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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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PhysiCell Studio Resource Report Resource Website 10+ mentions |
PhysiCell Studio (RRID:SCR_025311) | software resource, source code | 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. | create, execute, visualize, multicellular model, create initial positions of cells, | NSF ; NCI U01 CA232137; Breast Cancer Research Foundation ; Jayne Koskinas Ted Giovanis Foundation for Health and Policy ; European Commission |
PMID:37961612 | Free, Available for download, Freely available | SCR_025311 | 2026-02-14 02:09:07 | 15 | |||||||||
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pVACtools Resource Report Resource Website 10+ mentions |
pVACtools (RRID:SCR_025435) | software resource, software toolkit | 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. | Cancer immunotherapy tools, identify and visualize cancer neoantigens, | NCI U01CA209936; NCI U01CA231844; NCI U24CA237719; NHGRI R00HG007940; V Foundation for Cancer Research |
PMID:31907209 | Free, Freely available | SCR_025435 | 2026-02-14 02:09:03 | 27 | |||||||||
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MatrixEQTL Resource Report Resource Website 50+ mentions |
MatrixEQTL (RRID:SCR_025513) | data analysis software, software resource, data processing software, software application | Software tool for ultra fast eQTL analysis via large matrix operations. | expression Quantitative Trait Loci, fast eQTL analysis, large matrix operations, | NIMH R01 MH090936; NIEHS R01 ES015241; US Environmental Protection Agency ; NCI R01 CA138255; NSF ; Gillings Innovation Laboratory in Statistical Genomics |
PMID:22492648 | Free, Freely available, | SCR_025513 | Matrix Expression Quantitative Trait Loci | 2026-02-14 02:09:12 | 69 | ||||||||
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scGBM Resource Report Resource Website 1+ mentions |
scGBM (RRID:SCR_025518) | software resource, source code | 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. | Generalized bilinear models, model-based dimensionality reduction, scRNA-seq data, removing unwanted variation, | NCI T32CA009337; NCI R01CA240299 |
PMID:37162914 | Free, Available for download, Freely available, | SCR_025518 | 2026-02-14 02:09:19 | 2 | |||||||||
|
MRQy Resource Report Resource Website 1+ mentions |
MRQy (RRID:SCR_025779) | data analysis software, software resource, data processing software, software application | 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. | quantitative assessment, magnetic resonance imaging, computed tomography, imaging data, | NCI U24CA199374; NCI R01CA202752; NCI R01CA208236; NCI R01CA216579; NCI R01CA220581; NCI 1U01CA239055; NCI 1F31CA216935; NCI 1U01CA248226; NHLBI R01HL15127701A1; NIBIB 1R43EB028736; NCRR 1C06RR12463 |
PMID:33176026 | Free, Available for download, Freely available | SCR_025779 | 2026-02-14 02:09:06 | 1 | |||||||||
|
STAR-Fusion Resource Report Resource Website 10+ mentions |
STAR-Fusion (RRID:SCR_025853) | software resource, source code | 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. | identify candidate fusion transcripts, predict fusions, leverages chimeric and discordant read alignments, chimeric, discordant, read alignment, | Howard Hughes Medical Institute ; Klarman Cell Observatory ; NCI U24CA180922; NCI R50CA211461; NCI R21CA209940; NCI U01CA214846 |
PMID:31639029 | Free, Available for download, Freely available | SCR_025853 | 2026-02-14 02:09:28 | 33 | |||||||||
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MethylSig Resource Report Resource Website 1+ mentions |
MethylSig (RRID:SCR_025849) | software resource, software toolkit | 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. | whole genome DNA methylation analysis, whole genome DNA, DNA methylation, testing differentially methylated cytosines, whole-genome bisulfite sequencing, reduced representation bisulfite sequencing, | NCI R01CA158286; NIEHS P30 ES017885 |
PMID:24836530 | Free, Available for download, Freely available | SCR_025849 | 2026-02-14 02:09:28 | 3 | |||||||||
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Moffitt spatialGE Resource Report Resource Website 1+ mentions |
Moffitt spatialGE (RRID:SCR_025980) | software resource, web application | 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. | Moffitt Cancer Center, spatial transcriptomics data analysis, implementation of spatialGE R package, methods for visualization and spatial statistics analysis, tissue microenvironment and heterogeneity, spatial transcriptomics experiments, | NCI U01 CA274489; NCI T32 CA23339 |
DOI:10.1101/2024.06.27.601050 | Free, Freely available | SCR_025980 | Moffitt Cancer Center spatialGE, spatialGE | 2026-02-14 02:08:54 | 1 | ||||||||
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ArCH Resource Report Resource Website |
ArCH (RRID:SCR_025975) | ArCH | software resource, software toolkit | Software somatic variant calling pipeline designed to detect low variant allele fraction clonal hematopoiesjsonsis variants. | sequencing studies analysis, somatic variant calling, detect low variant allele fraction, clonal hematopoiesjsonsis variants, | Edward P. Evans Foundation ; American Society of Hematology ; NCI K08 CA241318; NCI P30 CA008748 |
PMID:38485690 | Free, Available for download, Freely available, | SCR_025975 | , ArCH: Artifact Filtering Clonal Hematopoiesis Variant Calling Pipeline, Artifact Filtering Clonal Hematopoiesis Variant Calling Pipeline | 2026-02-14 02:09:29 | 0 | |||||||
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TNBCtype Resource Report Resource Website |
TNBCtype (RRID:SCR_026238) | software resource, web application | Website for predicting the subtype of triple negative breast cancer sample based on its gene expression profile. | predicting subtype, triple negative breast cancer sample, gene expression profile, | NCI CA068485; NCI CA95131; NCI CA148375; NCI CA105436; NCI CA070856; NCI CA009385; American Cancer Society ; Komen Foundation |
PMID:22872785 | Free, Freely available | SCR_026238 | 2026-02-14 02:09:36 | 0 | |||||||||
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scVital Resource Report Resource Website |
scVital (RRID:SCR_026215) | software resource, source code, software application | 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. | embed scRNA-seq data, species-agnostic latent space, overcome batch effect, identify cell states shared between species, cross-species integration, scRNA-seq data, | NIA R01 AG054720; NCI K08 CA267072; NCI R01 CA290400; NCI P30 CA08748 |
DOI:10.1101/2024.12.20.629285 | Free, Available for download, Freely available | SCR_026215 | 2026-02-14 02:09:11 | 0 | |||||||||
|
DSigDB Resource Report Resource Website 50+ mentions |
DSigDB (RRID:SCR_026202) | data or information resource, database | 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. | gene sets, quantitative inhibition, drug induced, gene expression changes, data, drugs, compounds, | NCI P30CA046934; NCI P50CA058187 |
PMID:25990557 | Free, Freely available, | SCR_026202 | , Drug Signatures Database, drug SIGnatures DataBase | 2026-02-14 02:08:58 | 82 | ||||||||
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TRUST4 Resource Report Resource Website 1+ mentions |
TRUST4 (RRID:SCR_026162) | sequence analysis software, data processing software, data analysis software, source code, software application, software resource | 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. | analyze TCR and BCR sequences, de novo assembly, unselected RNA sequencing data, fluid and solid tissues, tumors, | NCI U01CA226196; NCI U24CA224316 |
PMID:33986545 | Free, Available for download, Freely available | SCR_026162 | 2026-02-14 02:09:10 | 4 | |||||||||
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FACETS Resource Report Resource Website 10+ mentions |
FACETS (RRID:SCR_026264) | data processing software, data analysis software, source code, software application, software resource | 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. | Allele-specific copy number, clonal heterogeneity analysis, estimating genome copy numbers, high throughput DNA sequencing data, Fraction and Copy number Estimate from Tumor/normal Sequencing, | NCI CA124514; NCI CA163251; NCI CA195365; NCI P01 CA129243; Susan G. Komen for the Cure ; NCI P30 CA008748 |
PMID:27270079 | Free, Available for download, Freely available, | SCR_026264 | 2026-02-14 02:09:36 | 12 | |||||||||
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Eastern Cooperative Oncology Group Performance Status Scale Resource Report Resource Website 1+ mentions |
Eastern Cooperative Oncology Group Performance Status Scale (RRID:SCR_026432) | portal, data or information resource, organization portal, narrative resource, standard specification | 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. | ECOG-ACRIN Cancer Research Group, patient’s performance status, assess patient functional status, conduct clinical trials, | NCI | Free, Freely available | SCR_026432 | ECOG Performance Status Scale | 2026-02-14 02:09:40 | 3 | |||||||||
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MeTPeak Resource Report Resource Website 10+ mentions |
MeTPeak (RRID:SCR_026533) | software resource, source code, software toolkit | Software package for finding the location of m6A sites in MeRIP-seq data. | finding location of m6A sites, MeRIP-seq data | NCI P30CA54174; NCI U54 CA113001; NIGMS R01 GM113245; Natural Science Foundation of China ; NSF |
PMID:27307641 | Free, Available for download, Freely available | SCR_026533 | 2026-02-14 02:09:37 | 10 | |||||||||
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HiGlass Resource Report Resource Website 10+ mentions |
HiGlass (RRID:SCR_026687) | software resource, source code, web application | Web-based visual exploration and analysis of genome interaction maps. | visual exploration and analysis, genome interaction maps, | NCI U01CA200059; NHGRI R00 HG007583; NHGRI U54 HG007963 |
PMID:30143029 | Free, Available for download, Freely available | SCR_026687 | 2026-02-14 02:09:41 | 45 | |||||||||
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AMICI Resource Report Resource Website |
AMICI (RRID:SCR_026913) | software resource, source code, software toolkit | 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. | high-performance sensitivity analysis, large ordinary differential equation models, | European Unions Horizon 2020 ; Federal Ministry of Education and Research of Germany ; German Research Foundation ; NCI U54 CA225088 |
PMID:33821950 | Free, Available for download, Freely available | SCR_026913 | Advanced Multilanguage Interface to CVODES and IDAS | 2026-02-14 02:09:21 | 0 | ||||||||
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OpenTOPAS Resource Report Resource Website 1+ mentions |
OpenTOPAS (RRID:SCR_026927) | software resource, source code, software application | 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. | Monte Carlo method, particle simulation, simulation of medical applications, ionizing radiation, | NCI R01 CA140735; NCI U24 CA215123 |
PMID:23127075 PMID:32247964 |
Free, Available for download, Freely available | https://opentopas.github.io/ | SCR_026927 | , TOPAS, TOol for PArticle Simulation | 2026-02-14 02:09:12 | 2 | |||||||
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apeglm Resource Report Resource Website |
apeglm (RRID:SCR_026951) | software resource, software toolkit | Software package provides Bayesian shrinkage estimators for effect sizes for variety of GLM models, using approximation of posterior for individual coefficients. | Bayesian shrinkage estimators, | NHGRI R01 HG009125; NCI P01 CA142538; NIEHS P30 ES010126; NIGMS R01 GM070335 |
PMID:30395178 | Free, Available for download, Freely available, | SCR_026951 | , Approximate Posterior Estimation for generalized linear model, Approximate posterior estimation for GLM | 2026-02-14 02:09:12 | 0 |
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