Search Results for: selected reaction monitoring

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...

The NCI Clinical Research Correlatives Core provides non-CLIA-certified spectral flow cytometric assays to support clinical trials conducted in the CCR. The core specializes in immunophenotyping and immune monitoring assays. Established Technologies Spectral flow cytometry (Cytek), Read More...

05/08/2025 - Attend this virtual seminar via Teams. The Division of Intramural Research (DIR) sponsors a monthly series of talks by intramural and special guest speakers celebrating genetics and genomics research. Speakers are selected by NHGRI Read More...

Following normalization, the next step is to find variable features. In most scRNA-seq experiments only a small proportion of the genes will be informative and biologically variable. A subset of cells with high cell to Read More...

To access the NIH Partek Flow server, go to https://partekflow.cit.nih.gov/flow and enter the user's NIH username and then password. Note User may have selected a password different than that Read More...

Information regarding Globus and how to obtain it can be found at https://hpc.nih.gov/docs/globus/setup.php . For those Globus already setup, goto https://www.globus.org to log in by clicking Read More...

From within the R_Class_June_2022, click on the application "Practicing R - Outside of Class". This will take you to a window that looks like this: On this screen click on the & Read More...

DAVID compares the overlap of user provided gene list to an annotation to the overlap of a background gene list to the same annotation. Thus, DAVID is really using the Fisher exact test to determine Read More...

DAVID compares the overlap of user provided gene list to an annotation to the overlap of a background gene list to the same annotation. Thus, DAVID is using the Fisher exact test to determine if Read More...

touch creates an empty file nano basic editor for creating small text files rm remove files or directories. Be careful! mkdir make a directory and rmdir (remove a directory with NO files) mv rename or Read More...

06/29/2023 - All biology research projects involve finding relevant literature and identifying related biological information. Often high school or new undergraduate students need guidance on how to effectively search for helpful information. For almost 35 years, the Read More...

11/17/2022 - Join Icahn School of Medicine at Mount Sinai’s Dr. Zeynep Gümüş to learn about a user-friendly tool she and her team are developing to enable researchers of all computational skill levels to 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...

Open Web Browser with link https://www.nomachine.com and Click Download now Mac OS X button. Navigate to Downloads folder on your Mac and double click the NoMachine DMG install file. In this example, Read More...

04/28/2021 - Register/Join In this public workshop, participants will have the opportunity to discuss the challenges and opportunities involved in establishing effective data management and sharing practices. The organizers encourage anyone working with data to Read More...

12/02/2020 - Register Visualizing biological data can be challenging. Heat maps are useful for showing the basic distribution of gene expression but interactivity is needed for additional, in-depth analysis. Clustergrammer2 is a visualization tool that allows Read More...

02/12/2020 - This two-day instructor-led course gives participants a broad study of networking options on Google Cloud Platform. Through presentations, demonstrations, and hands-on labs, learners explore and deploy GCP networking technologies, such as Google Virtual Private Read More...

Bioinformatics integrates biology, statistics, and computer science to develop and apply theory, methods, and tools for the collection, storage, and analysis of biological and related data. Some key application areas in bioinformatics include genomic and Read More...

Bioinformatics integrates biology, statistics, and computer science to develop and apply theory, methods, and tools for the collection, storage, and analysis of biological and related data. Some key application areas in bioinformatics include genomic and Read More...

We see a similar organization of information for other annotation categories. For instance, DAVID pulls information on biomolecular processes, functions, and pathways from several sources such as UniProt, GO, KEGG, Reactome, and Wikipathways. For Gene Read More...

Goto https://www.globus.org to log in by clicking on the "LOG IN" icon at the top right corner of the page. In the next page, select organziational affiliation from the drop Read More...

What is Xenium? Xenium is a high-resolution, imaging-based in situ spatial profiling technology from 10x Genomics that allows for simultaneous expression analysis of RNA targets (currently in range of 100’s) within the same tissue section. Read More...

The NIH Center for Human Immunology, Inflammation, and Autoimmunity (CHI) is a trans-NIH resource whose mission is to provide a collaborative hub of advanced translational immunology for NIH clinical and pre-clinical studies. This uniquely structured Read More...

Electron Microscopy Laboratory (EML) The EML offers investigators access to unique expertise and EM technologies that allow our partners to explore new avenues of research to enhance the knowledge of biological systems. To assist our Read More...

The EML offers investigators access to unique expertise and EM technologies that allow CCR Investigators to explore new avenues of research in order to enhance the knowledge of biological systems. To assist our customers, we Read More...

The Division of Veterinary Resources’ (DVR) mission is to contribute to the advancement of NIH biomedical research programs by providing excellence in animal care, customer service, and specialized research services to support intramural research efforts. Read More...

The Center for Advanced Tissue Imaging (CAT-I) is an NIAID and NCI supported effort involving collaborative studies between experts in the Laboratory of Immune System Biology, DIR, NIAID and investigators in the DIR, NIAID and Read More...

NanoString Technology The nCounter® Analysis System is an automated, multi-application, digital detection and counting system which directly profiles up to 800 molecules simultaneously from a single sample using a novel barcoding technology. Profile hundreds of mRNAs, Read More...

The Crystallization Facility provides an automated environment for setting up crystallization experiments in a high-throughput format, storing the resulting plates under controlled conditions, and monitoring the status of prepared droplets remotely. The Facility is in Read More...

The Stem Cell Unit (SCU) has established a database to which hESC lines, adult stem cells and induced pluripotent stem (iPS) cells may be directly compared. These data give scientists the information they need when Read More...

The Office of Collaborative Biostatistics, Office of the Clinical Director, is the statistical and data management component of CCR. The Section provides statistical leadership and data management consultation for CCR’s major clinical activities and Read More...

Back Services: Biophysics Facility offers ITC calorimeters as open-access instruments.  First-time users must complete a short training session before gaining access to the instrument reservation calendar.  Training includes performing a test experiment and Read More...

The Animal Diagnostic Laboratory (ADL) provides a full range of diagnostic capabilities, including microbiological cultures on various culture medium, microscopic screening for parasites such as mites and pinworms, molecular detection of pathogens, serological evaluation of Read More...

In support of Intramural Research Program (IRP) scientists, DOHS provides training, consulting, and resources to ensure that workers' risk to hazards and stresses in the laboratory environment is minimized. Our services include one-on-one consultation with Read More...

In support of Intramural Research Program (IRP) scientists, DOHS provides training, consulting, and resources to ensure that laboratory equipment is used and maintained properly and safely. We provide expert safety and health consulting support for Read More...

The NIH Clinical Center Pharmacy Department provides pharmaceutical care to inpatients and outpatients on NIH intramural research protocols at the NIH Clinical Center. The Clinical Center facility encompasses 200 inpatient beds, 93 day-hospital stations, and 15 clinics. Clinical 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 Antibody Characterization Laboratory (ACL) is the laboratory responsible for the development of well-characterized monoclonal antibody reagents. The NCI’s Office of Cancer Clinical Proteomics Research funds ACL as a resource to the entire cancer Read More...

The Blood Processing Core monitors viral load in patients with HIV and performs sequential studies using samples obtained from patients with cancer, AIDS, chronic granulomatous disease, or other diseases associated with immunologic dysfunction. The core 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...

This is part II of the article highlighting nf-core pipelines and specifically addresses the use of these pipelines in the DNAnexus cloud environment. Part I of the article can be found in the October 2023 topic 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...

01/27/2025 - NCI CCR Liver Cancer Program Seminar Series Dr. Sethupathy is professor of physiological genomics and chair of the Department of Biomedical Sciences at Cornell University. He leads a research lab focused on genome-scale and Read More...

In Seurat (since version 4), differential analysis requires a preprocessing step to appropriately scale the normalized SCTransform assay across samples: adp = PrepSCTFindMarkers(adp) Found 8 SCT models. Recorrecting SCT counts using minimum median counts: 8146 As covered earlier, Read More...

Step 1: Goto https://www.globus.org to log in by clicking on the "LOG IN" icon at the top right of the pages. After logging in, select organziational affiliation, which is National Institutes Read More...

Accessing Partek Flow at NIH and tips for data transfer Learning objectives Instructions for accessing Partek Flow NCI researchers can find instructions for accessing Partek Flow at https://bioinformatics.ccr.cancer.gov/btep/partek-flow-bulk-and-single-cell-rna-seq-data-analysis/ . But Read More...

Now we are ready to work with some of our first R commands. We are going to run commands directly from our R script rather than typing into the R console. Our first command will Read More...

To create an R object, you need a name, a value, and an assignment operator (e.g.,

DNAnexus Basics Setting up the R-Studio environment outside of Class hours These instructions should be followed if you are setting up the R-Studio Web environment outside the normal class hours. Log into DNAnexus Each student Read More...

This page uses content directly from the Biostars Handbook by Istvan Albert (https://www.biostarhandbook.com). Always remember to load the bioinformatics environment. conda activate bioinfo SAM files SAM format is TAB-delimited, line-oriented, human-readable text Read More...

This page uses content directly from the Biostars Handbook by Istvan Albert (https://www.biostarhandbook.com). Always remember to load the bioinformatics environment. conda activate bioinfo SAM files SAM format is TAB-delimited, line-oriented, human-readable text Read More...

{{Sdet}} Using e-utilities to programmatically grab the run info{{Esum}} esearch and efetch , can be used to query and pull information from Entrez . They aren't the easiest to understand or use, but you can Read More...

pwd (print working directory) ls (list) touch (creates an empty file) nano (basic editor for creating small text files) using the rm command to remove files. Be careful! mkdir (make a directory) and rmdir (remove Read More...

From the publication REDO: Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak First we get the project (PRJN) number from the publication: PRJNA257197 Next we're going to query the "sra& Read More...

Fisher Exact Test DAVID performs over representation analysis (ORA) at its core, which aims to find enriched molecular functions, pathways, or other annotations represented by the input gene list. In other words, many genes in Read More...

Fisher Exact Test DAVID performs over representation analysis (ORA) at its core, which aims to find enriched molecular functions, pathways, or other annotations represented by the input gene list. In other words, many genes in Read More...

Database for Annotation, Visualization and Integrated Discovery (DAVID) - an overview Before getting started, remember to be signed on to the DNAnexus GOLD environment. Lesson 17 review In the previous class, we got an overview of Read More...

How can we better automate downloads from the SRA? For example, what if we want the sequence files from the publication Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak First we need 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...

07/18/2023 - This workshop is for life scientists, including educators and research students, who would like to learn to use the command line for searching and fetching NCBI data. In this workshop, we will begin with Read More...

Getting a DNAnexus account - every student should go to the main DNAnexus web page (https://dnanexus.com/) and apply for a "free account". The BTEP staff will associate each account with the Read More...

Navigating DNAnexus DNAnexus is a Cloud-based platform for NextGen Sequence analysis for which CCR has a " site-license ". For this class we are using the platform to provide a uniform, stable, preinstalled interface for Read More...

Now we are ready to work with some of our first R commands. We are going to run commands directly from our R script rather than typing into the R console. Our first command will Read More...

Getting a DNAnexus account - every student should go to the main DNAnexus web page (https://dnanexus.com/) and apply for a "free account". The BTEP staff will associate each account with the Read More...

Navigating DNAnexus DNAnexus is a Cloud-based platform for NextGen Sequence analysis for which CCR has a " site-license ". For this class we are using the platform to provide a uniform, stable, preinstalled interface for Read More...

11/18/2022 - The Medical Rehabilitation Research Speaker Series provides an opportunity for selected NCMRR and NIH rehabilitation research grantees to share their research with colleagues from rehabilitation-related and other fields. This fourth session features NCMRR grantees 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...

NoMachine Installation for Biowulf To run programs with a graphical user interface (GUI) in a unix environment like Biowulf, you need to connect via a terminal emulator such as NoMachine. For example, if you want Read More...

R has a similar install and load method. If you wish to use a package in R , you can check if it's already installed by using the Package Manager. If it is listed, it Read More...

Installing Packages in R Installing P ackages in R in Console R has a similar install and load method. If you wish to use a package in R , you can check if it's already Read More...

11/16/2021 - Presenter: Rahul Satija, PhD, is a Core Faculty Member at the New York Genome Center (NYGC), with a joint appointment as Associate Professor at the Center for Genomics and Systems Biology at New York Read More...

06/07/2021 - A multidisciplinary network of researchers and clinicians dedicated to improving early detection, diagnosis, prognosis and treatment of liver cancer. Presenter: Shalev Itzkovitz, PhD Associate Professor Department of Molecular Cell Biology Weizmann Institute of Science Read More...

03/05/2021 - Overview: The Human Cell Atlas (HCA) is an ambitious global initiative that aims to create a comprehensive reference map of all human cells—the fundamental units of life—as a basis for both understanding Read More...

08/21/2020 - Abstract: Machine learning (ML) has emerged as an essential tool for building models which can be used to predict clinical outcomes for age-related diseases. A significant challenge of ML is knowing which algorithms and Read More...

02/28/2020 - https://cbiit.webex.com/recordingservice/sites/cbiit/recording/play/e688e94d71934c4183480167b05f0f67 The CIViC knowledgebase (www.civicdb.org) is an open access, open source, community-driven resource for Clinical Interpretation of Read More...

01/07/2020 - The CIViC knowledgebase (www.civicdb.org) is an open access, open source, community-driven resource for Clinical Interpretation of Variants in Cancer. The goal of CIViC is to enable precision medicine by providing an educational Read More...

02/26/2013 -   Comparison Study of NGS SNP Detection Tools Brief background and introduction for the current status of SNP detection field and each of the selected tools to be compared Description of our benchmark exome-seq data Read More...

In the chart view, we are presented with the disease(s) found in a particular database that our input genes map to. Notice that we can sort this list by gene count, percentage, p-value, or Read More...

Fisher Exact Test DAVID performs over representation analysis (ORA) at its core, which aims to find enriched molecular functions, pathways, or other annotations represented by the input gene list. With DAVID, we are essentially looking Read More...

Navigate back to the HPC OnDemand website by clicking "HPC OnDemand" at the top left corner. Then click on the "Jupyter" tab to launch a Jupyter Lab session. The subsequent page Read More...

Using e-utilities to programmatically grab the run info esearch and efetch, can be used to query and pull information from Entrez. They aren't the easiest to understand or use, but you can use them Read More...

Chart Report is an annotation term focused view which lists annotation terms and their associated genes under study. -- DAVID help documents As we have seen, you can view the Functional Annotation Chart for specific Read More...

Indices in R start with 1. Incorrect usage of indexing in data structures such as vectors or data frames will not necessarily result in an error, but will often lead to unexpected results. A general subscript Read More...

Indices in R start with 1. Incorrect usage of indexing in data structures such as vectors or data frames will not necessarily result in an error, but will often lead to unexpected results. A general subscript Read More...

The CLIA Molecular Diagnostics Laboratory (CMDL) provides an array of services for groups at the NIH Clinical Center, Fort Detrick, and Hood College, among others. They support cancer- and disease-related research by making Read More...

Back Services: Biophysics Facility offers DSC as an open-access instrument. First-time users must complete training before gaining access to the instrument reservation calendar. Location: Building 50, room 3123 Description: The differential scanning calorimeter measures the constant pressure Read More...

Clinical Support Laboratory – Cellular Immunology offers a spectrum of bioassays to assess cellular responses to antigens and mitogens including ELISPOT, cytotoxicity assays, and proliferation assays. Established Technologies Elispot Assays, Dual or Triple Color Fluorospot Assays, Read More...

The CCR-Frederick Flow Cytometry Core Facility provides research support to the Frederick-CCR community, including cytometry analysis and sorting services, instrument maintenance, new user training, and technical consultation. Typical Assays Performed by Core Instruments Immunophenotyping of Read More...

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 Department of Laboratory Medicine provides state-of-the-art laboratory testing in support of Clinical Center patient care and will serve as a center of excellence in research and training in laboratory medicine, particularly in areas which Read More...

The CCR Building 41 Flow Cytometry Core is a full-service facility within the Center for Cancer Research that supports over 150 users representing 26 laboratories. The Core Facility provides instrument and software training, technical expertise, assay development, and 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...

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 centrally funded Statistics team within the Advanced Biomedical Computational Science group at the Frederick National Lab provides statistical consultation and data analysis support for NCI laboratories. We have broad-range expertise in biomedically relevant areas Read More...

CREx News & Updates January 2022 Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More Site Spotlight NCI ANTIBODY CHARACTERIZATION LABORATORY (ACL) The ACL specializes in rigorously validating antibodies for signaling and Read More...

The Division of Veterinary Resources Animal Surgery has supported large animal research and clinical care for more than 40 years. DVR surgeons provide outstanding and highly specialized large animal (rabbits, ungulates, etc.) research support in a 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 Clinical Image Processing Service (CIPS) offers timely and accurate advanced image processing of diagnostic radiology images for clinical care, research, and training. CIPS’ functions include clinical services and scientific researches. Established Technologies: CIPS can Read More...

The Biophysics Core’s mission is to provide support in the study of macromolecular interactions, dynamics, and stability by offering consultations, training, professional collaborations, and instrument access. General Services: Multi-technique molecular interaction studies, Kinetic and Read More...

The Clinical Support Laboratory offers processing, tracking, and testing of a broad range of clinical samples. Support can begin at the early stages of clinical trial development to aid in developing a comprehensive strategy for 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...

The facilities at AIM are available for use by the entire NIH intramural research community. While we welcome users with any size imaging project, AIM specializes in large, yearlong (or longer), collaborative research efforts with Read More...

The Chemistry and Synthesis Center (CSC) of the National Heart, Lung, and Blood Institute (NHLBI) provides IRP scientists with targeted imaging probes and chemical tools that help accelerate cell-based assays, in vivo imaging studies, and Read More...

10/24/2024 - NIH Text Mining and Natural Language Processing SIG is pleased to welcome you to this special event featuring two extraordinary speakers focused on the applications of Deep Learning in Computational Biology.  & Read More...

Learning Objectives This tutorial was designed to demonstrate common secondary analysis steps in a scRNA-Seq workflow. We will start with a merged Seurat Object with multiple data layers representing multiple samples. Throughout this tutorial we Read More...

1. Introduction and Learning Objectives This tutorial has been designed to demonstrate common secondary analysis steps in a scRNA-Seq workflow. We will start with a merged Seurat Object with multiple data layers representing multiple samples that Read More...

Accessing Partek Flow at NIH and tips for data transfer Learning objectives After consulting this guide, participants will Know how to access Partek Flow at NIH. Be able to transfer data from NCI CCR Sequencing 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...

R Crash Course: A few things to know before diving into wrangling Learning the Basics Objectives 1. Learn about R objects 3. Learn how to recognize and use R functions 4. Learn about data types and accessors Console Read More...

Retrieve R "helper" scripts developed for Biostars environment. curl -O http://data.biostarhandbook.com/rnaseq/code/deseq1.r curl -O http://data.biostarhandbook.com/rnaseq/code/deseq2.r curl -O http://data.biostarhandbook. Read More...

Retrieve R "helper" scripts developed for Biostars environment. curl -O http://data.biostarhandbook.com/rnaseq/code/deseq1.r curl -O http://data.biostarhandbook.com/rnaseq/code/deseq2.r curl -O http://data.biostarhandbook. Read More...

Retrieve R "helper" scripts developed for Biostars environment. curl -O http://data.biostarhandbook.com/rnaseq/code/deseq1.r curl -O http://data.biostarhandbook.com/rnaseq/code/deseq2.r curl -O http://data.biostarhandbook. Read More...

Database for Annotation, Visualization and Integrated Discovery (DAVID) - an overview Lesson 17 review In the previous class, we got an overview of functional and pathway analysis, which help to put RNA sequencing results into biological Read More...

This page uses content directly from the Biostar Handbook by Istvan Albert. Review: * downloading data from SRA * decompressing tar files * e-utilities * fastq-dump Learn: * sra-stat * XML format * automating SRA downloads * working with comma-separated values (csv) format * Read More...

Lesson 7: Downloading the RNA-Seq Data and Dataset Overview Lesson Review pwd (print working directory) ls (list) touch (creates an empty file) nano (basic editor for creating small text files) using the rm command to remove Read More...

Lesson 6: sra-tools, e-utilities, and parallel This page uses some content directly from the Biostar Handbook by Istvan Albert. Lesson 5 Review: The majority of computational tasks on Biowulf should be submitted as jobs: sbatch or swarm Read More...

Lesson 6: Downloading data from the SRA For this lesson, you will need to login to the GOLD environment on DNAnexus. Lesson 5 Review: The majority of computational tasks on Biowulf should be submitted as jobs: sbatch Read More...

This page contains content taken directly from the Biostar Handbook (Istvan Albert). Always remember to activate the class bioinformatics environment. conda activate bioinfo For this data analysis, we will be using: Two commercially available RNA Read More...

This page contains content taken directly from the Biostar Handbook (Istvan Albert). Always remember to activate the class bioinformatics environment. conda activate bioinfo For this data analysis, we will be using: Two commercially available RNA Read More...

This page uses content directly from the Biostar Handbook by Istvan Albert. Obtain RNA-seq test data. The test data consists of two commercially available RNA samples: Universal Human Reference (UHR) and Human Brain Reference (HBR) . Read More...

Lesson 1: Introduction to Biowulf, Unix, and R Learning Objectives Learn about why you may want to use R on Biowulf. Refresh Unix and R skills. This lesson will not be hands on. Why use R 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...

Below, we assign the heatmap to the R object hm_ph. hm_ph {"x":{"data":[{"x":[4.875,2.875,null,2.875,2.875,null,2.875,1.75,null,1.75,1.75,null,1.75,1,null,1,1,null,1.75,2.5,null,2.5,2.5,null,2.5,2,null,2,2,null,2.5,3,null,3,3,null,2.875,4,null,4,4, Read More...

Below, we assign the heatmap to the R object hm_ph and we can import this back to R in the future. hm_ph {"x":{"data":[{"x":[4.875,2.875,null,2.875,2.875,null,2.875,1.75, Read More...

Visualizing clusters with heatmaps Objectives Introduce the heatmap and dendrogram as tools for visualizing clusters in data. Learn to construct cluster heatmap using the package pheatmap . Learn how to save a non-ggplot2 plot. Introduce ggplotify Read More...

Visualizing clusters with heatmaps Objectives Introduce the heatmap and dendrogram as tools for visualizing clusters in data. Learn how to work with the package pheatmap . Learn how to save a non-ggplot2 plot. Introduce ggplotify to 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...

08/10/2022 - For our next CDSL webinar we will have two fellows’ talks from Dr. Zisha Zhong and Arati Rajeevan . Zisha’s talk details: Title:  Multi-task Feature Learning to train Interpretable Encoders on Histopathology Images Digital Read More...

02/08/2021 - Dear colleagues, Coming Monday, Feb 8th, we'll be having a guest lecture by Prof. Vineet Bafna from UCSD. Abstract: Increase in the number of copies of tumor promoting (onco-) genes is a hallmark Read More...