Search Results for: 68 T2/Onc (Sleeping Beauty)

11/02/2023 - In this seminar, Dr. Furlan will share data using single cell genomic technologies after hematopoietic cell transplantation including the molecular approaches and computational tools they have used and developed as they relate to this Read More...

09/28/2023 - The Trapnell Lab at the University of Washington's  Department of Genome Sciences  studies how genomes encode the program of vertebrate development and how that program goes awry in disease. Read More...

After the merged expression counts table has been created, we can proceed with differential expression analysis. Let's use DESeq2 again for this. But first, let's move counts.csv (the merged salmon expression table) Read More...

08/22/2023 - This class of the Python Introductory Education Series will introduce participants to working with and wrangling tabular data using the package Pandas. A Biowulf account and knowledge of working on Biowulf is needed for Read More...

08/15/2023 - This is the first class of the Python Introductory Education Series. It is meant to provide an overview of the Python programming language. Critically, it will ensure that participants can sign onto Biowulf and Read More...

03/20/2025 - This class will serve as a review for essential Unix commands needed for bioinformatics. It is suitable for those who took BTEP's recent Bioinformatics for Beginners course series ( https://bioinformatics.ccr.cancer.gov/ Read More...

03/18/2025 - This class is not hands-on and will demonstrate to participants the use of IGV for visualizing alignment results from Next Generation Sequencing using RNA as an example. After this class, participants will be able Read More...

03/13/2025 - This session will introduce participants to visualizing alignment results from Next Generation Sequences using the Integrative Genomics Viewer (IGV). This step is important as scientists may want to highlight results from certain genomic locations Read More...

03/11/2025 - In this class, participants will get hands-on experience with generating and interpreting differential gene expression analysis results from bulk RNA sequencing. In addition, participants will learn to generate common plots used to visualize bulk Read More...

03/06/2025 - This class introduces participants to the first steps to differential expression analysis in bulk RNA sequencing which involves filtering out noise from (ie. genes without expression across samples) and performing QC on the gene Read More...

03/04/2025 - Alignment of RNA sequencing data enables researchers to identify where in the genome each sequence came from. However, it does not inform of how many sequences aligned to each genomic feature such as a Read More...

02/27/2025 - NGS produces millions of sequences per sample and the challenge is to identify where in the genome each sequence came from. Fortunately, there are aligners that help scientists with this task. After this class, Read More...

02/25/2025 - Quality assessment may reveal low quality sequences and/or contaminations such as adapters in NGS data. Therefore, it is important to perform cleanup to ensure that the input for downstream analyses tools is of Read More...

02/20/2025 - This class will introduce the first step in analyzing NGS data using bulk RNA sequencing as an example. After attending, participants will be able to describe the file format in which NGS data is Read More...

02/18/2025 - This class will introduce basic experimental and analytical considerations for bulk RNA sequencing, a technique that is used to profile gene expression at the tissue level. Information taught serves as the foundation for participants Read More...

12/12/2024 - This class will introduce bulk RNA sequencing analysis using Qiagen software. Participants will learn how to process FASTQ files and obtain differential expression using CLC Genomics Workbench as well as extract biological insight using Read More...

12/12/2024 - Knowledge of Unix command line is advantageous for scientists who are new to bioinformatics, as many tools are designed to run on Unix-like systems. High performance computing systems (e.g., NIH Biowulf) also require Read More...

11/20/2024 - ggplot2 is a popular R package for data visualization that uses layers to build high quality plots. There are over 100 packages that extend the functionality of ggplot2. This session of the BTEP Coding Club Read More...

11/19/2024 - 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 a point-and-click software hosted on Biowulf, the NIH Read More...

11/14/2024 - The accessibility of artificial intelligence/machine learning (AI/ML) tools has taken off in recent years. This democratization of advanced analytics has the potential to revolutionize predictive toxicology, especially for applications that generate massive, Read More...

11/07/2024 - Dr. Blackshaw's work investigates the molecular mechanisms controlling neurogenesis and cell fate specification in the vertebrate forebrain, with a particular focus on the retina. He currently focuses on the use of comparative S Read More...

10/30/2024 - In this session of the BTEP Coding Club, Emily Clough, PhD, GEO Curator, will explore updates to analysis tools available within the Gene Expression Omnibus (GEO), a public repository for gene expression and epigenomics Read More...

10/23/2024 - CellMinerCDB is an interactive public web application ( https://discover.nci.nih.gov/cellminercdb/ ) that simplifies access and exploration of cancer cell line pharmacogenomic data across different sources such as the National Cancer Institute (NCI), Read More...

10/09/2024 - This session will give an overview of the NCI Cancer Research Data Commons and the variety of available cancer data such as RNA expression and protein abundance. These data are hosted in openly accessible Read More...

10/08/2024 - Mass spectrometry is a powerful tool for analyzing protein regulation and function. This workshop, divided into two parts, will explain the fundamentals of mass spectrometry experiments and how proteins are identified. We will further Read More...

09/24/2024 - This class will introduce beginners or those looking for a refresher to Jupyter Lab, a platform used to organize code and analysis steps in one place. Jupyter Lab can be easily installed or run Read More...

09/19/2024 - Qiagen Ingenuity Pathway Analysis (IPA) is a point-and-click software that enables scientists to discern how genomic, transcriptomic, proteomic, and metabolomic changes influence molecular biology pathways and networks. This software is available to NCI investigators, Read More...

09/12/2024 - Telomere to telomere (T2T) genome assemblies represent a paradigm shift in comparative genomics, offering insights into chromosome structure, evolution, and function at the highest resolution. Dr. O'Neill's lab has made recent Read More...

09/11/2024 - Qlucore Omics Explorer is a point-and-click package available to NCI CCR scientists that enables visualization-based analysis of multi-omics data including RNA-seq, scRNA-seq, proteomics, metabolomics, as well as enabling the use of machine learning classification Read More...

08/29/2024 - Dr. Mardis is an internationally recognized expert in cancer genomics, with ongoing interests in the integrated characterization of cancer genomes, defining DNA-based somatic and germline interactions and RNA-based pathways, and immune microenvironments that lead Read More...

08/15/2024 - Qiagen’s CLC Genomics Workbench is a point-and-click software for analyzing multi-omics sequencing data including variant analysis, RNA sequencing, and ChIP sequencing. This class will demonstrate variant analysis using this software. Participants will be Read More...

08/08/2024 - The Elemento lab combines Big Data analytics with experimentation to develop entirely new ways to help prevent, diagnose, understand, treat and ultimately cure disease. Our research involves routine use of ultrafast DNA sequencing, proteomics, Read More...

07/24/2024 - Knowledge of Unix command line is advantageous for scientists who are new to bioinformatics, as many tools are designed to run on Unix-like systems. High performance computing systems (e.g., NIH Biowulf) also require Read More...

07/24/2024 - 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 Read More...

07/18/2024 - Long read sequencing holds an advantage over short read sequencing in areas such as structural variant and transcript isoform discovery.  This class will demonstrate long read analysis using Qiagen’s CLC Genomics Workbench, a Read More...

07/10/2024 - Qlucore Omics Explorer is a point-and-click software for analyzing various omics data including RNA sequencing (bulk and single cell), proteomics, and metabolomics. Participants will learn to perform QC, construct visualizations (ie. PCA, heatmap, volcano, Read More...

06/20/2024 - Dr. Irizarry will share findings demonstrating limitations of current workflows that are popular in single cell RNA-Seq data analysis. Specifically, he will describe challenges and solutions to dimension reduction, cell-type classification, and statistical significance Read More...

06/13/2024 - Qiagen CLC Genomics Workbench is a point-and-click bioinformatics software that runs on a personal computer and enables bulk RNA sequencing, ChIP sequencing, long reads, and variant analysis. NCI scientists can use CLC Genomics Workbench Read More...

06/12/2024 - Join us for an engaging training session where we will examine the similarities and differences between machine learning and statistical differential gene expression (DGE) analysis using Qlucore Omics Explorer. Qlucore Omics Explorer is a Read More...

06/06/2024 - The Brooks Lab developed a computational tool called FLAIR (Full-Length Alternative Isoform Analysis of RNA) to produce confident transcript isoforms from long-read RNA-seq data with the aim of alternative isoform detection and quantification. With Read More...

05/23/2024 - An exciting opportunity at the intersection of the biomedical sciences and machine learning stems from the growing availability of large-scale multi-modal data (imaging-based and sequencing-based, observational and perturbational, at the single-cell level, tissue-level, and Read More...

05/23/2024 - 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, Read More...

05/16/2024 - Qiagen CLC Genomics Workbench is a point-and-click bioinformatics software that runs on a personal computer and enables bulk RNA sequencing, ChIP sequencing, long reads, and variant analysis. NCI scientists can use CLC Genomics Workbench Read More...

05/08/2024 - Qlucore Omics Explorer is a point-and-click software that enables analysis of RNA sequencing (bulk and single cell), proteomics and metabolomics data. It’s machine learning capabilities also allow for classification of cell types. This Read More...

05/02/2024 - The explosion of biomedical big data and information in the past decade or so has created new opportunities for discoveries to improve the treatment and prevention of human diseases. As such, the field of Read More...

04/11/2024 - Informaticians aim to bring the right information to the forefront at the right time to improve decision-making. Dr. Greene's  lab develops computational methods that integrate distinct large-scale datasets to extract the rich and Read More...

04/04/2024 - Although generative artificial intelligence (AI), a’la ChatGPT, is receiving a lot of “attention” these days, there are many other options for using AI to support biomedical research.  In order to help analyze and Read More...

03/01/2024 - Jens Rittscher is Professor of Engineering Science at the University of Oxford with his appointment held jointly between the Institute of Biomedical Engineering and the Nuffield Department of Medicine. He is a group leader Read More...

02/28/2024 - 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 Read More...

02/21/2024 - 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 Read More...

A function in R (or any computing language) is a short program that takes some input and returns some output. An R function has three key properties: Functions have a name (e.g. dir, getwd); Read More...

01/24/2024 - This is the second lesson of the Introduction to Unix on Biowulf, January 2024 series. After this lesson, participants will  Know how to get help with Unix commands Know how to transfer data from local Read More...

01/22/2024 - This is the first lesson in the Introduction to Unix on Biowulf, January 2024 series. In this lesson, participants will learn to log onto Biowulf and receive an overview of Unix command line as well Read More...

There are many steps that can be taken following subsetting (i.e., filtering by rows and columns); one of which is reordering rows. In the tidyverse, reordering rows is largely done by arrange() . Arrange will Read More...

12/13/2023 - In this session we will take a closer look at the usage and all configuration options for Venn diagram and Pie chart in Qlucore. Also, we will look at variable list manipulations like compare Read More...

11/29/2023 - In this session we will take a closer look at the usage and all configuration options for heatmaps and PCA (sample and variable) plots in Qlucore. Also, we will look at easy and cool Read More...

10/25/2023 - Partek Flow is your start-to-finish solution for analyzing high dimensional multi-omics sequencing data. It is a point-and-click software and is suitable for those who wish to avoid the steep learning curve associated with analyzing Read More...

10/11/2023 - Partek Flow is your start-to-finish solution for analyzing high dimensional multi-omics sequencing data. It is a point-and-click software and is suitable for those who wish to avoid the steep learning curve associated with analyzing Read More...

09/28/2023 - This is Lesson 4 of the Fall 2023 Introduction to Unix on Biowulf Series . Registering for this class will get you signed up for all four sessions in this course. Please make sure that you can Read More...

09/27/2023 - Partek Flow is your start-to-finish solution for analyzing high dimensional multi-omics sequencing data. It is a point-and-click software and is suitable for those who wish to avoid the steep learning curve associated with analyzing Read More...

09/21/2023 - This is Lesson 3 of the Fall 2023 Introduction to Unix on Biowulf Series . Registering for this class will get you signed up for all four sessions in this course. Please make sure that you can Read More...

09/14/2023 - This is Lesson 2 of the Fall 2023 Introduction to Unix on Biowulf Series . Registering for this class will get you signed up for all four sessions in this course. Please make sure that you can Read More...

09/13/2023 - Partek Flow is your start-to-finish solution for analyzing high dimensional multi-omics sequencing data. It is a point-and-click software and is suitable for those who wish to avoid the steep learning curve associated with analyzing Read More...

09/08/2023 - Hybrid Seminar Friday, September 8, 2023 • 9:00-10:00 a.m. Building 549 Auditorium (In-person attendance encouraged)   Speaker: Brian Kelsall, M.D. Senior Investigator, Mucosal Immunobiology Section Laboratory of Molecular Immunology National Institutes of Allergy Read More...

09/07/2023 - This is Lesson 1 of the Fall 2023 Introduction to Unix on Biowulf Series. Registering for this class will get you signed up for all four sessions in this course. Please make sure that you can Read More...

The bulk RNA-Seq test data we've been working with is in FASTQ format. We'd like to do a BLAST search on a couple of these sequences. Data must be in FASTA format to Read More...

This page uses content directly from the Biostar Handbook by Istvan Albert. Always remember to activate the bioinfo environment when working on Biostar class materials. conda activate bioinfo The bulk RNA-Seq test data we've Read More...

BBDuk is another tool that can be used for adapter and quality trimming. In addition, BBDuk can be used to filter out contaminations, perform GC filtering, filter for length, etc. (see https://jgi.doe.gov/ Read More...

08/29/2023 - This class will wrap up the Python Introductory Education Series by showing participants how to create data visualizations. A Biowulf account and knowledge of working on Biowulf is needed for this class. Meeting link: Read More...

08/17/2023 - In the second class of the Python Introductory Education Series, participants will start to dive into Python. Participants will walk away with knowledge of common Python data types and structures, how to assign variables, Read More...

06/21/2023 - 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 Read More...

06/15/2023 - Are you interested in analyzing your own data, but you lack coding experience? No problem. There are several proprietary -omics solutions available to researchers within the Center for Cancer Research (CCR). If you have Read More...

06/14/2023 - Partek Flow is your start-to-finish solution for analyzing high dimensional multi-omics sequencing data. It is a point-and-click software and is suitable for those who wish to avoid the steep learning curve associated with analyzing Read More...

06/07/2023 - " New Violin plot, more statistical tests, and even more info for 3D PCA in Qlucore 3.9 " We are excited to share the new Qlucore Omics Explorer version 3.9 with you! It brings to you Read More...

06/06/2023 - Welcome to Learning Unix on Biowulf. This course consists of four one-hour lessons that will run weekly on Tuesdays from 1 -2 PM starting May 16. Subsequent lessons will be held on May 23, May 30, and June 6. Read More...

05/30/2023 - Welcome to Learning Unix on Biowulf. This course consists of four one-hour lessons that will run weekly on Tuesdays from 1 -2 PM starting May 16. Subsequent lessons will be held on May 23, May 30, and June 6. Read More...

05/23/2023 - Welcome to Learning Unix on Biowulf. This course consists of four one-hour lessons that will run weekly on Tuesdays from 1 -2 PM starting May 16. Subsequent lessons will be held on May 23, May 30, and June 6. Read More...

05/16/2023 - Welcome to Introduction to Unix on Biowulf. This course consists of four one-hour lessons that will run weekly on Tuesdays from 1 -2 PM starting May 16. Subsequent lessons will be held on May 23, May 30, and Read More...

05/03/2023 - Partek Flow is your start-to-finish solution for analyzing high dimensional multi-omics sequencing data. It is a point-and-click software and is suitable for those who wish to avoid the steep learning curve associated with analyzing Read More...

04/12/2023 - Partek Flow is your start-to-finish solution for analyzing high dimensional multi-omics sequencing data. It is a point-and-click software and is suitable for those who wish to avoid the steep learning curve associated with analyzing Read More...

04/06/2023 - Az imuth is a web application that uses an annotated reference dataset to  automate the processing, analysis, and interpretation of a new single-cell RNA-seq experiment . Azimuth leverages a  'reference-based mapping' pipeline that inputs a Read More...

03/30/2023 - AI Models of Cancer and Precision Medicine: Building a Mind for Cancer The long-term objective of the Ideker Lab is to create artificially intelligent, mechanistic models of cancer and neurodegenerative diseases for translation of Read More...

A function in R (or any computing language) is a short program that takes some input and returns some output. An R function has three key properties: Functions have a name (e.g. dir, getwd); Read More...

01/25/2023 - Bulk RNA-Seq data analysis - learn all about expression counts (raw counts, FPKM, RPKM, TMM, TPM, CPM). Those of you, who are hands-on with RNA-seq, or even simply reading publications on this know there Read More...

09/27/2022 - Course Objectives: This 12-week long course is for scientists wanting to learn basic bioinformatics skills. Material will be taught at a beginner to intermediate level. There are no pre-requisites. Learners will: Learn Unix skills Read More...

09/22/2022 - The avalanche of easy-to-create genomics data has impacted almost all areas of medicine and science, from cancer patients and microbial diagnostics to molecular monitoring for astronauts in space. In this lecture, new discoveries from Read More...

07/26/2022 - Meeting Link: https://cbiit.webex.com/cbiit/j.php?MTID=m62ed494c9292a59c0f158b2c60f08263 Join us for an introduction to bioinformatics resources for NCI CCR researchers. We will look Read More...

Learning Objectives To understand: 1. the difference between R and RStudioIDE. 2. how to work within the RStudio environment including: creating an Rproject and Rscript navigating between directories using functions obtaining help how R can enhance data Read More...

Introduction to dplyr and the %>% Objectives Today we will begin to wrangle data using the tidyverse package, dplyr . To this end, you will learn: how to filter data frames using dplyr how to employ Read More...

Lesson 11: Merging FASTQ quality reports and data cleanup Before getting started, remember to be signed on to the DNAnexus GOLD environment. Lesson 10 Review In the previous lesson, we learned about the structure of the FASTQ Read More...

Lesson 16: RNA sequencing review and classification based analysis Before getting started, remember to be signed on to the DNAnexus GOLD environment. Review In the previous classes, we learned about the steps involved in RNA sequencing Read More...

Introduction to R and RStudio IDE Objectives To understand: 1. the difference between R and RStudioIDE. 2. how to work within the RStudio environment including: creating an Rproject and Rscript navigating between directories using functions obtaining help 3. Read More...