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https://health.ucdavis.edu/cancer/research/sharedresources/cmp.html

Provides services to support the development and implementation of clinical trials at UC Davis Comprehensive Cancer Center. Oversees high quality collection, processing, and analysis of clinical specimens,typically but not exclusively blood specimens, for pharmacokinetic and pharmacodynamics studies. Conducts preclinical modeling of novel anti cancer agents to test hypotheses and develop scientific rationale required for translation of laboratory concepts into clinical trials, including assessment of DM/PK/PD properties.

Proper citation: University of California Davis Health Molecular Pharmacology Shared Resource Core Facility (RRID:SCR_023588) Copy   

•   Source: SciCrunch Registry

https://med.stanford.edu/cancer/research/shared-resources/biostatistics_research_informatics.html

Core provides statistical support to SCI members by engages them on their data related needs. Specifically, BSR members assist researchers at each stage of study’s lifecycle, including project design, mid study evaluation and interpretation and reporting of results. In addition, BSR members mentor SCI investigators in research methods. BSR assists with development and review of proposed studies and planning of research related data management systems.

Proper citation: Stanford University School of Medicine Cancer Institute Biostatistics Shared Resource Core Facility (RRID:SCR_023696) Copy   

•   Source: SciCrunch Registry

https://github.com/broadinstitute/ichorCNA

Software tool that quantifies tumor content in cfDNA from 0.1× coverage whole-genome sequencing data without prior knowledge of tumor mutations. Used to simultaneously segment genome, predict large scale copy number alterations, and estimate tumor fraction of ultra low pass whole genome sequencing sample.

Proper citation: ichorCNA (RRID:SCR_024768) Copy   

•   Source: SciCrunch Registry

https://maayanlab.cloud/drugmonizome/#/

Database with search engine for querying annotated sets of drugs and small molecules for performing drug set enrichment analysis.

Proper citation: Drugmonizome (RRID:SCR_024821) Copy   

•   Source: SciCrunch Registry

https://cbc.app.vumc.org/tnbc/

Website for predicting the subtype of triple negative breast cancer sample based on its gene expression profile.

Proper citation: TNBCtype (RRID:SCR_026238) Copy   

•   Source: SciCrunch Registry

https://github.com/j-rub/scVital

Software tool to embed scRNA-seq data into species-agnostic latent space to overcome batch effect and identify cell states shared between species. Deep learning algorithm for cross-species integration of scRNA-seq data.

Proper citation: scVital (RRID:SCR_026215) Copy   

•   Source: SciCrunch Registry

https://dsigdb.tanlab.org/DSigDBv1.0/

Online database provides collection of gene sets based on quantitative inhibition and/or drug-induced gene expression changes data of drugs and compounds. Allows users to search, view and download drugs/compounds and gene sets.

Proper citation: DSigDB (RRID:SCR_026202) Copy   

•   Source: SciCrunch Registry

https://github.com/liulab-dfci/TRUST4

Software tool to analyze TCR and BCR sequences using unselected RNA sequencing data, profiled from fluid and solid tissues, including tumors. Performs de novo assembly on V, J, C genes including the hypervariable complementarity-determining region 3 and reports consensus contigs of BCR/TCR sequences. TRUST4 then realigns the contigs to IMGT reference gene sequences to identify the corresponding gene and CDR3 details. TRUST4 supports both single-end and paired-end bulk or single-cell sequencing data with any read length.

Proper citation: TRUST4 (RRID:SCR_026162) Copy   

•   Source: SciCrunch Registry

https://github.com/mskcc/facets

Software tool for estimating genome copy numbers from high throughput DNA sequencing data. Allele-specific copy number and clonal heterogeneity analysis tool for high-throughput DNA sequencing. Used to implement Fraction and Copy number Estimate from Tumor/normal Sequencing.

Proper citation: FACETS (RRID:SCR_026264) Copy   

•   Source: SciCrunch Registry

https://ecog-acrin.org/resources/ecog-performance-status/

ECOG Performance Scale describes patient’s level of functioning in terms of their ability to care for themself, daily activity, and physical ability (walking, working, etc.). Standard criteria for measuring how the disease impacts patient’s daily living abilities. Used to assess the functional status of patient.

Proper citation: Eastern Cooperative Oncology Group Performance Status Scale (RRID:SCR_026432) Copy   

•   Source: SciCrunch Registry

https://github.com/compgenomics/MeTPeak

Software package for finding the location of m6A sites in MeRIP-seq data.

Proper citation: MeTPeak (RRID:SCR_026533) Copy   

•   Source: SciCrunch Registry

https://github.com/higlass/higlass

Web-based visual exploration and analysis of genome interaction maps.

Proper citation: HiGlass (RRID:SCR_026687) Copy   

•   Source: SciCrunch Registry

https://github.com/AMICI-dev/AMICI/

Software toolbox implemented in C++/Python/MATLAB that provides efficient simulation and sensitivity analysis routines tailored for scalable, gradient-based parameter estimation and uncertainty quantification. Used for high-performance sensitivity analysis for large ordinary differential equation models.

Proper citation: AMICI (RRID:SCR_026913) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/bioc/html/apeglm.html

Software package provides Bayesian shrinkage estimators for effect sizes for variety of GLM models, using approximation of posterior for individual coefficients.

Proper citation: apeglm (RRID:SCR_026951) Copy   

•   Source: SciCrunch Registry

https://github.com/OpenTOPAS/OpenTOPAS

Software Monte Carlo tool for particle simulation. Used for simulation of medical applications of ionizing radiation with the Monte Carlo method. Allows to assemble and control library of simulation objects (geometry components, particle sources, scorers, etc.) with no need to write C++ code and without knowledge of underlying Geant4 Simulation Toolkit.

Proper citation: OpenTOPAS (RRID:SCR_026927) Copy   

•   Source: SciCrunch Registry

https://github.com/mskilab-org/JaBbA

Software tool to infer junction-balanced genome graphs with high fidelity. Builds genome graph based on junctions and read depth from whole genome sequencing, inferring optimal copy numbers for both vertices (DNA segments) and edges (bonds between segments).

Proper citation: JaBba (RRID:SCR_027134) Copy   

•   Source: SciCrunch Registry

https://github.com/dpeerlab/Palantir/

Algorithm to align cells along differentiation trajectories. Models trajectories of differentiating cells by treating cell fate as probabilistic process and leverages entropy to measure cell plasticity along the trajectory. Generates high-resolution pseudo-time ordering of cells and, for each cell state, assigns probability of differentiating into each terminal state.

Proper citation: Palantir (RRID:SCR_027194) Copy   

•   Source: SciCrunch Registry

https://www.med.unc.edu/microscopy/

Core provides training, assistance and services in light microscopy, electron microscopy and image analysis. UNC core facility that is part of Department of Pathology and Laboratory Medicine, and are light microscopy core for Lineberger Comprehensive Cancer Center.

Proper citation: University of North Carolina at Chapel Hill Microscopy Services Laboratory Core Facility (RRID:SCR_017913) Copy   

•   Source: SciCrunch Registry

http://www.med.unc.edu/csb/unc-peptides

Core offers services for: High quality synthetic peptides, stable isotope labeled peptides, peptides with PTM and fluorescent and affinity tags, synthesis of peptide libraries. Analysis of synthetic peptides. Purification, lyophilization and aliquoting of synthetic peptides.

Proper citation: North Carolina University at Chapel Hill School of Medicine High Throughput Peptide Synthesis and Array Core Facility (RRID:SCR_017837) Copy   

•   Source: SciCrunch Registry

https://www.med.unc.edu/csb/mx/

Core provides support and infrastructure necessary to initiate and successfully complete structural biology or structural chemistry project. Offers services in Crystallization,X-Ray DiffractionData Collection,Structure Determination and Refinement.

Proper citation: North Carolina University at Chapel Hill School of Medicine Macromolecular X-Ray Crystallography Core Facility (RRID:SCR_017839) Copy   

•   Source: SciCrunch Registry