René's URL Explorer Experiment

{"@context":"https://schema.org","@type":"DiscussionForumPosting","headline":"Project 7: Visualization of single cell RNA-seq data from tens of thousands of cells in real time","articleBody":"**Project:**\nCharacterizing the transcriptome of individual cells is fundamental to understanding complex biological systems. Recent developments in single cell RNA sequencing (scRNA-seq) technologies have enabled profiling of tens of thousands of cells in a single sample. However, existing analysis tools are designed for datasets with much lower cell numbers, and to be used by people with a programming background, limiting their adoption. There is a strong need for an intuitive user interface to facilitate real-time data visualization and interpretation by biologists to accelerate the discovery cycle of scRNA-seq analysis. We propose to develop a visualization framework that can be used for scRNA-seq data from tens of thousands of cells in real time. As a starting point, we can use the Python interactive visualization library bokeh to display scRNA-seq data. While the goal is to design a framework that is compatible with scRNA-seq data from most technologies, we will use scRNA-seq data from 10x Genomics as a demonstration dataset. It includes a 68k scRNA-seq data from peripheral blood mononuclear cells (PBMCs) and 8k scRNA-seq data from bone marrow samples of a healthy individual and a patient with acute myeloid leukemia. Some basic functions the visualization framework should support are: 1) dynamic visualization of cells by principal components and clustering; 2) coloring of expression of specific markers in cells; 3) selection of a subset of cells; 4) identification of cluster-specific markers; and 5) visualization compatibility for multiple samples. Participants are encouraged to explore and add other functionalities. The data has been processed by the 10x single-cell pipeline, and output files (matrices, principal component and clustering outputs) have been saved in text files. Team members are expected to familiarize themselves with these output files before the hackathon. Team members should also be familiar with applications of single cell RNA-seq. In addition, team members should become familiar with bokeh. The proposed schedule is to sketch out an interface and functionalities on Day 1. Day 2 and part of Day 3 will be used for implementation and evaluation, and end of Day 3 is used for demo.    \n\n**Project Lead:**\nGrace Zheng / @gracezheng / Industry Professional / 10x Genomics\n","author":{"url":"https://github.com/ttimbers","@type":"Person","name":"ttimbers"},"datePublished":"2016-06-13T15:04:17.000Z","interactionStatistic":{"@type":"InteractionCounter","interactionType":"https://schema.org/CommentAction","userInteractionCount":11},"url":"https://github.com/4/hackseq_projects_2016/issues/4"}