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
Atac Seq Analysis Pipeline is CCBR's pipeline to calls peaks for ATACseq datasets.
NCI CCR
Genomics Workflows
Alternate SpliCing EveNt Tools; multi-sample alternative splicing identification
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 genotypopes 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
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
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
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
Interactive visualization and analysis results of virion counting on RNAscope and DNAscope images; GitHub repo
NCI OD-Frederick
Image Analysis
Extracts sub-images defined on Aperio SVS images and saves these sub-images to separate TIFF image files for downloading; 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
A resource group which provides a mechanism for CCR researchers to obtain many different types of bioinformatics assistance to further their research goals
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
Genome Analysis Unit Provides bioinformatics assistance to CCR investigators by engaging in long-term collaborative projects; Developing custom tools and pipelines and by providing training opportunities
NIAID
Other Resources
The NIAID Collaborative Bioinformatics Resource is a group with expertise in a broad range of bioinformatics topics to provide a mechanism for researchers to obtain bioinformatics assistance.
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.
NCI DCTD
Scientific Catalogs
NCI's Proteome Characterization Laboratory (PCL) at FNLCR develops and implements standardized proteomic measurements (comprehensive and targeted) for approved projects.
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