Workshops

Start your new year by signing up for your individual experimental design session to discuss how the latest advancements in Chromium Single Cell, Visium Spatial, and Xenium In Situ platforms from 10x Genomics can help you push the boundaries of your research. Uncover molecular insights, dissect cell-type differences, investigate the adaptive immune system, detect novel subtypes and biomarkers, and map the epigenetic landscape cell by cell. We hope to see you and learn about your research and discuss ways to get you started!

Please email christine.kao@10xgenomics.com to schedule an appointment.

The vast complexities of biology require approaches to build a complete picture, starting from single cells to tissues and beyond. At 10x Genomics, we provide single cell, spatial, and in situ technologies that fuel scientific discoveries and drive exponential progress. Unravel highly complex biological systems, while bringing into focus the details that matter most.

Sign up for your individual session to discuss how Chromium Single Cell, Visium Spatial, and Xenium In Situ platforms from 10x Genomics can help you push the boundaries of your research. Uncover molecular insights, dissect cell-type differences, investigate the adaptive immune system, detect novel subtypes and biomarkers, and map the epigenetic landscape cell by cell. Enabling deeper insight into cancer, immunology, neuroscience, and developmental biology, 10x Genomics gives researchers the ability to see biology in new ways.

Please email christine.kao@10xgenomics.com to schedule your 1:1 session.

This workshop will introduce data analysis workflow with both sequencing and imaging based spatial transcriptomics platforms, using 10x Visium HD and Xenium as examples. The topics will include an overview of preprocessing and data visualization with both 10x proprietary software and the state-of-the-art open-source software. New topics will be discussed including analysis, spatial neighborhood analysis and integration with image data. A guided tour will be provided on how to run the latest visualization and data exploration tools to support spatial transcriptomics via both the command line and the Jupyterhub of HPC3. Attendees are encouraged to bring their own project data for analysis and discussion.

Introduction to 10x Genomics Visium and Xenium Spatial Platform Data Analysis Workflow and Analytical Tools (Jenny Wu, PhD)

Interactive Computing on the HPC3 for Spatial Omics (Ivan Chang, PhD)

Are you ready to dive deep into your single cell or spatial data? Join us for a 10x Genomics Data Analysis Q&A Session!

What to Expect:

● Personalized Guidance: Register for a dedicated 1:1 one-hour slot

● Deep Dive: Bring your own single cell or spatial data for a focused, in-depth analysis session.

● Expert Support: Get your questions answered and gain valuable insights into your research.

How to Participate:

1. Register: Book your time with christine.kao@10xgenomics.com

2. Bring Your Data: Come prepared with your single cell or spatial data for an interactive session. Don’t miss this opportunity to advance your data analysis skills with 10x Genomics!

We hope to see you and learn about your research!

Single-cell RNA sequencing (scRNA-seq) offers researchers comprehensive insights into biological systems and finds applications in diverse fields such as developmental biology, oncology, and immunology. Yet analyzing single cell data – and generating biological insights from these data – can be challenging because of the data processing and expertise required. 

Join our hands-on workshop and get direct experience using Trailmaker, Parse Biosciences’ intuitive single cell data analysis platform. Whether you’re new to single cell analysis or looking to accelerate your data-to-figure pipeline, this interactive session will equip you with the skills to go from FASTQ files to publication-ready figures.

CONFIDENTLY ANALYZE YOUR SINGLE CELL DATA – NO CODING REQUIRED

The vast complexities of biology require approaches to build a complete picture, starting from single cells to tissues and beyond. At 10x Genomics, we provide single cell, spatial, and in situ technologies that fuel scientific discoveries and drive exponential progress. Unravel highly complex biological systems, while bringing into focus the details that matter most.

Sign up for your individual session to discuss how Chromium Single Cell, Visium Spatial, and Xenium In Situ platforms from 10x Genomics can help you push the boundaries of your research. Uncover molecular insights, dissect cell-type differences, investigate the adaptive immune system, detect novel subtypes and biomarkers, and map the epigenetic landscape cell by cell. Enabling deeper insight into cancer, immunology, neuroscience, and developmental biology, 10x Genomics gives researchers the ability to see biology in new ways.

Please email christine.kao@10xgenomics.com to schedule your 1:1 session.

In this workshop, you will be introduced to the single cell gene expression analysis journey. Analysis begins at experimental design. Together, we will explore a set of neutrophil data starting with the 10x Cloud Analysis platform for raw data processing. From there, we will assess the data quality using the Cell Ranger web summary and then move into the Loupe Browser for our initial analysis. To wrap things up, each participant will have the opportunity to map out their own analysis journey moving forward by sitting down with members of the 10x Genomics team. Bring your laptop and power cord for this full day interactive hands-on workshop.

The event is free, but registration is required.

Agenda:

Introduction to the workshop and housekeeping

10x Genomics Single Cell Portfolio overview

10x Genomics Cloud Analysis: From FASTQs to quantitative biological information with Cell Ranger

Introduction to Single Cell RNA-Seq Data Analysis

Quality Assessment: Interpreting the Cell Ranger Web Summary

Loupe Analysis: Quality control and rapid data exploration

Wrap up and planning your individual journey with option to meet with the 10x team individually

Single cell RNA-Seq has become a required tool in today’s genomics research. Droplet-based approaches are effective, but struggle against flexibility, high costs, and scale. The Evercode technology enables you to conduct scalable, high-quality single cell with no instrument required. Learn more by stopping by our onsite office hours. Plus, donuts and coffee will be available for all!

Contact srickey@parsebiosciences.com to book a 20-30 minute meeting.

This workshop will introduce the applications of deep neural networks to genomics including variant calling, motif discovery, analysis of gene expression, single cell and image analysis using deepVariant, deepBind, cellpose, etc. We will introduce basic concepts in ML and discuss common model architectures and training. We will also touch upon foundation models in single cell analysis such as scGPT. A hands-on session is emphasized and will showcase how to use Python to train a simple model on HPC3 and perform common analysis tasks in genomics.

Attendees are encouraged to bring their own project data for analysis and discussion.

Introduction to Deep Learning Applications in Genomics (Jenny Wu, PhD)

Training ML/DL Models on HPC3 (Ivan Chang, PhD)

Sign up for your individual session to discuss how the latest advancements in Chromium Single Cell, Visium Spatial, and Xenium In Situ platforms from 10x Genomics can help you push the boundaries of your research. Uncover molecular insights, dissect cell-type differences, investigate the adaptive immune system, detect novel subtypes and biomarkers, and map the epigenetic landscape cell by cell. We hope to see you and learn about your research!

Please email christine.kao@10xgenomics.com to schedule an appointment.