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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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InfectiousPathogenDetector2 Resource Report Resource Website 1+ mentions |
InfectiousPathogenDetector2 (RRID:SCR_026220) | IPD2, IPD 2.0 | data processing software, software application, data analysis software, source code, software resource | IPD2 is updated version of InfectiousPathogenDetector, in-silico GUI-based automated pathogen analysis pipeline for seamless analysis of data from heterogenous NGS platforms. IPD performs integrated variants analysis, along with systematic quantification of pathogen genomes. IPD additionally has an in-built SARS-CoV-2 analysis module, for assignment of viral clades of the samples analyzed and an automated report generation. | PMID:33985433 | Free, Available for download, Freely available | SCR_026220 | Infectious Pathogen Detector (IPD) 2.0 | 2026-08-14 09:29:46 | 1 | |||||||||
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SpaSNE Resource Report Resource Website 1+ mentions |
SpaSNE (RRID:SCR_026223) | source code, software application, software resource | Software extension of t-distributed stochastic neighbor embedding, the spatially resolved t-SNE (SpaSNE) designed to preserve both global gene expression and spatial structure for spatially resolved profiling data. Gives comprehensive low-dimensional visualization that could best reflect the molecular similarities of cells and the spatial interactions between cells. | global gene expression, spatial structure, spatially resolved profiling data, low-dimensional visualization, | Free, Available for download, Freely available | SCR_026223 | 2026-08-14 09:29:13 | 1 | |||||||||||
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NIST Chemistry WebBook Resource Report Resource Website 50+ mentions |
NIST Chemistry WebBook (RRID:SCR_026225) | database, data or information resource | Database that provides access to organic compounds data compiled and distributed by NIST under the Standard Reference Data Program. | National Institute of Standards and Technology U.S. Department of Commerce, Standard Reference Data Program, organic compounds data, | Free, Freely available | SCR_026225 | National Institute of Standards and Technology Chemistry WebBook | 2026-08-14 09:29:46 | 76 | ||||||||||
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WinSCP Resource Report Resource Website 1+ mentions |
WinSCP (RRID:SCR_026226) | software application, software resource | Free file manager, SSH File Transfer Protocol, File Transfer Protocol, WebDAV, Amazon S3, and secure copy protocol client for Microsoft Windows. | file manager, SSH File Transfer Protocol, File Transfer Protocol, WebDAV, Amazon S3, secure copy protocol client, Microsoft Windows, | Free, Available for download, Freely available | SCR_026226 | 2026-08-14 09:29:24 | 5 | |||||||||||
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University of Louisville School of Medicine Molecular Modeling Core Facility Resource Report Resource Website 1+ mentions |
University of Louisville School of Medicine Molecular Modeling Core Facility (RRID:SCR_026183) | service resource, access service resource, core facility | Core offers services including molecular modeling of proteins and nucleic acids, virtual drug screening, computational biophysics. | ABRF, molecular modeling, proteins, nucleic acids, virtual drug screening, computational biophysics, |
is listed by: ABRF CoreMarketplace has parent organization: University of Louisville; Kentucky; USA |
ABRF_2993 | https://coremarketplace.org/?FacilityID=2993&citation=1 | https://louisville.edu/medicine/cancer-research/cores-and-facilities-1/mole-model | SCR_026183 | 2026-08-14 09:29:46 | 1 | ||||||||
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2015 PQStat Statistical Calculation Software Resource Report Resource Website 1+ mentions |
2015 PQStat Statistical Calculation Software (RRID:SCR_026338) | data processing software, software application, data analysis software, software resource | Software application for statistical calculation. | Statistical calculation, statistics, | Restricted | SCR_026338 | 2026-08-14 09:29:14 | 7 | |||||||||||
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University of California San Francisco Clinical Cancer Genomics Laboratory Core Facility Resource Report Resource Website 1+ mentions |
University of California San Francisco Clinical Cancer Genomics Laboratory Core Facility (RRID:SCR_026219) | CCGL | service resource, access service resource, core facility | Core performs standard-of-care and advanced molecular testing for patients with cancer, and to provides special expertise in solid tumors. Services include targeted gene sequencing, microsatellite instability testing, fluorescence in situ hybridization (FISH), and next-generation sequencing (NGS). CCGL is staffed with board-certified surgical pathologists and board-certified molecular pathologists who can properly evaluate the quality of samples submitted for testing as well as make correlations between the pathologic diagnosis of a tumor and the molecular findings in the tumor. | ABRF, advanced molecular testing, patients with cancer, expertise in solid tumors, targeted gene sequencing, microsatellite instability testing, fluorescence in situ hybridization, next-generation sequencing, |
is listed by: ABRF CoreMarketplace has parent organization: University of California at San Francisco; California; USA |
ABRF_3000 | https://coremarketplace.org/?FacilityID=3000&citation=1 | SCR_026219 | UCSF Clinical Cancer Genomics Laboratory (CCGL), University of California San Francisco Clinical Cancer Genomics Laboratory (CCGL) | 2026-08-14 09:29:12 | 2 | |||||||
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Conditional AutoRegressive Deconvolution Resource Report Resource Website 1+ mentions |
Conditional AutoRegressive Deconvolution (RRID:SCR_026310) | CARD | software toolkit, source code, software resource | Software R package for spatial transcriptomics. Deconvolution method that combines cell-type-specific expression information from single-cell RNA sequencing (scRNA-seq) with correlation in cell-type composition across tissue locations. | Deconvolution method, spatial transcriptomics, cell-type-specific expression, single-cell RNA sequencing, cell-type composition across tissue locations, | NIGMS R01GM126553; NHGRI R01HG011883; NIGMS R01GM144960 |
PMID:35501392 | Free, Available for download, Freely available | SCR_026310 | , CARD: Conditional AutoRegressive Deconvolution, Conditional autoregressive-based deconvolution | 2026-08-14 09:29:25 | 3 | |||||||
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Medical College of Wisconsin Oxford Instruments Center for Advanced Microscopy Electron Microscopy Core Facility Resource Report Resource Website 1+ mentions |
Medical College of Wisconsin Oxford Instruments Center for Advanced Microscopy Electron Microscopy Core Facility (RRID:SCR_026315) | service resource, access service resource, core facility | Institutionally available research service unit managed on behalf of the Medical College by the Department of Cell Biology, Neurobiology and Anatomy. OCAM-EM encompasses both Light and Electron Microscopy services. | ABRF, Light and Electron Microscopy services, |
is listed by: ABRF CoreMarketplace has parent organization: Medical College of Wisconsin; Wisconsin; USA |
Restricted | ABRF_3006 | https://coremarketplace.org/?FacilityID=3006&citation=1 | SCR_026315 | , Medical College of Wisconsin MCW-Oxford Instruments Center for Advanced Microscopy- Electron Microscopy Core, MCW-Oxford Instruments Center for Advanced Microscopy- Electron Microscopy Core | 2026-08-14 09:29:47 | 3 | |||||||
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University of Alberta Precision Human Health Laboratory Core Facility Resource Report Resource Website 1+ mentions |
University of Alberta Precision Human Health Laboratory Core Facility (RRID:SCR_026314) | PHHL | service resource, access service resource, core facility | Core to advance understanding of mechanism of vascular dysfunction in chronic disease, identify how vascular dysfunction contributes to exercise intolerance, evaluate how exercise training improves vascular dysfunction and exercise intolerance using innovative clinical trial designs. | ABRF, vascular dysfunction, chronic disease, clinical trial designs, |
is listed by: ABRF CoreMarketplace has parent organization: University of Alberta; Alberta; Canada |
ABRF_2561 | https://coremarketplace.org/?FacilityID=2561&citation=1 | SCR_026314 | , PHHL - Precision Human Health Laboratory, University of Alberta PHHL - Precision Human Health Laboratory | 2026-08-14 09:29:14 | 1 | |||||||
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FireBrowse Resource Report Resource Website 100+ mentions |
FireBrowse (RRID:SCR_026320) | data or information resource, portal, disease-related portal, topical portal | Portal provides access to cancer genomic data from variety of analyses: clinical, copy number, miR, miRseq, mRNA, mRNAseq, mutation and pathway analyses. Provides comprehensive suite of interdependent analyses of those data, including: correlations, clustering, and GISTIC and MutSigCV. Companion portal to the Broad Institute GDAC Firehose analysis pipeline, and was developed to cull and analyze data generated by The Cancer Genome Atlas (TCGA), which characterizes and identifies genomic patterns in human cancer models. | cancer genomics data, clinical annotations, DNA copy number, miR, miRseq, mRNA, mRNAseq, analyze data, |
has parent organization: Broad Institute works with: The Cancer Genome Atlas works with: Broad Institute GDAC Firehose |
cancer | Free, Freely available, | http://firebrowse.org/tutorial/FireBrowse-Tutorial.pdf, | SCR_026320 | 2026-08-14 09:29:14 | 131 | ||||||||
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Collaborative Cohort of Cohorts for COVID-19 Research Resource Report Resource Website 1+ mentions |
Collaborative Cohort of Cohorts for COVID-19 Research (RRID:SCR_026322) | C4R | data or information resource, topical portal, disease-related portal, portal | Portal provides information about nationwide study of more than 50,000 individuals to determine factors that predict disease severity and long-term health impacts of COVID-19. | nationwide study, determine factors, predict disease severity, long-term health impacts, COVID-19 | COVID-19 | NHLBI ; NINDS ; NIA |
SCR_026322 | 2026-08-14 09:29:25 | 1 | |||||||||
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SqueezeCall Resource Report Resource Website 1+ mentions |
SqueezeCall (RRID:SCR_026321) | source code, software application, software resource | Software tool as Nanopore basecalling using Squeezeformer network to improve basecalling accuracy over recurrent neural network (RNN)-based model and Transformer-based models. | Nanopore basecalling, improve basecalling accuracy, | Free, Available for download, Freely available, | SCR_026321 | 2026-08-14 09:29:47 | 1 | |||||||||||
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DSigDB Resource Report Resource Website 100+ mentions |
DSigDB (RRID:SCR_026202) | database, data or information resource | 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 | 2026-08-14 09:29:12 | 165 | ||||||||
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watvina Resource Report Resource Website 1+ mentions |
watvina (RRID:SCR_026282) | source code, software application, software resource | Software tool as implicit or explicit water model based docking with Autodock vina engine, supporting pharmacophore /position constrained docking.Facilitates drug design with support for explicit or implicit waters, pharmacophore or position-constrained docking, and external torsion parameters (akin to amber/gaff/charmm force fields). Water Model supported protein-ligand docking with Autodock Vina engine. | Water Model, protein-ligand docking, Autodock Vina engine, | Free, Available for download, Freely available, | SCR_026282 | 2026-08-14 09:29:14 | 7 | |||||||||||
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HapHiC Resource Report Resource Website 10+ mentions |
HapHiC (RRID:SCR_026284) | source code, software application, software resource | Software fast, reference-independent, allele-aware scaffolding tool based on Hi-C data. Allele-aware scaffolding tool that uses Hi-C data to scaffold haplotype-phased genome assemblies into chromosome-scale pseudomolecules. | reference-independent, allele-aware scaffolding tool, performance on chromosome assignment, contig ordering and orientation, Hi-C data, scaffold haplotype-phased genome assemblies, chromosome-scale pseudomolecules, | National Natural Science Foundation of China | PMID:39103456 | Free, Available for download, Freely available | SCR_026284 | 2026-08-14 09:29:25 | 27 | |||||||||
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Qualimap 2 Resource Report Resource Website 10+ mentions |
Qualimap 2 (RRID:SCR_026258) | software application, software resource | Software platform-independent application written in Java and R that provides both Graphical User Inteface and command-line interface to facilitate quality control of alignment sequencing data and its derivatives like feature counts. Used for advanced multi-sample quality control for high-throughput sequencing data. | ChIP-seq, RNA-seq, quality control of alignment, advanced multi-sample quality control, high-throughput sequencing data, | DOI:10.1093/bioinformatics/btv566 | Free, Available for download, Freely available | SCR_026258 | 2026-08-14 09:29:46 | 14 | ||||||||||
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Fluxfix Resource Report Resource Website 1+ mentions |
Fluxfix (RRID:SCR_026259) | data access protocol, software resource, web service, source code | Web isotopologue analysis tool for metabolomics experiment. Used to compute tracer analysis. Transforms raw mass spec AUC values into the percent representation of each isotopologue measured. | transform raw mass spec AUC values, percent representation, isotopologue measure, | Free, Freely available | https://github.com/sophietrefely/traceranalysis | SCR_026259 | 2026-08-14 09:29:24 | 3 | ||||||||||
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MuSiCal Resource Report Resource Website 1+ mentions |
MuSiCal (RRID:SCR_026265) | software toolkit, source code, software resource | Software Python toolkit for mutational signature analysis. Used to estimate mutational signatures from somatic mutations in genome. | mutational signature analysis, estimate mutational signatures, somatic mutations in genome, | Free, Available for download, Freely available, | SCR_026265 | Mutational Signature Calculator | 2026-08-14 09:29:25 | 1 | ||||||||||
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FACETS Resource Report Resource Website 10+ mentions |
FACETS (RRID:SCR_026264) | data processing software, software application, data analysis software, source code, 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 | 2026-08-14 09:29:46 | 22 |
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