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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Michigan Genomics Initiative Resource Report Resource Website 1+ mentions |
Michigan Genomics Initiative (RRID:SCR_023556) | MGI | material storage repository, service resource, project portal, portal, data or information resource, storage service resource, biobank | Collaborative research effort among physicians, researchers, and patients at the University of Michigan with goal of combining patient electronic health record data with corresponding genetic data to gain novel biomedical insights. Biobank linking genotypes and electronic clinical records in Michigan Medicine patients. MGI participants agree to provide study team with access to EHR data for clinical information and biospecimen including blood or saliva. | combining patient electronic health record data, genetic data, genotypes, electronic clinical records | has parent organization: Michigan State University; Michigan; USA | PMID:36819667 | Restricted | SCR_023556 | 2026-08-11 09:44:36 | 6 | ||||||||
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VarFish Resource Report Resource Website 1+ mentions |
VarFish (RRID:SCR_023710) | data analysis software, data processing software, software resource, software application | Web application for quality control, filtering, prioritization, analysis, and user based annotation of DNA variant data with focus on rare disease genetics. Comprehensive DNA variant analysis for diagnostics and research. | Genetics, Variant Call Format, Filtering, Quality control, | Berlin Institute of Health Charité funds ; Stiftung Charité |
DOI:10.1093/nar/gkaa241 | Free, Available for download, Freely available | https://github.com/bihealth/varfish-server | SCR_023710 | 2026-08-11 09:44:37 | 2 | ||||||||
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DendroX Resource Report Resource Website 1+ mentions |
DendroX (RRID:SCR_023434) | software application, source code, software resource, data processing software, 4d visualization software, data visualization software | Web application for multi-level multi-cluster selections in dendrogram. Provides interactive visualization of dendrogram in which users can divide dendrogram at any level and into any number of clusters. | cluster, heatmap, visualization, dendrogram, cluster analysis, TypeScript | Second Military Medical University 2017JZ11; Shanghai Jiading District Health Commission 2020-ZD-01 |
Free, Available for download, Freely available | https://frlender.github.io/dendrox-app/ | SCR_023434 | 2026-08-11 09:44:38 | 1 | |||||||||
|
UCSC Cell Browser Resource Report Resource Website 100+ mentions |
UCSC Cell Browser (RRID:SCR_023293) | web service, software resource, data access protocol | Web based tool to visualize gene expression and metadata annotation distribution throughout single cell dataset or multiple datasets. Interactive viewer for single cell expression. You can click on and hover over cells to get meta information, search for genes to color on and click clusters to show cluster specific marker genes. | visualize gene expression, metadata annotation distribution, single cell data viewer, cluster specific marker genes, single cell expression, |
is related to: Allen Institute for Brain Science is related to: BRAIN Initiative Cell Atlas Network has parent organization: University of California at Santa Cruz; California; USA |
NHGRI 5U41HG002371; NHGRI 1U41HG010972; NHGRI 5R01HG010329; NIMH U01MH114825; NINDS K99 NS111731; NIMH RF1MH121268; NIMH DP2MH122400; Silicon Valley Community Foundation ; California Institute for Regenerative Medicine ; University of California Office of the President Emergency COVID-19 Research Seed Funding ; Chan Zuckerberg Initiative Foundation ; Simons Foundation ; Brain and Behavior Research Foundation |
PMID:34244710 | Free, Freely available | https://cellbrowser.readthedocs.io/en/master/, https://github.com/maximilianh/cellBrowser | SCR_023293 | 2026-08-11 09:44:25 | 155 | |||||||
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FunGAP Resource Report Resource Website 1+ mentions |
FunGAP (RRID:SCR_023213) | FunGAP | software application, simulation software, software resource | Software tool to predict protein coding genes in fungal genome assembly. Performs gene prediction on given genome assembly and RNA-seq reads. Runs multiple gene predictors, evaluates all predicted genes, and assembles gene models that are highly supported by homology to known sequences. | Genome annotation, predict protein-coding genes, fungal genome assembly, RNA-seq reads, gene prediction | Rural Development Administration ; Republic of Korea ; School of Life Sciences and Biotechnology for BK21 PLUS ; Korea University |
PMID:28582481 | Free, Available for download, Freely available | SCR_023213 | Fungal Genome Annotation Pipeline | 2026-08-11 09:44:31 | 2 | |||||||
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roifile Resource Report Resource Website 1+ mentions |
roifile (RRID:SCR_023331) | software toolkit, software resource, software library | Software Python package to read, write, create, and plot ImageJ ROI format, an undocumented and ImageJ application specific format to store regions of interest, geometric shapes, paths, text, and whatnot for image overlays. | Python package, plot ImageJ ROIs, store regions of interest, geometric shapes, paths, text, image overlays | Free, Available for download, Freely available | SCR_023331 | 2026-08-11 09:44:36 | 1 | |||||||||||
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LOHHLA Resource Report Resource Website 1+ mentions |
LOHHLA (RRID:SCR_023690) | data analysis software, data processing software, software resource, software application | Software tool to evaluate HLA loss using next-generation sequencing data. Computational tool to determine HLA allele-specific copy number from sequencing data. | evaluate HLA loss, Human Leukocyte Antigen loss, next-generation sequencing data, determine HLA allele-specific copy number, sequencing data, | Cancer Research UK ; University College London Hospitals Biomedical Research Centre ; European Union Seventh Framework Programme ; UK Medical Research Council ; Wellcome Trust ; Rosetrees Trust ; NovoNordisk Foundation ; Prostate Cancer Foundation ; Breast Cancer Research Foundation ; European Research Council ; Marie Curie Network PloidyNet |
PMID:29107330 | Restricted | SCR_023690 | Loss Of Heterozygosity in Human Leukocyte Antigen | 2026-08-11 09:44:41 | 6 | ||||||||
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oncoboxlib Resource Report Resource Website 1+ mentions |
oncoboxlib (RRID:SCR_023722) | software toolkit, software resource, software library | Software library to calculate Pathways Activation Levels. It takes file that contains gene symbols in HGNC format, their expression levels for one or more samples and calculates PAL values for each pathway in each sample. | calculate Pathways Activation Levels, Pathways Activation Levels, gene symbols, HGNC format, gene expression levels, PAL values calculation, | is related to: OncoboxPD | Russian Foundation for basic research | PMID:33633781 | Free, Available for download, Freely available | SCR_023722 | oncoboxlib | 2026-08-11 09:44:42 | 2 | |||||||
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Harmony Resource Report Resource Website 10+ mentions |
Harmony (RRID:SCR_023543) | data analysis software, data processing software, software resource, software application | Software tool designed by PerkinElmer for high content screening systems. Used to quantify complex cellular phenotypes. High content analysis software. | PerkinElmer, high content screening systems, quantify complex cellular phenotypes, | Restricted | SCR_023543 | Harmony High-Content Imaging and Analysis Software, Harmony 5.0, Harmony 5.1 | 2026-08-11 09:44:35 | 22 | ||||||||||
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Enroll-HD Resource Report Resource Website 10+ mentions |
Enroll-HD (RRID:SCR_023300) | data or information resource, topical portal, portal, disease-related portal | Clinical research platform and longitudinal observational study for Huntington’s Disease families intended to accelerate progress towards therapeutics. Collaboration between Huntington’s disease families, clinicians, and researchers to accelerate progress toward effective treatments. | Clinical Research, clinical trails, Huntington’s Disease families, therapeutics, effective treatments, | Huntington’s disease | Cure HD Initiative Foundation | Free, Freely available | SCR_023300 | 2026-08-11 09:44:35 | 13 | |||||||||
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GRIMER Resource Report Resource Website 1+ mentions |
GRIMER (RRID:SCR_023265) | data analysis software, data processing software, software resource, software application | Software tool to perform analysis of microbiome studies and generates portable and interactive dashboard integrating annotation, taxonomy and metadata with focus on contamination detection. | microbiome studies analysis, interactive dashboard, integrating annotation, integrating taxonomy, integrating metadata | Free, Available for download, Freely available | SCR_023265 | 2026-08-11 09:44:25 | 1 | |||||||||||
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GE Volume Viewer Resource Report Resource Website 1+ mentions |
GE Volume Viewer (RRID:SCR_023417) | software application, data processing software, software resource, data visualization software | Software tool to provide data 3D visualization and processing. Used for reading and comparing CT, MR, 3D X-ray, PET, and PET/CT datasets. | GE Healthcare, 3D image processing, 3D image visualization, 3D image | Restricted | SCR_023417 | Volume Viewer | 2026-08-11 09:44:27 | 2 | ||||||||||
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SViCT Resource Report Resource Website 1+ mentions |
SViCT (RRID:SCR_023656) | data analysis software, data processing software, software resource, software application | Software tool for detecting structural variations from cell free DNA containing low dilutions of circulating tumor DNA. | detecting structural variations, cell free DNA, cfDNA, circulating tumor DNA low dilutions, ctDNA | Natural Sciences and Engineering Research Council Discovery Grant ; Terry Fox Research Institute New Frontiers Program Project Grant ; Natural Sciences and Engineering Research Council Discovery Frontiers Program ; National Science Foundation ; NIGMS GM108348; Indiana University Grant Challenges Program ; Precision Health Initiative |
PMID:30759232 | Free, Available for download, Freely available | SCR_023656 | Structural Variant detection in Circulating Tumor DNA | 2026-08-11 09:44:29 | 1 | ||||||||
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Slide-seq Pipeline Resource Report Resource Website 1+ mentions |
Slide-seq Pipeline (RRID:SCR_023379) | data analysis software, data processing software, software resource, software application | Software pipeline developed in collaboration with BRAIN Initiative Cell Census Network and BRAIN Initiative Cell Atlas Network. Supports processing of spatial transcriptomic data generated with Slide-seq commercialized as Curio Seeker assay. | single cell data, spatial transcriptomics, barcode correction, reads alignment, aligns reads to genome, |
is related to: BICCN has parent organization: Broad Institute is organization facet of: BRAIN Initiative Cell Atlas Network |
NIH New Innovator Award ; NIH Early Independence Award ; Schmidt Fellows Program at the Broad Institute ; Hertz Graduate Fellowship ; National Science Foundation Graduate Research Fellowship Program |
PMID:30923225 | Free, Available for download, Freely available | https://github.com/broadchenf/Slideseq/tree/master/BeadSeq%20Code | https://github.com/broadinstitute/warp/tree/master/pipelines/skylab/slideseq | SCR_023379 | Slide-seq, slideseq, SlideSeq, SlideSeq Pipeline | 2026-08-11 09:44:33 | 2 | |||||
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metaGOflow Resource Report Resource Website 1+ mentions |
metaGOflow (RRID:SCR_023674) | data analysis software, data processing software, software resource, software application | Software pipeline for marine Genomic Observatories data analysis. Used to address challenges of analysis of European Marine Omics Biodiversity Observation Network data. | Genomic Observatories, marine, marine biodiversity, metagenomic samples, | Free, Available for download, Freely available | SCR_023674 | 2026-08-11 09:44:41 | 1 | |||||||||||
|
Scaffold Resource Report Resource Website 100+ mentions |
Scaffold (RRID:SCR_014321) | portal, topical portal, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 1,2023. Visualize and validate complex MS/MS proteomics experiments | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_014321 | 2026-08-11 09:42:48 | 186 | ||||||||||||
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Google Looker Studio Resource Report Resource Website 1+ mentions |
Google Looker Studio (RRID:SCR_023549) | web service, software resource, data access protocol | Former name Google Data Studio, is online tool for converting data into customizable informative reports and dashboards introduced by Google on March 15, 2016 as part of enterprise Google Analytics 360 suite. Online service for graphic data visualization. | Google Analytics 360 suite, graphic data visualization, converting data, reports and dashboards, data visualization | Free, Freely available | SCR_023549 | Google Data Studio, , Looker Studio | 2026-08-11 09:44:35 | 2 | ||||||||||
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PhysiCOOL Resource Report Resource Website 1+ mentions |
PhysiCOOL (RRID:SCR_023305) | PhysiCOOL | software toolkit, software resource, software library | Software Python library tailored to perform model calibration studies with PhysiCell. Generalized framework for model Calibration and Optimization Of modeLing projects. | perform model calibration studies, PhysiCell, Calibration and Optimization, modeling projects, | Free, Available for download, Freely available | SCR_023305 | Physi Calibration and Optimization Of modeLing | 2026-08-11 09:44:35 | 1 | |||||||||
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NanoString GeoMx Tools Resource Report Resource Website 10+ mentions |
NanoString GeoMx Tools (RRID:SCR_023424) | data analysis software, data processing software, software resource, software application | Software package contains tools for analyzing data from NanoString GeoMx Digital Spatial Profiler. Provides functions to read, quality control and normalize starting from Nanostring DCC and PKC files generated from NanoString GeoMx DSP. Contains definition of NanoStringGeoMxSet class which inherits from Biobase’s ExpressionSet class and NanoStringRCCSet class. | NanoString GeoMx Digital Spatial Profiler, Nanostring DCC, PKC files, NanoString GeoMx DSP, Biobase ExpressionSet class, NanoStringRCCSet class, | Free, Available for download, Freely available | https://bioconductor.org/packages/GeomxTools/ | SCR_023424 | GeoMxTools | 2026-08-11 09:44:27 | 41 | |||||||||
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DeepCT Resource Report Resource Website 1+ mentions |
DeepCT (RRID:SCR_023302) | data analysis software, data processing software, software resource, software application | Software tool can learn complex interconnections of epigenetic features and infer unmeasured data from any available input. Can learn cell type-specific properties, build biologically meaningful vector representations of cell types, and utilize these representations to generate cell type-specific predictions of effects of non-coding variations in human genome. | interconnections of epigenetic features, infer unmeasured data, human genome | DOI:10.1101/2021.12.31.474623 | Free, Available for download, Freely available | SCR_023302 | 2026-08-11 09:44:32 | 1 |
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