Search Results for: Qlucore

08/29/2023 - In this introductory session, we will look at a biologist-friendly way to analyze RNAseq data in Qlucore, integrated GSEA, and then taking results into NDEx + Cytoscape for biological network analysis.

08/22/2023 - In this introduction webinar, broken down into two 40 minute sessions one week apart, we will look at a biologist-friendly way to analyze RNAseq data in Qlucore, integrated GSEA, and then taking results into NDEx + 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...

04/06/2022 - Gene set enrichment analysis (GSEA) is a statistical method that can be used to determine if gene sets are differentially expressed in different phenotypes. Qlucore Omics Explorer has implemented the GSEA method in a Read More...

02/20/2020 - Attendance at this hands-on workshop will be limited to 20 people. NCI/CCR: To get access to Qlucore, put a request into NCI at Your Service under Get Help https://service.cancer.gov/Get Help Read More...

02/20/2020 - Learn how to easily analyze your gene expression data yourself - using Qlucore Omics Explorer NCI/CCR:To get access to Qlucore, put a request into NCI at Your Service under Get Help https:// Read More...

09/26/2019 - Qlucore Omics Explorer is an interactive analysis and visualization tool that helps the user to find groups, structures, variable networks and discriminating variables. You can use your own data and analyze public data. Omics Read More...

10/25/2017 - BTEP encourages researchers with high-throughput data from NGS or mutiple sources to attend this hands-on workshop on Qlucore Omics Explorer (QOE), which handles various types of data with the platform-independent data import Wizard module. Read More...

02/23/2023 - In this session we will go over a visual, dynamic, and interactive way to work with OMICs data using public leukemia GEO gene expression data sets. We will approach the data with confirmatory and 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...

02/23/2022 - We will go over  data clean up, visualization, clustering (tSNE, UMAP, 3D PCA) and cluster identification using your markers. Qlucore supports automatic import of 10x data, user-friendly visualization, easier cluster ID and visual statistics. Read More...

03/30/2021 - Register Presenter: Yana Stackpole, PhD (Qlucore Training and Support) Description: In this session we will go over a visual, dynamic and interactive way to work with OMICs data using public leukemia GEO gene expression Read More...

05/11/2022 - Many new studies include RNA sequencing data. In this webinar we will go through the process of downloading and importing SRA data using the SRA toolkit, how to use an aligner to convert fastq Read More...

04/11/2019 - https://cbiit.webex.com/recordingservice/sites/cbiit/recording/8a6265d50fb241b292cdcaeb6f20aa1b/playback

06/29/2022 - THIS EVENT HAS BEEN RESCHEDULED FROM 6/22 TO 6/29 AT 11:00 AM USING THE SAME MEETING LINK. We will go over RNA-seq from experimental design,  data import options, data normalization options, to to statistical tests and biological Read More...

Qlucore Omics Explorer has extensive documentation. To access these, users will need to create an account on the Qlucore Omics website. There are also webinars that showcase the use of various workflows. BTEP also hosts Read More...

Contact Yana Stackpole (Qlucore) for help with support and training. If you need help with some aspect of your data analysis with Qlucore Omics Explorer, 30 minute training sessions can be booked directly with Yana via Read More...

You must submit a request through service.cancer.gov to obtain access to Qlucore Omics Explorer. This software requires access to a floating license server (OSTR has 5 licenses). Please be sure to close the application Read More...

Standard formats generally accepted: BAM GTF QUANT.sf (Qlucore) GEDATA (Qlucore) CEL CHP BioArray Software Environment TXT CSV GEO SRA CYTOBAND 10X GENOMICS (requires barcodes.tsv, features.tsv, matrix.mtx)

Slides: Qlucore Omics Explorer Qlucore Omics Explorer v3.8 Features Overview

Geneious Prime can not be used for epigenetic analysis. Please see Partek Flow or CLC Genomics Workbench for this functionality. This package does not support pathway or gene ontology analyses. Please see Partek Flow, Partek Read More...

Check out additional information on Qlucore Omics Explorer, including useful links, in the BTEP Resource pages.

OSTR provides CCR investigators with access to a variety of software licenses for genomic, proteomic, pathway analysis and data visualization tools. These software are funded by OSTR and made available at no cost to CCR 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...

Gene Set Enrichment Analysis (GSEA) EnrichmentMap REVIGO (reducing and visualizing gene ontology) Pathview iPathwayGuide (proprietary) Qiagen IPA (proprietary, CCR license) Qlucore (proprietary, CCR license) GeneMANIA CellNetAnalyzer PARADIGM

01/12/2023 - Join us for an introduction to bioinformatics resources for NCI CCR researchers. We will look at the information available on the BTEP website, such as the: NIH Bioinformatics Calendar Training opportunities Upcoming events New Read More...

Qlucore Omics Explorer does not perform upstream tasks in Next Generation Sequencing such as quality control, read mapping, or deriving gene expression counts. Use Partek Flow, Qiagen CLC Genomics Workbench, or Geneious Prime.

Qlucore Omics Explorer specializes in taking tabular omics data (e.g, RNA sequencing read counts) and producing robust visualizations. If an investigator is interested only in visualizations rather than tabular outputs, this would be the Read More...

Announcements are in the form of "news", including updated information about online learning resource licenses (Coursera, Dataquest) and available NGS analysis software packages (Partek Flow, Qlucore, Qiagen, etc.), and "bulletins". The Read More...

Qlucore Omics Explorer (Qlucore) is a graphical user interface (GUI) based package used to generate visualizations, elucidate biological function, and classify samples as well as cells for omics data. {{Sdet}}{{Ssum}}Listing of Analysis Functions{{ Read More...

Images PNG JPG BMP TIF Tabular data GEDATA (Qlucore)

The goals of the Bioinformatics Training and Education Program within NCI/CCR are: To make researchers aware of the bioinformatics resources available to them, To provide training and guidance on these resources regularly and at Read More...

02/22/2024 - Join us for an introduction to bioinformatics resources for NCI CCR researchers.  Featuring:  NIH Bioinformatics Calendar Programming Classes (R, Unix, Python) Class documentation Website resources working on high performance compute cluster (Biowulf/Helix) Next-Gen Read More...

NCI scientists have many choices available to them for bioinformatic analyses of Next Generation Sequencing (NGS) data. While some require expertise in programming, others provide a more user-friendly, point-and-click interface. These options include programs for Read More...

on the front page is the NIH Bioinformatics Calendar (search by topic, or organizer, info on current, future and past events) Licenses are available to online learning platforms (Dataquest and Coursera), where you can learn Read More...

Includes ‘gene set scoring’ methods such as GSEA, which first compute DE scores for all genes measured, and subsequently compute gene set scores by aggregating the scores of contained genes. --- Geistlinger et al. 2021 GSEA 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...

02/08/2016 - BTEP Workshop on Data Visualization, Exploration and Analysis NOTE: This is a Bring Your Own Computer (BYOC) class, and will be simultaneously shared via GoToMeeting with attendees at the Advanced Technology Research Facility (ATRF) Read More...

06/02/2015 - This workshop will cover some basic concepts involved in the integration of different types of NGS data in order to obtain a better overall picture of the underlying biology. Specifically, the course will examine Read More...

{{Sdet}}{{Ssum}}Gene expression by microarray{{Esum}} CLC Genomics Workbench What file types can I start my analysis with? Affymetrix Gene Chip (CHP, NetAFFx, CEL) Illumina BeadChip TSV CSV Partek Flow What file types can Read More...

Gene Set Enrichment Analysis (GSEA) EnrichmentMap REVIGO (reducing and visualizing gene ontology) Pathview iPathwayGuide (proprietary) Qiagen IPA (proprietary, CCR license) Qlucore (proprietary, CCR license) GeneMANIA CellNetAnalyzer PARADIGM

Below is a list of licensed software available for use by CCR Researchers. Linked software pages include a brief description of each software, recommendations, things to know, input data types, output data types, access information, Read More...

Analyzing your data WITHOUT coding experience: Bioinformatics Licensed Software is a two-hour event featuring four guest speakers from popular commercial software accessible by individuals affiliated with the Center for Cancer Research (CCR). Guest speakers will Read More...

{{Sdet}}{{Ssum}}Pathway, network, and gene ontology{{Esum}} Partek Flow What file types can I start my analysis with? FASTQ BAM TXT Partek Genomics Suite What file types can I start my analysis with? BAM Read More...

Includes ‘gene set scoring’ methods such as GSEA, which first compute DE scores for all genes measured, and subsequently compute gene set scores by aggregating the scores of contained genes. --- Geistlinger et al. 2021 GSEA Read More...

Most BTEP courses include detailed course materials including lesson content, additional resources, and lesson associated data. These course materials are listed here so that learners can easily return to and review concepts taught in class Read More...

Following Cell Ranger and/or other pre-processing tools, you will have a gene-by-cell counts table for each sample. The three most popular frameworks for analyzing these count matrices include: R ( Seurat ). Seurat, brought to you Read More...

Whether you are measuring mRNA expression, protein expression, DNA methylation, expressed miRNAs, protein binding to DNA or RNA, etc., you will likely end up with a list of genes or gene products from which you Read More...

A common question posed to the Bioinformatics Training and Education Program (BTEP) is “How can I learn R and Python to analyze my data?”. First, it’s important to state that learning any programming language Read More...

05/22/2017 - Driven by the decreasing costs and increasing performance of next-generation sequencing (NGS) technologies, the amount of available genomic data has grown exponentially in recent years.  While most of the analyses of these data is Read More...

03/18/2014 - The Cancer Genome Atlas (TCGA) is a large-scale study that has catalogued genomic data accumulated from more than 20 different types of cancer including mutations, copy number variation, mRNA and miRNA gene expression, and DNA Read More...

Includes ‘gene set scoring’ methods such as GSEA, which first compute DE scores for all genes measured, and subsequently compute gene set scores by aggregating the scores of contained genes. --- Geistlinger et al. 2021 These Read More...

There are several tools and packages available for performing GSEA, including but not limited to the following: GSEA software: The original GSEA software developed by the Broad Institute, which provides a user-friendly interface for performing Read More...

Listed below are the video recordings of past BTEP events (classes, seminars, workshops). Videos are hosted on various servers and may play slightly differently. Some videos may be downloaded for local viewing. Recorded Videos of Read More...

This lesson provides an introduction to R in the context of single cell RNA-Seq analysis with Seurat. Learning Objectives Learn about options for analyzing your scRNA-Seq data. Learn about resources for learning R programming. Learn Read More...

Gene ontology and pathway analysis Objectives Determine potential next steps following differential expression analysis. Tour geneontology.org and understand the three main ontologies. Learn about different methods and tools related to functional enrichment and pathway Read More...

Syllabus for “Bioinformatics for Beginners" Instructors: Co-Instructors: To participate in these courses, you need a computer, reliable internet connection and a web browser. All classes and help sessions will be held online. This class Read More...