Tools   Select Another Resource Report Type

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://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://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

https://pvactools.readthedocs.io/en/latest/

Software toolkit to identify and visualize cancer neoantigens. Cancer immunotherapy tools suite consisting of following tools: pVACseq as cancer immunotherapy pipeline for identifying and prioritizing neoantigens from VCF file; pVACbind as cancer immunotherapy pipeline for identifying and prioritizing neoantigens from FASTA file; pVACfuse as tool for detecting neoantigens resulting from gene fusions; pVACvector as tool designed to aid specifically in construction of DNA-based cancer vaccines; pVACview as application based on R Shiny that assists users in reviewing, exploring and prioritizing neoantigens from results of pVACtools processes for personalized cancer vaccine design.

Proper citation: pVACtools (RRID:SCR_025435) 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://github.com/kbolton-lab/ArCH

Software somatic variant calling pipeline designed to detect low variant allele fraction clonal hematopoiesjsonsis variants.

Proper citation: ArCH (RRID:SCR_025975) 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://www.bioconductor.org/packages/release/bioc/html/methylSig.html

Software R package as whole genome DNA methylation analysis pipeline. Used for testing differentially methylated cytosines or regions in whole-genome bisulfite sequencing or reduced representation bisulfite sequencing experiments. Several options exist for either site-specific or sliding window tests, and variance estimation.

Proper citation: MethylSig (RRID:SCR_025849) 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://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