way to compare groups. They are intuitive: viewers can see samples’ medians, distribution, and variabilities with a quick glance. They allow comparing samples of different sizes; for example, a set of 50 data points with a set of 30. They don’t even […]

    Data visualization and analysis, Venn diagrams
    Proportional Venn diagram in 1 minute with BioVinci
    by biomembers • May 11, 2018 November 8, 2018

    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 […]

    Box plots, Data visualization and analysis, Violin plots
    How to craft a figure legend for scientific papers
    by Linh Ngo • May 10, 2018 October 29, 2020

    Writing a scientific paper? Preparing for publication? Making a poster for a conference tomorrow? Let’s face it: People will skim through the body text of your paper/poster, and only look at the figures. We all love figures. They catch eyes, they deliver information effectively, they highlight your results. Figures are […]

    Data visualization and analysis, Heatmap
    How to build a hierarchical clustering heatmap with BioVinci?
    by biomembers • May 8, 2018 November 14, 2018

    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 […]

    Data visualization and analysis
    Log base 2 or e or 10?
    by biomembers • April 26, 2018 November 9, 2020

    When your data span a large range, the graphs tend to get ugly. Values either crowd at the bottom or spread out at the top — a problem called poor resolution. The rate of changes is hard to display, since the graph usually has a very long tail, or a very […]

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