NCI OD-Frederick
ABCS Publications
List of peer-reviewed publications by ABCS researchers
NCI OD-Frederick
Biomedical Annotations
Genomic location based annotations; Variant impact analysis; Annotate variants in VCF and BED formats; Recognizes codon and protein variant formats
NCI OD-Frederick
Biomedical Annotations
Gene based identifer conversions; Organism wide; Ortholog conversions; Recognizes hundreds of data types
NCI OD-Frederick
Biomedical Annotations
Visualize protein annotations from UniProt; Comparisons across ortholog sequences; Visualize custom annotations on protein sequences
NCI OD-Frederick
Biomedical Annotations
non-B DNA annotations; External and custom annotations from in-house algorithms; All mammalian genomes; Annotate custom sequences
NCI DCTD
Biomedical Data Integration
Local instance of cBioPortal with CTEP and NIH authentication supporting the National Clinical Lab Network (NCLN) studies
NCATS
Biomedical Data Integration
Rare disease and associated gene details, related variant annotations, literature mining using language models
USACEHR/WRAIR
Biomedical Data Integration
Data sharing for ongoing collaborations; Raw, temporary and analyzed files; Clinical data analytics; Interactive tracking of samples and assays status
NCI CSSI
Data Analysis and Management
Data sharing using standardized metadata; Open access and controlled access; Ontologically enhanced searches; Flexible downloads and API access
NCI OD-Frederick
Data Analysis and Management
Computes Ki values from experimentally determined IC50 values for inhibitors of enzymes that obey classic Michaelis-Menten kinetics and protein-ligand interactions
NCI CCR
Data Analysis and Management
Pro-Viral Sequence Database; meta-analysis of HIV RNA and proviral sequences in donors on antiretroviral therapy
NCI CCR
Data Analysis and Management
Retrovirus Integration Database; query retrovirus integration sites in host genomes
NCI CCR
Data Analysis and Management
Tumor IsomiR Encyclopedia for querying and comparing isomiR expression across TCGA and TARGET miRNA datasets
NCI CCR
Genomics Workflows
Alternate SpliCing EveNt Tools; multi-sample alternative splicing identification
NCI CCR
Genomics Workflows
Atac Seq Analysis Pipeline is CCBR's pipeline to calls peaks for ATACseq datasets
NCI CCR
Genomics Workflows
Cut And Run anaLysIS pipeLinE; prediction tool for murine cancer neoantigens
NCI CCR
Genomics Workflows
Docker containers for ATACSeq, ChIPSeq, ExomeSeq, RNASeq; to be executed on the DNANexus cloud platform; GitHub repo
NCI CCR
Genomics Workflows
Haplotype inference program; Expectation-Maximization algorithm; uses a natural format for input genotypes and output haplotypes; GitHub repo
NCI CCR
Genomics Workflows
Individual-nucleotide resolution Cross-Linking and ImmunoPrecipitation; multi-sample peak identification and annotation analysis; differential analysis using DIFFBIND and MANORM
NCI CCR
Genomics Workflows
Integrated Single Cell RNA-Seq analysis pipeline; multi-sample differential expression analysis; marker gene and subpopulation identification; GitHub repo
NCI CCR
Genomics Workflows
This pipeline processes long-read (LR) sequencing data to identify somatic mutations including single nucleotide variants (SNVs), structural variants (SVs), and copy number alterations (CNAs) using various bioinformatics tools
NCI CCR
Genomics Workflows
MicroArray Analysis Pipeline, also known as MAAPster, is a comprehensive Shiny application and R package that performs transcriptome analysis of human or mouse Affymetrix gene expression data
NCI CCR
Genomics Workflows
Mouse nEoanTigen pRedictOr; prediction tool for murine cancer neoantigens
NCI CCR
Genomics Workflows
Workflow for handling small RNA sequencing analysis
NCI CCR
Genomics Workflows
MNase-seq Analysis PipeLinE: multi-sample DYAD fragment identification and quantification
NCI CCR
Genomics Workflows
Next Gen Sequencing analysis pipeline for structural variant and copy number variation detection, annotation and visualization: GitHub repo
NCI CCR
Genomics Workflows
Provides a graphical interface for configuring and executing RNA-Seq, Exome-Seq and sc-RNA-Seq analysis pipelines on the NIH biowulf cluster
NCI CCR
Genomics Workflows
The project utilizes the innovative Polylox barcode system in conjunction with PacBio sequencing and 10X cell barcodes for high-resolution lineage tracing and cell tracking
NCI CCR
Genomics Workflows
The ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) pipeline analyzes paired-end sequencing data and identify regions of open chromatin (peaks)
NCI CCR
Genomics Workflows
Workflow for handling long-read transcriptomic (LR_Transcriptome) sequencing analysis
NCI CCR
Genomics Workflows
The SF Long Read Variant Analysis Pipeline (SF_LR_VAP) integrates a suite of advanced tools and methodologies for the comprehensive analysis of long-read sequencing data, from raw reads to annotated variants
NCI CCR
Genomics Workflows
In the SF Multiplexed Arrays Sequencing (SF_MAS-SC) workflow, full-length cDNA sequences are processed and classified against a reference annotation database. This workflow identifies novel genes and isoforms, and outputs count matrices at both the gene and isoform levels.
NCI CCR
Genomics Workflows
TRna AbundaNce QUantification pIpeLine is a Snakemake pipeline which quantifies tRNA using the mim-tRNAseq tool
NCI OD-Frederick
Image Analysis
Semi-automatic classification guided 3D volumetric image data visualization tool; GitHub repo
NCI OD-Frederick
Image Analysis
GitHub page for Predicting survival of rhabdomyosarcoma patients based on deep-learning of hematoxylin and eosin images manuscript
NCI OD-Frederick
Image Analysis
Interactive visualization and analysis results of virion counting on RNAscope and DNAscope images; GitHub repo
NCI OD-Frederick
Image Analysis
Central imaging informatics platform for collaborators to interface with IVG; Adjust parameters; Download results; GitHub repo
NCI OD-Frederick
Other Resources
Git Repo with code and data from several ABCS projects including the biomarker discovery kit, image analysis and NGS workflows
NCI OD-Frederick
Other Resources
Details on computational science, programming and statistics trainings available to NCI researchers
NCI OD-Frederick
Other Resources
Web interface listing ABCS web applications and code repositories; Hosts small applications
NCI CCR
Other Resources
CCR Bioinformatics is an integrated portal for CCR bioinformatics resources including Bioinformatics Training & Education Program (BTEP), CCR Collaborative Bioinformatics Resource (CCBR), Genome Analysis Unit (GAU), and NCI Bioinformatics Community (NCI BC)
NCI CCR
Other Resources
The CCR Genomics core provides investigators from NCI and other institutes within NIH with access to genomic technologies and Next-Generation Sequencing (NGS) with rapid turnaround on smaller-scale projects or projects that are not ready for production
NCI CCR
Other Resources
The Center for Molecular Microscopy (CMM) develops and utilizes new techniques and emerging technologies for high resolution 3-D electron microscopy in structural biology (high resolution imaging) and cell biology (volume EM)
NCI CCR
Other Resources
NCI Optical Microscopy Laboratories provide advanced cancer research through optical measurements and analysis
NCI CCR
Other Resources
An open core dedicated to developing and implementing cutting edge protein-based technologies to facilitate discovery, translational and clinical research
NCI CCR
Other Resources
The Molecular Targets Program (MTP) provides the focus and infrastructure that enables CCR investigators to pursue molecularly targeted drug discovery research by promoting an interdisciplinary, collaborative, team-oriented approach to identifying and validating potential cancer-pertinent targets
NCI DCTD
Other Resources
The OCCPR Author Management System (OAMS) is an online resource for tracking publication authors across the DCTD community
NCI CCR
Other Resources
Explores and evaluates the latest technologic advancements and then makes them available to all CCR investigators
NCI DCTD
Scientific Catalogs
An NCI community resource that provides access to a large number of standardized renewable affinity reagents and accompanying characterization data
NCI DCTD
Scientific Catalogs
A voluntary scientific organization that provides a forum for collaboration among some of the world’s leading cancer and proteogenomic research centers
USACEHR/WRAIR
Visual Analytics and Analysis
Transcriptomics analysis; Differentially expressed genes/metabolites/proteins; Categorize longitudinal data sets; Pathway and functional references
USACEHR/WRAIR
Visual Analytics and Analysis
Network visualization of complex data sets; Interactive and customizable; Upload and visualize multiple aspects of custom data