Search Results for: comparative genomic hybridization

"Keep raw data separate from analyzed data" -- datacarpentry.org For large genomic data sets, you may want to include a project folder with two main subdirectories (i.e., raw_data and data_ Read More...

12/07/2023 - This hands-on workshop will introduce the Ingenuity Pathway Analysis (IPA) and CLC Genomics Workbench tools, which are available to access from the NIH Library. IPA can be used identify biological relationships, mechanisms, pathways, functions, Read More...

10/23/2023 - Do you use the Cancer Research Data Commons’ (CRDC’s) Genomic Data Commons (GDC) for downloading molecular, clinical, and/or imaging data? Do you download large quantities of data? Attend Read More...

10/03/2023 - Presented as part of the Sequencing Strategies for Population and Cancer Epidemiology Studies (SeqSPACE) Webinar Series Dr. Kushal Dey is an Assistant Member and Josie Robertson Investigator in the Department of Computational and Systems Read More...

Genomic variations are typically categorized into different classes and are often denoted with a shortened acronym: SNP, a single nucleotide polymorphism - A change of a single base. INDEL, an insertion or a deletion - Read More...

This page uses context taken directly from the Biostar Handbook by Istvan Albert. Remember to activate the class bioinformatics environment. conda activate bioinfo Introduction to Genomic Variation Genomic variations are typically categorized into different classes Read More...

Generating VCF Files (Simulated data) VCF files are produced by running a variant caller on one or more BAM alignment files. We will download the ebola genome (AF086833) into a "refs" directory, create Read More...

Molecular Cytogenetics Core Facility facilitates the assessment of structural and numerical genomic changes in pre-cancer and cancer research models. This core provides comprehensive support for the cytogenetic analysis of cells from human and research animal Read More...

Seaborn is a popular Python plotting package, which is the tool that will be introduced in this lesson. Seaborn is an extension of and builds on Matplotlib and is oriented towards statistical data visualization. However, Read More...

Seaborn is a popular Python plotting package, which is the tool that will be introduced in this lesson. Seaborn is an extension of and builds on Matplotlib and is oriented towards statistical data visualization. However, Read More...

07/01/2025 - Learn how to vi ualize equencing and analy i re ult effectively. Thi e ion de cribe the application of the web-ba ed interactive OmicCirco in R hiny to con truct circular plot with 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...

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...

04/26/2024 - Dear Colleagues,    In this webinar, you'll get an introduction to WebMeV. WebMeV aims to democratize bioinformatics analysis for biological sciences researchers.   The maturation of many bioinformatics processes Read More...

For visualizing the HBR and UHR alignment results, we will use the built in Human hg38 genome. To do this, we will just goto the genome selection box and select hg38 (Figure 2). In Figure 3, we Read More...

Data Simulation We'll download a reference sequence from NCBI (AF086833, ebola genome), place it in a refs directory that we create, and create a "bam" index using "bwa". mkdir -p Read More...

The Molecular Pathology Unit is intended to spearhead opportunities for bridging basic and clinical research efforts by more precisely optimizing the development, characterization, and utilization of models of human disease. The initiative approach includes both Read More...

06/10/2021 - Meeting Link:  https://cbiit.webex.com/cbiit/j.php?MTID=mc11b56eb7f7e732aa44c78427402dd2e Abstract: Long read, single molecule sequencing from Pacific Biosciences (PacBio) and Oxford Nanopore are revolutionizing Read More...

09/04/2020 - Speakers: Dave Clements, Galaxy Community Manager, Johns Hopkins University, Steven Weaver, Senior Programmer Analyst, Temple University Galaxy is an open web-based platform for data integration and analysis in the life sciences. Galaxy makes sophisticated Read More...

02/27/2020 - The Annotation, Visualization and Impact Analysis (AVIA) is an application developed to guide, prioritize and summarize genomic variants. AVIA maintains and aggregates dozens of publicly available variant annotation databases and predictions from impact analysis Read More...

The UCSC Genome Browser is the "goto tool" for viewing sequence data in a genomic context. It's wide variety of supported organisms and data types, coupled with its responsive performance make it Read More...

02/14/2024 - Explore the intricate world of pathway analysis with Reactome. Reactome is an open-source, manually-curated and peer-reviewed biological pathway knowledgebase, free and open to the public. We will provide you an overview of the contents Read More...

The Genomics Technology Laboratory is an integrated, high-throughput molecular biology laboratory focusing on the development of genetics and genomics technologies, data analysis, and information management tools, in support of CCR Investigators. The laboratory develops integrated Read More...

The Genomics Laboratory (formerly Laboratory of Molecular Technology) is an integrated, high-throughput molecular biology laboratory focusing on the development of genetics and genomics technologies, together with associated laboratory automation systems, data analysis, and information management Read More...

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...

06/22/2022 - Cancer origination and progression is a complex process that can be viewed as a somatic evolutionary progression with clonal cellular expansion(s) driven by accumulation of survival-/evasion-beneficial genomic mutations, alongside constantly changing selective Read More...

06/17/2025 - In thi webinar, Dr . Weng and Abdennur will be pre enting on the integrative analy i and vi ualization platform for cancer regulatory genomic .

06/06/2025 - The la t decade ha demon trated the power of genomic to unravel the etiology of complex trait and di ea e . The va t majority of genomic tudie have been ba ed on Read More...

03/13/2025 - UCSC Xena showcases seminal cancer genomics datasets from The Cancer Genome Atlas (TCGA) and the Pan-Cancer Atlas, as well as the Genomic Data Commons, Pan-cancer Atlas of Whole Genomes, and the International Cancer Genome Read More...

01/10/2025 - NIH DIRECTORS SEMINAR SERIES In this presentation, Dr. Scholz will discuss the approach to tackling complex neurodegenerative diseases using modern genomic tools, focusing on Lewy body dementia, a major research area in her lab. 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...

06/14/2024 - Data Sharing and Reuse Seminar Series Please join us for the June Data Sharing and Reuse Seminar where Micahel Schatz, Ph.D. will be presenting "BioDIGS: BioDiversity and Informatics for Genomics Scholars. This Read More...

03/20/2024 - Dear Colleagues,   cBioPortal is an open-access resource for interactive exploration of multidimensional cancer genomics data sets, currently providing access to data from >200,000 tumor samples collected from >400 published cancer Read More...

There are a number of other file types you may be interested in. For genomic specific formats, you will likely need to install specific packages; check out Bioconductor for packages relevant to bioinformatics. For information Read More...

Reference genome or transcriptome Annotation files (gff or gtf) that tells us the genomic features (ie. gene, transcript, etc.) Raw sequencing files in FASTQ (or fq) format

{{Sdet}} Solution{{Esum}} Reference genome or transcriptome Annotation files (gff or gtf) that tells us the genomic features (ie. gene, transcript, etc.) Raw sequencing data in FASTQ (or fq) format {{Edet}}

Many tools (like a bazillion) for biological data analysis are freely available and supported on Unix systems Useful for working with big data, like genomic sequence files To use the NIH High Performance Cluster (HPC) Read More...

Many tools (like a bazillion) for biological data analysis are freely available and supported on Unix systems Useful for working with big data, like genomic sequence files To use the NIH High Performance Cluster (HPC) Read More...

Reads not perfect Duplicate molecules (PCR artifacts skew quantitation) Multimapped reads - Some regions of the genome are thus classified as unmappable Aligners try very hard to align all reads, therefore fewest artifacts occur when Read More...

CCR staff have access to a number of resources Biowulf (Helix) - CIT maintained large cluster with a huge software library (Unix command line) CCBR Pipeliner (Biowulf) Partek Flow (Local Web Service) DNAnexus (Cloud Solution) Read More...

Biomarker Discovery with Morphological Context:  Changing how tissue specimens are analyzed < https://youtu.be/mVhfZq8ppbc What is Digital Spatial Profiling? GeoMx Digital Spatial Profiler is a novel platform developed by NanoString. Digital Spatial Read More...

The FNLCR Molecular Histopathology Laboratory (MHL) provides comprehensive veterinary pathology support for animal health monitoring, biomarker discovery and validation, drug development, genomics, and proteomics on a cost recovered basis. The MHL is organized into multiple Read More...

Discover expert help with analysis, processing applications, and licensed software packages.

Mass Spectrometry Section of the Collaborative Protein Technology Resource (Bldg. 37) Core Capabilities: Identification of proteins in complexes, organelles, subcellular fractions, or fluids. Global relative protein quantitation. Quantitation by isotopic labeling of cells in culture (SILAC) Read More...

The NCI High-Throughput Imaging Facility (HiTIF) works in a collaborative fashion with NCI/NIH Investigators by providing them with the necessary expertise, instrumentation, and software to develop and execute advanced High-Throughput Imaging (HTI) assays. These Read More...

Protein Characterization Laboratory (PCL) offers various technologies to CCR investigators to characterize proteins and metabolites. The laboratory develops and applies state-of-the-art analytical technologies, primarily mass spectrometry, liquid chromatography, and Surface Plasmon Resonance (SPR), to advance Read More...

CREx News & Updates August 2022 Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More Site Spotlight NCATS Functional Genomics Laboratory (FGL) FGL is designed to help NIH Investigators use the latest Read More...

Protein Characterization Laboratory (PCL) offers various technologies to CCR investigators to characterize proteins and metabolites. The laboratory develops and applies state-of-the-art analytical technologies, primarily mass spectrometry, liquid chromatography, and Surface Plasmon Resonance (SPR), to advance Read More...

CREx News & Updates June 2021 Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More NIH Collaborative Research Exchange (CREx) News Site Spotlight FACILITY HIGHLIGHTS Visit here to learn about services from Read More...

CREx News & Updates April 2022 Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More Click below to learn how easy it is to navigate the CREx platform. These short videos will Read More...

NISC’s role within NHGRI, and more broadly across NIH, aims to advance genome sequencing and its many applications, with a goal not simply to produce sequence data, but to produce the infrastructure required to Read More...

07/23/2025 - This presentation will explore the next emerging stage where biobanking is characterised by being part of system - Biobanking 4.0. Biobanking has always been about data generation with tissue specimens providing the biological and genomic Read More...

07/21/2025 - Profe or Angela Brook i a leader in the development and application of high-throughput genomic and computational approache to inve tigate gene regulation. Her re earch focu e on characterizing mutation impacting RNA expre Read More...

06/26/2025 - Join u for a webinar introducing MIRA, a Python oftware package de igned for the analy i of ingle-cell RNA- eq, ATAC- eq, and multimodal data. Di cover how MIRA help decode the ci Read More...

06/20/2025 - Emerging artificial intelligence—e pecially generative model and deep learning—i tran forming biomedical and biological cience. In thi talk, Profe or Juexin Wang of Indiana Univer ity will pre ent ca e tudie Read More...

05/22/2025 - It took over $3 billion and 13 years to sequence the first human genome. Today, we can sequence a genome in a single day for less than $1,000.  That incredible technological advancement has led to the generation Read More...

04/14/2025 - Gene set analysis (GSA) is essential in genomic research, yet traditional methods often lack transparency and produce contextually irrelevant results, making interpretation challenging. While large language models (LLMs) offer a promising solution for result 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...

12/04/2024 - Galaxy is a web-based computational workbench for analyzing and visualizing biomedical datasets that is used by thousands of scientists daily. &nbsp; Galaxy enables accessible, reproducible, and scalable biomedical data science by any scientist 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...

08/13/2024 - NCI staff are welcome to register for an upcoming Childhood Cancer Data Initiative (CCDI) webinar titled, "CCDI Federated Data: Enhancing Data Discoverability," where you can learn about one of the newest advancements 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...

06/18/2024 - 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 Read More...

03/29/2024 - This first of five webinars will introduce NIH&rsquo;s All of Us Research Program, including the program&rsquo;s mission and core values. Learn about the current size and diversity of Read More...

03/13/2024 - Dear Colleagues, &nbsp;&nbsp; UCSC Xena is a web-based visual integration and exploration tool for multi-omic data and associated clinical and phenotypic annotations. &nbsp; Xena showcases seminal cancer genomics datasets from Read More...

Bioconductor packages are divided into four types: software annotation data experiment data workflows. Software packages themselves can be subdivided into packages that provide infrastructure (i.e., classes) to store and access data, and packages that Read More...

01/03/2024 - on Wednesday, January 3rd at noon in Building 41, Conference Room C507/C509 and online. In-person attendance is encouraged.&nbsp; Dr. Larson's research is focused on&nbsp;understanding gene expression in eukaryotic Read More...

We can use the airway package to see how this container works, including how to access and subset the data. What is the airway package? There are data sets available in R to practice with Read More...

11/14/2023 - Dr. Ting Wang is a Sanford C. and Karen P. Loewentheil Distinguished Professor of Medicine at the McDonnell Genome Institute, Washington University School of Medicine in St. Louis. Dr. Wang&rsquo;s lab Read More...

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...

In this lesson, we will continue to learn about RNA sequencing analysis using the Human Brain Reference (HBR) and Universal Human Reference (UHR) datasets . In particular, we will Get to know the HBR and UHR Read More...

In this lesson, we will continue to learn about RNA sequencing analysis using the Human Brain Reference (HBR) and Universal Human Reference (UHR) datasets . In particular, we will Get to know the HBR and UHR Read More...

To use various tools for functional analysis, you will need a list of annotated genes. Gene annotations come in a variety of flavors and not all flavors are compatible with every tool. For example, Gene Read More...

Pathway Analysis IPA (Qiagen - CCR License) Future talk Functional Analysis Gene Set Enrichment Analysis (GSEA) https://www.gsea-msigdb.org/gsea/index.jsp DAVID https://david.ncifcrf.gov/ Enrichr https://maayanlab.cloud/Enrichr/ Other Types Read More...

In Lesson 9, we got a short introduction on what IGV can do. It allows us to visualize genomic data such as reference genomes and how features such as genes and transcripts align to them. A Read More...

The Integrative Genome Viewer (IGV) is an open-source genome browser created and maintained by the Broad Institute. We will be using this to visualize genomic data. To obtain IGV, please submit a ticket through service. Read More...

Instructions for installing IGV The Integrative Genome Viewer (IGV) is an open-source genome browser created and maintained by the Broad Institute. We will be using this to visualize genomic data. To obtain IGV, please submit Read More...

Step 1 for generating bigWig files is to convert the BAM alignment results to a bedGraph (with extension bg) file that contains coverage along genomic regions. Enhancing your vocabulary: BED file - this is also known Read More...

Step 1 for generating bigWig files is to convert the BAM alignment results to a bedGraph file that contains coverage along genomic regions. Enchancing your vocabulary: BED file - this is also known as Browser Extensible Read More...

Due to time constraints, we will not be going over the creation of bigWig files in class. The information below is for your reference and you can view these during your spare time. In Lesson 9, Read More...

Variant annotation means predicting the effects of genetic variants (SNPs, insertions, deletions, copy number variations (CNV) or structural variations (SV)) on the function of genes, transcripts, and protein sequence, as well as regulatory regions. The Read More...

Resources Tertiary Analysis - Biological Meaning Pathway Analysis IPA (Qiagen - CCR License) Future talk Functional Analysis Gene Set Enrichment Analysis (GSEA) https://www.gsea-msigdb.org/gsea/index.jsp DAVID https://david.ncifcrf.gov/ Enrichr Read More...

Change in the ~/biostar_class/hbr_uhr/hbr_uhr_hisat2 folder for this portion of the class. cd ~/biostar_class/hbr_uhr/hbr_uhr_hisat2 Now that we have our SAM files generated for the 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...

Lesson 17: RNA sequencing review 2 Learning objectives This lesson will serve as comprehensive review of Module 2. We will spend roughly the first hour reviewing the Module 2 material the second hour answering specific questions from the poll Read More...

Change in the ~/biostar_class/hbr_uhr/hbr_uhr_hisat2 folder for this portion of the class. cd ~/biostar_class/hbr_uhr/hbr_uhr_hisat2 Now that we have our SAM files generated for the 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...

After assessing the quality of our raw sequencing data and performing cleanup if necessary the step that follows alignment the raw sequencing data to a genome or transcriptome. What tools can we use? {{Sdet}} Answer{{ Read More...

While we can always download reference genomes and reference transcriptomes from repositories such as NCBI or Ensembl, we will use gffread to create one from the chromosome 22 genome (22.fa) that we have used when analyzing Read More...

Let's align an RNA-Seq sample using the "splice aware" aligner hisat2. First we will need to create the indices. Use this format: hisat2-build REFERENCE_GENOME INDEX_PREFIX Like this: hisat2-build Read More...

Let's align an RNA-Seq sample using the "splice aware" aligner hisat2. First we will need to create the indices. Use this format: hisat2-build REFERENCE_GENOME INDEX_PREFIX Like this: hisat2-build Read More...

Let's align an RNA-Seq sample using the "splice aware" aligner hisat2. First we will need to create the indices. Use this format: hisat2-build REFERENCE_GENOME INDEX_PREFIX Like this: hisat2-build Read More...

Our operational objectives are to provide state-of-the-art OMICS technologies in support of the Genetics Branch (GB) investigators and collaborators. Research Services Wet Lab Single cell isolation from fresh, frozen, and FFPE tissue, DNA/RNA extractions Read More...

CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More New NIH Resource Resources Advance your research with the NIH Mouse Imaging Facility (MIF) The NIH Mouse Imaging Read More...

What is Visium FFPE v2 with CytAssist? Visium FFPE v2 is sequencing-based spatial profiling technology developed by 10x Genomics. This assay can take mouse or human tissue sections on normal glass slides as input and Read More...

CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More New NIH Resource Resources Derive Greater Insights and Accelerate your Research Using Bioinformatic Tools! CREx is an NIH Read More...

CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More New Resources on CREx NCI CLIA Molecular Diagnostics Laboratory (CMDL) The NCI CMDL is available to assist all Read More...

The NHLBI Transgenic Core’s main mission is to keep up with the latest advancements in genome engineering technologies and to provide state-of-the-art services to assist NIH scientists in generating genetically engineered animal models. In Read More...

CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More Technology Event Biophysical Methods for Protein Interactions Monday, May 15 – Friday, May 19, 2023 This workshop will review the strategies of Read More...

CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More New CREx User Survey The CREx Team is carrying out a CREx User Survey. We would greatly appreciate Read More...

CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More New CREx User Survey The CREx Team is carrying out a CREx User Survey. If you haven’t Read More...

The Genomics and Pharmacology Facility is part of the NCI's Center for Cancer Research (CCR), within the Developmental Therapeutics Branch. Its mission is to manage and assess molecular interaction data obtained through multiple platforms, increase Read More...

The Advanced Biomedical Computational Sciences (ABCS) group provides technology development, scientific consultation, collaboration and training, research, software development, and high-performance computing support. ABCS encompasses specialized groups focusing on machine learning applied to the interpretation of 2 Read More...

CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More NIH Research Festival The NIH Research Festival highlights the groundbreaking science and the vibrant NIH community driving our Read More...

The Pan-Microbial Serology Facility (PMSF) is part of the Center for Cancer Research (CCR) at the National Cancer Institute (NCI). The PMSF focuses on determining individualized pan-microbial immune profiles associated with human diseases including immunological Read More...

Proteomic Data Common (PDC) represents the NCI’s largest public repository of proteogenomic comprehensive tumor datasets, essentially a Proteogenomic Cancer Atlas. It was developed to advance our understanding of how proteins help shape the risk, Read More...

Cores & Facilities From centralized laboratories to collaborative resources and technologies available to CCR Investigators. NCI Cores Centralized laboratories providing broad access to cutting-edge technologies and specialized expertise. Browse NCI Cores Collaborative Resources are technologies and Read More...

CREx News & Updates February 2022 Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More Site Spotlight ORS Division of Veterinary Resources (DVR) DVR is the central NIH lab animal support program Read More...

CREx News & Updates December 2021 Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More Site Spotlight FACILITY HIGLIGHTS Learn more about services from the STRIDES Initiative. VIEW STRIDES INITIATIVE NIH Cores Read More...

Supplemental Technology Award Review System (STARS) Overview STARS Request Form STARS System The Supplemental Technology Award Review System (STARS) is a web-based interface for submission and review of S&S supplement requests by CCR Read More...

The CCR Genomics Core is located in Building 41 on the NIH Bethesda campus. The primary goal of the Core is to provide investigators from CCR/NCI and other NIH Institutes access to genomic technologies and Read More...

The introduction of DNA sequencing instruments capable of producing millions of DNA sequence reads in a single run has profoundly altered the landscape of genetics and cancer biology. Complex questions can now be answered at Read More...

The computational chemistry and protein modeling team in the Advanced Biomedical Computational Science (ABCS) group provides novel solutions in structural modeling and computational chemistry. Computational scientists in the group collaborate with NCI researchers by using Read More...

Long read sequencing was recently named 2022’s method of the year by Nature Methods . Long read sequencing technologies, those that generate sequence reads with lengths of 10s of kilobases or longer have several advantages over Read More...

BTEP strives to maintain links to resources that should be of interest to CCR Bioinformatics Community.  Some of the resources to will be accessible through more than one of these lists, but since the lists 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...

Register now for an upcoming seminar on January 22, 2025 , “Revealing Tumor-Promoting Signals in Breast Cancer Subtypes: A NIDAP Analysis of Single-Cell Data” . This one-hour talk will feature guest speaker and NIDAP developer, Josh Meyer, who will Read More...

Cancer research is a complex and data-intensive field. Cloud computing offers a powerful solution for researchers to store, analyze, and share large datasets efficiently. In this month’s topic spotlight, we will explore cloud resources Read More...

Please see https://bioinformatics.ccr.cancer.gov/btep/self-learning/ to sign up for a license. Contact ncibtep@nih.gov with any questions about obtaining a license. Did you know that CCR researchers have access to Read More...

Partek Flow enables scientists to build comprehensive workflows for analyzing multi-omics high throughput sequencing data including DNA and variant calling, bulk and single cell modalities for RNA, ChIP, and ATAC, spatial transcriptomics, CITE, and immune Read More...

Learning Objectives Learn about data structures including factors, lists, data frames, and matrices. Load, explore, and access data in a tabular format (data frames) Learn to write out (export) data from the R environment Data Read More...

This lesson will introduce data wrangling with R. Attendees will learn to filter data using base R and tidyverse (dplyr) functionality. Learning Objectives Understand the concept of tidy data. Become familiar with the tidyverse packages. Read More...

Objectives To explore Bioconductor, a repository for R packages related to biological data analysis. To learn about options for report generation with R: RMarkdown and Quarto. Introducing Bioconductor Bioconductor is both an open source project Read More...

As you can see from the image, there are several accessor functions to access the data from the object: assays() - access matrix-like experimental data (e.g., count data). Rows are genomic features (e.g., Read More...

Objectives To explore Bioconductor, a repository for R packages related to biological data analysis. To better understand S4 objects as they relate to the Bioconductor core infrastructure. To learn more about a popular Bioconductor S4 Read More...

Data import and reshape Objectives 1. Learn to import multiple data types 2. Data reshape with tidyr : pivot_longer() , pivot_wider() , separate() , and unite() Installing and loading packages So far we have only worked with objects that 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...

STAR 2-pass mode --sjdbGTFfile is the path to the file with annotated transcripts in standard GTF format, STAR extracts splice junctions from this file, improves accuracy of mapping. Using annotations is highly recommended whenever they Read More...