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http://code.google.com/p/annotare/

A software tool for annotating biomedical investigations and the resulting data, then producing a MAGE-TAB file. This software is a standalone desktop which features: an editor function, an annotation modifier, incorporation of terms from biomedical ontologies, standard templates for common experiment types, a design aid to help create a new document, and a validator that checks for syntactic and semantic violations.

Proper citation: Annotare (RRID:SCR_000319) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/release/bioc/html/nondetects.html

Software R package to model and impute non-detects in results of qPCR experiments.Used to directly model non-detects as missing data.

Proper citation: nondetects (RRID:SCR_001702) Copy   

•   Source: SciCrunch Registry

https://www.nationwidechildrens.org/research/areas-of-research/biopathology-center/about

Provides services related to biospecimen procurement, banking, processing, and distribution. Housed biospecimen collections are from biorepositories of National Cancer Institute funded Children’s Oncology Group, NRG Oncology-Columbus (formerly the GOG Tissue Bank), SWOG, Pediatric Division of Cooperative Human Tissue Network, and Biospecimen Core Resource of Center for Cancer Genomics, as well as numerous biospecimen collections sponsored by funded NCH investigators. Cooperative Human Tissue Network is one of six institutions funded by National Cancer Institutes to access to remnant human tissues for biomedical researchers throughout the United States and Canada. Offers expertise in tissue preparation and preservation to meet the research needs of basic and applied scientists.

Proper citation: Nationwide Children’s Hospital Abigail Wexner Research Institute Biopathology Center Core Facility (RRID:SCR_023260) Copy   

•   Source: SciCrunch Registry

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

Provides expertise in design, analysis and reporting of cancer related studies, including basic, translational, clinical and population based research. BSR affiliated faculty and staff work with investigators from the earliest stages of study planning. The shared resource is especially committed to mentoring early career cancer researchers.

Proper citation: University of California Davis Health Biostatistics Shared Resource Core Facility (RRID:SCR_023585) Copy   

•   Source: SciCrunch Registry

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

Provides high throughput screening platform to discover unique chemical probes against biological targets using various one bead one compound and one bead two compound combinatorial libraries.Interacts closely with resource users on optimization of the lead compounds via focused libraries and standard medicinal chemistry techniques. Provides custom synthesis of telodendrimer based micellar nanoparticle platform for efficient drug delivery.

Proper citation: University of California Davis Health Combinatorial Chemistry and Chemical Biology Shared Resource Core Facility (RRID:SCR_023584) Copy   

•   Source: SciCrunch Registry

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://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://www.npatlas.org

Open access knowledge base for microbial natural products discovery. Database of microbially derived natural product structures. Provides coverage of bacterial and fungal natural products to visualize chemical diversity. Includes compounds and contains referenced data for structure, compound names, source organisms, isolation references, total syntheses, and instances of structural reassignment. Interactive web portal permits searching by structure, substructure, and physical properties. Provides mechanisms for visualizing natural products chemical space and dashboards for displaying author and discovery timeline data. Atlas has been developed under FAIR principles.

Proper citation: Natural Products Atlas (RRID:SCR_025107) Copy   

•   Source: SciCrunch Registry

https://github.com/PhysiCell-Tools/PhysiCell-Studio

Software graphical tool to allow easy editing of (XML) model, create initial positions of cells, run simulation, and visualize results. To contribute, fork and make PRs to the development branch. Used to create, execute, and visualize multicellular model using PhysiCell.

Proper citation: PhysiCell Studio (RRID:SCR_025311) Copy   

•   Source: SciCrunch Registry

http://www.bios.unc.edu/research/genomic_software/Matrix_eQTL/

Software tool for ultra fast eQTL analysis via large matrix operations.

Proper citation: MatrixEQTL (RRID:SCR_025513) Copy   

•   Source: SciCrunch Registry

https://github.com/phillipnicol/scGBM

Software application for model-based dimensionality reduction of scRNA-seq data. Quantifies uncertainty in each cell's latent position and leverages these uncertainties to assess confidence associated with given cell clustering. On real and simulated single-cell data produces low-dimensional embeddings that better capture relevant biological information while removing unwanted variation. Used for model-based dimensionality reduction for single-cell RNA-seq with generalized bilinear models.

Proper citation: scGBM (RRID:SCR_025518) Copy   

•   Source: SciCrunch Registry

https://github.com/ccipd/MRQy

Software quality assurance and checking tool for quantitative assessment of magnetic resonance imaging and computed tomography data. Used for quality control of MR imaging data.

Proper citation: MRQy (RRID:SCR_025779) Copy   

•   Source: SciCrunch Registry

https://spatialge.moffitt.org/

Web application, a user friendly, point-and-click implementation of spatialGE R package. Contains collection of methods for visualization and spatial statistics analysis of tissue microenvironment and heterogeneity using spatial transcriptomics experiments. Used for user-friendly analysis of spatial transcriptomics data.

Proper citation: Moffitt spatialGE (RRID:SCR_025980) Copy   

•   Source: SciCrunch Registry

https://github.com/STAR-Fusion/STAR-Fusion

Software tool to leverage chimeric and discordant read alignments identified by STAR aligner to predict fusions. Component of Trinity Cancer Transcriptome Analysis Toolkit. Used to identify candidate fusion transcripts supported by Illumina reads. Maps junction reads and spanning reads to reference annotation set.

Proper citation: STAR-Fusion (RRID:SCR_025853) 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://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/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