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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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imcRtools Resource Report Resource Website 10+ mentions |
imcRtools (RRID:SCR_027613) | software toolkit, image processing software, image analysis software, data processing software, software application, software resource | Software R package that supports the handling and processing of IMC multiplex imaging data. Used for handling and analysing imaging mass cytometry data. | imaging, mass cytometry, imaging mass cytometry data, mass cytometry data, | Free, Available for download, Freely available | https://github.com/BodenmillerGroup/imcRtools | SCR_027613 | 2026-08-14 09:29:37 | 34 | ||||||||||
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sandwich Resource Report Resource Website 1+ mentions |
sandwich (RRID:SCR_027691) | software application, software resource | Object-oriented software for model-robust covariance matrix estimators. Starting out from the basic robust Eicker-Huber-White sandwich covariance methods include: heteroscedasticity-consistent (HC) covariances for cross-section data; heteroscedasticity- and autocorrelation-consistent (HAC) covariances for time series data (such as Andrews' kernel HAC, Newey-West, and WEAVE estimators); clustered covariances (one-way and multi-way); panel and panel-corrected covariances; outer-product-of-gradients covariances; and (clustered) bootstrap covariances. All methods are applicable to (generalized) linear model objects fitted by lm() and glm() but can also be adapted to other classes through S3 methods. | covariance matrix estimators, Eicker-Huber-White sandwich covariance, sandwich covariance, | Free, Available for download, Freely available | SCR_027691 | sandwich:Robust Covariance Matrix Estimators | 2026-08-14 09:29:48 | 1 | ||||||||||
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Icahn School of Medicine at Mount Sinai Human Immune Monitoring Center Core Facility Resource Report Resource Website 1+ mentions |
Icahn School of Medicine at Mount Sinai Human Immune Monitoring Center Core Facility (RRID:SCR_027571) | service resource, access service resource, core facility | Core provides team of experts in the characterization of immune profiles and treatment responses across a diverse range of diseases, such as cancer, autoimmunity, allergy, and neuro-immune disorders. Offers equipment in the field for research at Genomic, cellular and proteomic analysis. Develops assays to balance innovation with protocols and operating procedures to ensure data quality and reproducibility. | ABRF, characterization of immune profiles and treatment responses, equipment, assays |
is listed by: ABRF CoreMarketplace has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA |
ABRF_5607 | https://https://coremarketplace.org/?FacilityID=5607&citation=1 | SCR_027571 | , Icahn School of Medicine at Mount Sinai Mount Sinai Human Immune Monitoring Center, Mount Sinai Human Immune Monitoring Center | 2026-08-14 09:29:37 | 2 | ||||||||
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GCAT Workflow Resource Report Resource Website 1+ mentions |
GCAT Workflow (RRID:SCR_027692) | software application, software resource, source code | Software cancer genome and RNA sequencing data analysis pipeline that detects genomic variants and transcriptomic changes. | cancer genome, RNA sequencing data analysis, detect genomic variants, detect transcriptomic changes, | Free, Available for download, Freely available | SCR_027692 | 2026-08-14 09:29:37 | 1 | |||||||||||
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Integrative Prediction Strategy Resource Report Resource Website 1+ mentions |
Integrative Prediction Strategy (RRID:SCR_027608) | data processing software, software repository, software application, data analysis software, software resource, source code | Software with approach that leverages machine learning and network biology to predict brain gene expression from blood-derived features. | predict brain gene expression, blood-derived features, | Free, Available for download, Freely available | https://doi.org/10.5281/zenodo.17477450 | SCR_027608 | Integrative Prediction Strategy (IPS) | 2026-08-14 09:29:37 | 1 | |||||||||
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ltm:Latent Trait Models under IRT Resource Report Resource Website 1+ mentions |
ltm:Latent Trait Models under IRT (RRID:SCR_027664) | ltm | software toolkit, source code, software resource | Software R package for analysis of multivariate dichotomous and polytomous data using latent trait models under the Item Response Theory approach. | Analysis of multivariate dichotomous and polytomous data, latent trait models, Item Response Theory approach, | Free, Available for download, Freely available | https://github.com/drizopoulos/ltm | SCR_027664 | Latent Trait Models | 2026-08-14 09:29:57 | 1 | ||||||||
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lavaan Resource Report Resource Website 10+ mentions |
lavaan (RRID:SCR_027663) | software toolkit, source code, software resource | Software R package for latent variable analysis. Used to estimate variety of multivariate statistical models. Fit a variety of latent variable models, including confirmatory factor analysis, structural equation modeling and latent growth curve models. | latent variable analysis, confirmatory factor analysis, structural equation modeling, latent growth curve models, | Free, Available for download, Freely available | https://github.com/yrosseel/lavaan | SCR_027663 | lavaan: Latent Variable Analysis | 2026-08-14 09:29:37 | 15 | |||||||||
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RCy3 Resource Report Resource Website 1+ mentions |
RCy3 (RRID:SCR_027668) | software toolkit, source code, software resource | Software R package in Bioconductor that communicates with Cytoscape via its REST API, providing access to the full feature set of Cytoscape from within the R programming environment. RCy3 has been redesigned to streamline its usage and future development as part of a broader Cytoscape Automation effort.Network biology using Cytoscape from within R. | Network biology using Cytoscape from within R, network biology, Cytoscape, R | works with: Cytoscape | NIGMS P41GM103504; Google Summer of Code |
PMID:31819800 | Free, Available for download, Freely available | https://bioconductor.org/packages/release/bioc/html/RCy3.html, https://zenodo.org/records/3473421 | SCR_027668 | RCy3: Network biology using Cytoscape from within R | 2026-08-14 09:29:37 | 9 | ||||||
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Augusta University Proteomics and Mass Spectrometry Core Facility Resource Report Resource Website 1+ mentions |
Augusta University Proteomics and Mass Spectrometry Core Facility (RRID:SCR_027673) | service resource, access service resource, core facility | Facility for characterization and expression level quantitation of proteins (isolated or in an extract) and small molecules/metabolites by mass spectrometry (MS) and/or chromatography. Services include protein identification, labeled and label-free comparative proteomics by Orbitrap mass spectometry, protein/small molecule quantification using targeted mass spectometry (PRM and SRM/MRM mass spectometry), high throughput protein immune-protein assays (384-well Luminex/ELISA assay), etc. | ABRF, protein identification, labeled and label-free comparative proteomics, Orbitrap mass spectometry, protein/small molecule quantification, targeted mass spectometry, high throughput protein immune-protein assays, |
is listed by: ABRF CoreMarketplace has parent organization: Augusta University; Georgia; USA |
Open | ABRF_5654 | https://coremarketplace.org/RRID:SCR_027673/?citation=1 | SCR_027673 | 2026-08-14 09:29:57 | 6 | ||||||||
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Solarbio Resource Report Resource Website 10+ mentions |
Solarbio (RRID:SCR_027671) | reagent supplier, commercial organization, antibody supplier, material resource | Commercial vendor and service provider of laboratory reagents and antibodies located in Beijing, China. Supplier of scientific instrumentation, reagents and consumables, and software services. | laboratory reagents, antibodies, instrumentation, software services, | SCR_027671 | 2026-08-14 09:29:47 | 22 | ||||||||||||
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ImmuCellAI Resource Report Resource Website 10+ mentions |
ImmuCellAI (RRID:SCR_027645) | source code, software application, software resource | Software tool for comprehensive T‐Cell subsets abundance prediction and its application in cancer immunotherapy. | Cell subsets abundance prediction, predicting immunotherapy response, cancer immunotherapy estimate, immune cells, gene expression dataset, | National Natural Science Foundation of China | PMID:32274301 | Free, Available for download, Freely available | https://github.com/lydiaMyr/ImmuCellAI | SCR_027645 | Immune Cell Abundance Identifier | 2026-08-14 09:29:37 | 12 | |||||||
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PathoFact2 Resource Report Resource Website 1+ mentions |
PathoFact2 (RRID:SCR_027650) | software application, software resource | Software integrative pipeline for antimicrobial resistance genes, virulence factors, toxins, and biosynthetic gene clusters prediction in metagenomes. Used for predicting microbiome-based pathogenicity and resistance to better understand and address challenges posed by antimicrobial resistance and infectious diseases. | predicting microbiome-based pathogeni, antimicrobial resistance genes, virulence factors, toxin-related proteins, biosynthetic gene clusters, metagenomes | Pélican grant from the Mie and Pierre Hippert-Faber Pélican Foundation ; Luxembourg National Research Fund FNR CORE/23/BM/15886415; European Research Council ERC-CoG 863664; Luxembourg National Research Fund FNR CORE/23/BM/15886415; Luxembourg Government CoVaLux program |
DOI:10.1101/2024.12.09.627531 | Free, Available for download, Freely available | SCR_027650 | PathoFact 2.0 | 2026-08-14 09:29:37 | 4 | ||||||||
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Atlantis Resource Report Resource Website 1+ mentions |
Atlantis (RRID:SCR_027648) | database, data or information resource | Integrative database for human proteome structural and functional sites. Used for understanding role of specific residues in protein structures, complexes, and interaction networks. Integrates various structural and functional annotation layers for each residue, offering comprehensive understanding of protein functionality. | human proteome, protein structures, protein complexes, protein interaction, protein structural and functional sites, | Free, Freely available | SCR_027648 | 2026-08-14 09:29:56 | 3 | |||||||||||
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multiVIB Resource Report Resource Website 1+ mentions |
multiVIB (RRID:SCR_027589) | source code, software application, software resource | Software tool as comprehensive framework for integration of single-cell omics data with probabilistic contrastive learning. | integration of single-cell omics data, probabilistic contrastive learning, | has parent organization: Broad Institute | Free, Available for download, Freely available | SCR_027589 | 2026-08-14 09:29:37 | 1 | ||||||||||
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tidygraph Resource Report Resource Website 1+ mentions |
tidygraph (RRID:SCR_027617) | software toolkit, source code, software resource | Software R package as Tidy API for graph manipulation. Graph can be thought of as two tidy data frames describing node and edge data respectively. Used to manipulate these two virtual data frames using API defined in the 'dplyr' package, as well as provides tidy interfaces to a lot of common graph algorithms. | Tidy API, graph manipulation, node and edge data, | Free, Available for download, Freely available, | https://github.com/thomasp85/tidygraph | SCR_027617 | 2026-08-14 09:29:56 | 7 | ||||||||||
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Allen Institute Taxonomy Standard Resource Report Resource Website 1+ mentions |
Allen Institute Taxonomy Standard (RRID:SCR_027629) | AIT | standard specification, data or information resource, narrative resource | Compartmentalized schema for storing all required aspects of taxonomy. Fields in AIT schema are associated to broad category term which form piece of whole AIT file format. | Compartmentalized schema, taxonomy, AIT file format, | Free, Freely available | SCR_027629 | Allen Institute Taxonomy schema, Allen Institute Taxonomy Standard (AIT) | 2026-08-14 09:29:56 | 1 | |||||||||
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Ccube Resource Report Resource Website 1+ mentions |
Ccube (RRID:SCR_027721) | software toolkit, source code, software resource | Software R package for clustering and estimating cancer cell fractions (CCF) of somatic variants (SNVs/SVs) from bulk whole genome/exome data. Used for estimating cancer cell fractions . | Single nucleotide variant, cancer, estimating cancer cell fractions, | DOI:10.1101/484402v1 | Free, Available for download, Freely available | SCR_027721 | 2026-08-14 09:29:38 | 1 | ||||||||||
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DPClust Resource Report Resource Website 10+ mentions |
DPClust (RRID:SCR_027723) | software toolkit, source code, software resource | Software R package containing methods for sub-clonal reconstruction through SNVs and/or CNAs from whole genome or whole exome sequencing data. | Clonality, copy number variation, SNV, sub-clonal reconstruction, whole genome sequencing data, whole exome sequencing data, | Free, Available for download, Freely available | SCR_027723 | 2026-08-14 09:29:49 | 22 | |||||||||||
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ClusterSV Resource Report Resource Website 1+ mentions |
ClusterSV (RRID:SCR_027722) | source code, software application, software resource | Software application to group genetic structural variant rearrangements into rearrangement clusters and footprints. Used in the PCAWG-6 project. | structural variant, rearrangement region, group genetic structural variant rearrangements, rearrangement clusters and footprints, | Free, Available for download, Freely available | SCR_027722 | 2026-08-14 09:29:57 | 5 | |||||||||||
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SpatialProteomics Resource Report Resource Website 1+ mentions |
SpatialProteomics (RRID:SCR_027835) | source code, software application, software resource | Software graphical and containerized spatial proteomics workflow. End-to-end containerized spatial proteomics analysis workflow with QuPath integration. Consists of cell segmentation, batch correction, unsupervised clustering, validation of clusters on the image, and cell type clustering results visualization. | graphical and containerized spatial proteomics workflow, spatial proteomics analysis, spatial proteomics workflow, QuPath integration, | Free, Available for dowload, Freely available, | SCR_027835 | 2026-08-14 09:29:58 | 1 |
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