ncibtep@nih.gov

Bioinformatics Training and Education Program

BTEP Coding Club Seminar Series

2024 Seminar Series

The BTEP Coding club is an initiative to provide more tailored bioinformatics training to the NCI community. Each month we will feature a 1-hour demo / tutorial of a bioinformatics tool, software, skill, or platform. Tutorials / demos will range in experience level from beginner to advanced. We welcome suggestions from the NCI community. Email us at ncibtep@nih.gov if there is a specific topic you would like to see featured.

BTEP Coding Club Documentation: https://bioinformatics.ccr.cancer.gov/docs/btep-coding-club/

Getting Started with Partek Flow at NIH

  • When: July 24, 2024
  • Delivery: Online
  • Presented By: Joe Wu (BTEP)
  • Partek Flow enables scientists to construct analysis workflows for multi-omics sequencing data including DNA, bulk and single cell RNA, spatial transcriptomics, ATAC and ChIP. It is hosted on Biowulf, the NIH high performance computing system and suitable for those with little command line knowledge to conduct analyses through a point-and-click interface utilizing Biowulf’s immense compute power, rather than a personal computer that may not have the power for analyzing large genomic datasets. This Coding Club helps scientists with no or limited experience get started using Partek Flow. Participants will learn to acquire access to, transfer data to, and import data into projects on the NIH Partek Flow server. A Partek Flow account is not required for participation.

    Meeting link:
    https://cbiit.webex.com/cbiit/j.php?MTID=ma36cfbd1ac621ea0882fb46f1938cb55 
    Meeting number:
    2310 377 6819
    Password:
    ZbVR7YPk?64

    Join by video system
    Dial 23103776819@cbiit.webex.com
    You can also dial 173.243.2.68 and enter your meeting number.

    Join by phone
    1-650-479-3207 Call-in number (US/Canada)
    Access code: 2310 377 6819


Accessing and Downloading TCGA Data Archived

  • When: June 18, 2024
  • Delivery: Online
  • Presented By: Alex Emmons (BTEP)
  • The Cancer Genome Atlas (TCGA) was a landmark cancer genomics program that molecularly characterized over 20,000 primary cancer and matched normal samples spanning 33 cancer types. This resulted in a massive open-source dataset that continues to uncover revelations regarding the molecular underpinnings of various cancers. This BTEP Coding Club session demonstrates how to access and download TCGA data from the Genomic Data Commons (GDC).  Other means of accessing, analyzing, and downloading TCGA data will also be discussed.  

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Version control with Git Archived

  • When: May 23, 2024
  • Delivery: Online
  • Presented By: Desiree Tillo (GAU, BTEP)
  • Versioning enables researchers to track changes in coding projects. This Coding Club introduces Git (https://git-scm.com), an open-source software used to perform versioning on a personal computer. At the end of this class, participants will:

    • Understand the importance of versioning
    • Describe Git
    • Know how to access Git
      • Be aware of resources that helps with Git installation on personal computer
      • Be aware of the availability of Git on Biowulf, the NIH high performance computing system
    • Define repository
    • Know the steps involved in the versioning process including
      • Initiating a new repository
      • Understanding the difference between tracked and untracked files
      • Excluding files from being tracked
      • Staging files with changes
      • Commiting changes and writing commit messages
      • Viewing commit logs
    • Compare between versions of code
    • Revert to a previous version of code
    Meeting link:
    https://cbiit.webex.com/cbiit/j.php?MTID=m8d56b3aff91ddd2e6df839d05dda6a8f
     
    Meeting number:
    2319 013 9531
    Password:
    dnAnqfP$642
    Join by video system
    Dial 23190139531@cbiit.webex.com
    You can also dial 173.243.2.68 and enter your meeting number.
    Join by phone
    1-650-479-3207 Call-in number (US/Canada)
    Access code: 2319 013 9531
speaker series image

An Introduction to DAVID for Functional Enrichment Analysis Archived

  • When: March 27, 2024
  • Delivery: Online
  • Presented By: Brad Sherman, Weizhong Chang
  • DAVID (the Database for Annotation, Visualization and Integrated Discovery) provides a comprehensive set of functional annotation tools for investigators to understand the biological meaning behind large lists of genes acquired from high-throughput assays such as RNA-Seq, Proteomics, Microarray, etc.  In this BTEP Coding Club session, developers from DAVID (Weizhong Chang and Brad Sherman) will give an overview of DAVID and provide training on key tools including functional annotation tools (table, chart, and clustering), gene functional classification, gene ID conversion, gene name batch viewer, and the newly developed ortholog conversion tool.

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Version control using Git (Cancelled) Archived

  • When: February 28, 2024
  • Delivery: Online
  • Presented By: Joe Wu (BTEP)
  • Versioning enables researchers to track changes in coding projects. This Coding Club session will introduce Git (https://git-scm.com), an open-source software used to perform versioning locally and enables users to upload code to web repositories such as GitHub. At the end of this class, participants will

    • Be able to describe Git
    • Be able to use Git to
      • Create coding projects 
      • Save and track changes to code
      • Upload code to GitHub
      • Revert to/view previous versions of code
      • Perform basic collaboration tasks

     

    Installation of software is not needed to participate.

    Meeting information:

    Meeting link:
    https://cbiit.webex.com/cbiit/j.php?MTID=meadb08ed71552393fe486073a7a7ffc5 
    Meeting number:
    2308 646 3414
    Password:
    VRjdm9A5y$4

    Join by video system
    Dial 23086463414@cbiit.webex.com
    You can also dial 173.243.2.68 and enter your meeting number.

    Join by phone
    1-650-479-3207 Call-in number (US/Canada)
    Access code: 2308 646 3414

    Global call-in options
    https://cbiit.webex.com/webappng/sites/cbiit/meeting/info/e453fc36a706405db9991abd0f97f7bb#

speaker series image

Version control using Github Archived

  • When: February 21, 2024
  • Delivery: Online
  • Presented By: Joe Wu (BTEP), Nadim Rizk (CBIIT)
  • Versioning enables researchers to track changes in coding projects. This Coding Club session will introduce the versioning tool GitHub (https://github.com). At the end of this class, participants will

    • Become familiar with options available for using GitHub at NCI
    • Be able to use GitHub to
      • Create coding projects 
      • Track changes in code
      • Revert to a previous version of code
      • Collaborate with the project team

     

    Installation of software is not needed to participate.

    This class will be followed by one addressing versioning using Git on February 28, 2024 from 11 AM to 12 PM. See https://bioinformatics.ccr.cancer.gov/btep/classes/version-control-using-git for information and registration.

    Meeting information:

    Meeting link:
    https://cbiit.webex.com/cbiit/j.php?MTID=meadb08ed71552393fe486073a7a7ffc5 
    Meeting number:
    2308 646 3414
    Password:
    VRjdm9A5y$4

    Join by video system
    Dial 23086463414@cbiit.webex.com
    You can also dial 173.243.2.68 and enter your meeting number.

    Join by phone
    1-650-479-3207 Call-in number (US/Canada)
    Access code: 2308 646 3414

    Global call-in options
    https://cbiit.webex.com/webappng/sites/cbiit/meeting/info/e453fc36a706405db9991abd0f97f7bb#

speaker series image

Documenting Your Analysis with Quarto Archived

  • When: January 24, 2024
  • Delivery: Online
  • Presented By: Alex Emmons (BTEP)
  • Documenting your data analysis is a crucial step toward making your research reproducible. In this session of the BTEP Coding Club, we will learn how to get started using Quarto with RStudio for report generation. 

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2023 Seminar Series

The BTEP Coding club is an initiative to provide more tailored bioinformatics training to the NCI community. Each month we will feature a 1-hour demo / tutorial of a bioinformatics tool, software, skill, or platform. Tutorials / demos will range in experience level from beginner to advanced. We welcome suggestions from the NCI community. Email us at ncibtep@nih.gov if there is a specific topic you would like to see featured.

BTEP Coding Club Documentation: https://bioinformatics.ccr.cancer.gov/docs/btep-coding-club/

Creating R / Python templates for the NIH Integrated Data Analysis Platform (NIDAP) Archived

  • When: December 6, 2023
  • Delivery: Online
  • Presented By: Alexei Lobanov (CCBR)
  • NIDAP, the NIH Integrated Data Analysis Platform, is a cloud-based and collaborative data aggregation and analysis platform. The NIDAP platform hosts user-friendly bioinformatics workflows (Bulk RNA-Seq, scRNA-Seq, Digital Spatial Profiling) and other component analysis and visualization tools that have been created and maintained by the NCI developer community based on open-source tools.
     
    In this BTEP Coding Club session, Alexei Lobanov, bioinformatics analyst with CCBR, will demonstrate how to create NIDAP templates, GUI-like environments that allow users to run the same code on new datasets using a point-and-click approach, from source code (R or python).
     
    Why create a NIDAP template? 1) “Templatizing” your code is easy and allows users / collaborators with no coding skills to efficiently use your code. 2) Pre-made templates encourage efficiency and reproducibility. Templates allow the user to easily create custom workflows and pipelines that can be shared with collaborators and/or applied to future data sets.
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Visualizing multi-dimensional omics data with circular plots in R package OmicCircos Archived

  • When: November 15, 2023
  • Delivery: Online
  • Presented By: Chunhua Yan (CBIIT CGBB), Ying Hu (CBIIT CGBB)
  • This session introduces two versions of the R/ Bioconductor package OmicCircos to generate high-quality circular plots for visualizing multi-dimensional omics data:

    1. coding in the R environment for programmers;
    2. point-and-click OmicCircos R Shiny app on the Cancer Genomics Cloud (CGC) for non-programmers. 

     

    Meeting number:2310 050 3184

    Password:3sfNDMBq*66

    Join by phone

    1-650-479-3207 Call-in number (US/Canada)

    Access code: 2310 050 3184

Accessing data from and Submitting data to the Gene Expression Omnibus (GEO) Archived

  • When: October 18, 2023
  • Delivery: Online
  • Presented By: Joshua Meyer (CCBR)
  • This October session of the BTEP Coding club will feature a tutorial on how to access data from GEO as well as how to submit data to GEO. 

     

     


Using rMATS for differential alternative splicing detection Archived

  • When: September 20, 2023
  • Delivery: Online
  • Presented By: Alexei Lobanov (CCBR)
  • This session of the BTEP Coding Club will focus on the tool rMATS for differential alternative splicing event detection from RNA-Seq data. This 1-hour demo will provide a detailed overview of rMATS including why you may want to use it, how to use it, and how to interpret and further use resulting outputs. 

    https://rnaseq-mats.sourceforge.io/

    Multivariate Analysis of Transcript Splicing (MATS)

    MATS is a computational tool to detect differential alternative splicing events from RNA-Seq data. The statistical model of MATS calculates the P-value and false discovery rate that the difference in the isoform ratio of a gene between two conditions exceeds a given user-defined threshold. From the RNA-Seq data, MATS can automatically detect and analyze alternative splicing events corresponding to all major types of alternative splicing patterns. MATS handles replicate RNA-Seq data from both paired and unpaired study design.


Using EnhancedVolcano and ComplexHeatmap to visualize -omics data Archived

  • When: August 16, 2023
  • Delivery: Online
  • Presented By: Joe Wu (BTEP)
  • Heatmaps and volcano plots are common data visualizations in bioinformatic analyses of genomic data, such as bulk RNA-seq. While both plot types can be used to visualize gene expression, heatmaps can be used to examine expression data across samples, and in combination with clustering techniques, reveal potential patterns in the data. Volcano plots demonstrate the direction, distribution, and statistical significance of gene expression between experimental conditions (example tumor vs. non-tumor, or drug treated vs. non-treated). In this coding club, we will demonstrate how to construct these plots using the R/Bioconductor tools ComplexHeatmap and EnhancedVolcano.

     

     


A Beginners Guide to Troubleshooting R Code Archived

  • When: July 19, 2023
  • Delivery: Online
  • Presented By: Alex Emmons (BTEP)
  • This session of the BTEP Coding Club will focus on strategies for overcoming errors, warnings, and other common problems with R code. In this 1-hour tutorial targeting beginner R users, we will discuss commonly observed errors, how to find help, and how to approach and debug R code. 


BTEP Coding Club: Submitting Scripts to the Biowulf Batch System Archived

  • When: June 21, 2023
  • Delivery: Online
  • Presented By: Joe Wu (BTEP)
  • Biowulf is the high-performance computing cluster (HPC) at NIH. In addition to its vast compute power, Biowulf has hundreds of bioinformatics tools and databases for analyzing Next Generation Sequencing (NGS) data. This coding club will provide participants the foundations for harnessing Biowulf’s computing power to analyze NGS data. Participants will learn to request computing resources on and to submit scripts to the Biowulf system. This class is not hands-on so no need to obtain a Biowulf account prior to attending.

     

    Meeting link:
    https://cbiit.webex.com/cbiit/j.php?MTID=m39e6aa973e1500fbac8d3516e23cfaf8


    Meeting number:
    2317 419 7733
    Password:
    yKZJuSQ*983
    Host key:
    520526

    Join by video system
    Dial 23174197733@cbiit.webex.com
    You can also dial 173.243.2.68 and enter your meeting number.


    Join by phone
    1-650-479-3207 Call-in number (US/Canada)
    Access code: 2317 419 7733
    Host PIN: 2784

    Global call-in numbers:
    https://cbiit.webex.com/webappng/sites/cbiit/meeting/info/431acd8d9e5f4ad79e425d4832178a31#


Functional Enrichment Analysis with clusterProfiler Archived

  • When: May 17, 2023
  • Delivery: Online
  • Presented By: Alex Emmons (BTEP)
  • Functional enrichment analysis is used to understand the biological context of gene lists or differential expression results. There are a multitude of tools available for this purpose. clusterProfiler is a popular R / Bioconductor package supporting over-representation analysis (ORA) and gene set enrichment analysis (GSEA) using up-to-date biological knowledge of genes and biological processes (GO and KEGG) and support for thousands of organisms. The latest version of clusterProfiler (v. 4.6.2) also provides a tidy interface for visualizing resulting output.

    This May 2023 session of the BTEP Coding Club will provide an overview and demo of many of the key features of the clusterProfiler R package. 


Documenting Data Analysis with Jupyter Lab Archived

  • When: April 19, 2023
  • Delivery: Online
  • Presented By: Joe Wu (BTEP)
  • This BTEP coding club will introduce beginners to Jupyter Notebook, a platform to organize code and analysis steps in one place. Jupyter Notebook can be easily installed or run in a web browser, and supports several languages such as R and Python. It provides a way to keep track of all steps in an analysis and a place for collaboration. Come learn what Jupyter Notebook can do for you. This class will not be hands-on so need to install anything to attend.


VLOOKUP in excel and the R programming equivalent Archived

  • When: March 15, 2023
  • Delivery: Online
  • Presented By: Alex Emmons (BTEP)
  • Do you use excel's VLOOKUP function often to merge tables or search for subsets of data in large NGS data files? If so, you may be interested in a more programmatic solution. Join us for a lesson on performing VLOOKUP in excel followed by a more reproducible solution with R programming. Whether you are interested in merging a list of gene ids with a table of functional annotations or searching for unique matches of known T-Cell Receptor sequences among output from a 10X TCR sequencing run, this tutorial will likely be useful to you.  

    This tutorial will kick off the BTEP Coding Club, which features monthly 1-hour tutorials of bioinformatics tools, software, or skills. Email us at ncibtep@nih.gov if you would like to see a topic featured by the BTEP Coding Club.