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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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dREG Resource Report Resource Website 1+ mentions |
dREG (RRID:SCR_027012) | source code, software application, software resource | Software tool for detecting regulatory elements using GRO-seq and PRO-seq. | detecting regulatory elements, GRO-seq, PRO-seq | NHGRI 5R01HG007070; NIDDK R01 DK058110 |
PMID:25799441 | Free, Available for download, Freely available | SCR_027012 | 2026-08-14 09:29:36 | 1 | |||||||||
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Baylor College of Medicine BCM Mass Spectrometry Proteomics Core Facility Resource Report Resource Website 1+ mentions |
Baylor College of Medicine BCM Mass Spectrometry Proteomics Core Facility (RRID:SCR_027015) | service resource, access service resource, core facility | Core provides services including project evaluation and design, sample processing and biochemical purifications, mass spectrometry measurements, data processing, and bioinformatics analysis performed by the experienced core personnel. | ABRF, project evaluation and design, sample processing, biochemical purifications, mass spectrometry measurements, data processing, |
is listed by: ABRF CoreMarketplace has parent organization: Baylor College of Medicine; Houston; Texas |
ABRF_3248 | https://coremarketplace.org/?FacilityID=3248&citation=1 | SCR_027015 | BCM Mass Spectrometry Proteomics Core | 2026-08-14 09:29:36 | 6 | ||||||||
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yFiles Layout Algorithms Resource Report Resource Website 1+ mentions |
yFiles Layout Algorithms (RRID:SCR_026961) | software toolkit, algorithm resource, software resource | Software suite of algorithms used for arranging and visualizing graph structures. They provide variety of layout styles, such as hierarchical, organic, tree, circular, and orthogonal, each optimizing for different criteria and visualization needs. | arranging and visualizing graph structures, arrange Cytoscape networks, hierarchical, organic, tree, circular, orthogonal, styles, | works with: Cytoscape | Restricted | https://www.yworks.com/products/yfiles-layout-algorithms-for-cytoscape | SCR_026961 | yWorks GmbH yFiles Layout Algorithms | 2026-08-14 09:29:26 | 3 | ||||||||
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Foldseek Resource Report Resource Website 10+ mentions |
Foldseek (RRID:SCR_027018) | source code, software application, software resource | Software tool for fast and sensitive comparisons of large structure sets. Used for comparisons of large protein structure sets, supporting monomer and multimer searches, as well as clustering. It runs on CPU, supports GPU acceleration for faster searches, and optionally allows ultra-fast and sensitive comparisons directly from protein sequence inputs using a language model, bypassing the need for structures. | comparisons of large structure sets, protein structure sets, monomer and multimer searches, clustering | Free, Available for download, Freely available | SCR_027018 | 2026-08-14 09:29:51 | 15 | |||||||||||
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pcangsd Resource Report Resource Website 1+ mentions |
pcangsd (RRID:SCR_026956) | source code, software application, software resource | Software framework for analyzing low-depth next-generation sequencing data in heterogeneous/structured populations using principal component analysis. | analyzing low-depth next-generation sequencing data, heterogeneous populations, structured populations, principal component analysis, | Novo Nordisk Foundation ; Independent Research Fund Denmark |
PMID:34587903 | Free, Available for download, Freely available | SCR_026956 | PCAngsd | 2026-08-14 09:29:51 | 1 | ||||||||
|
READ Resource Report Resource Website 10+ mentions |
READ (RRID:SCR_026958) | software application, software resource | Software tool to infer family relationships for degraded samples. Used to infer degree of relationship (up to second degree, i.e. nephew/niece-uncle/aunt, grandparent-grandchild or half-siblings) for pair of low-coverage individuals. | infer family relationships, degraded samples, infer degree of relationship, | European Research Council ; Swedish Research Council ; Uppsala Multidisciplinary Center for Advanced Computational Science |
PMID:29684051 | Free, Freely available | SCR_026958 | Relationship Estimation from Ancient DNA | 2026-08-14 09:29:26 | 24 | ||||||||
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SemiBin Resource Report Resource Website 10+ mentions |
SemiBin (RRID:SCR_026896) | source code, software application, software resource | Software command tool for metagenomic binning with deep learning, handles both short and long reads. Used for metagenomic binning at contig level which uses deep contrastive learning. | command tool, metagenomic binning, contig level, short and long reads, | National Natural Science Foundation of China ; Shanghai Municipal Science and Technology Major Project |
PMID:35484115 PMID:37387171 |
Free, Available for download, Freely available | SCR_026896 | SemiBin2 | 2026-08-14 09:29:34 | 20 | ||||||||
|
CheckM2 Resource Report Resource Website 50+ mentions |
CheckM2 (RRID:SCR_026897) | source code, software application, software resource | Software tool to predict completeness and contamination of genomic bins. Used for predicting genome quality of metagenome-assembled genomes. Assessing microbial genome quality using machine learning. | predicting genome quality, metagenome-assembled genomes, genomic bins, microbial genome quality, | PMID:37500759 PMID:38514780 |
Free, Available for download, Freely available, | SCR_026897 | 2026-08-14 09:29:25 | 72 | ||||||||||
|
xTB Resource Report Resource Website 1+ mentions |
xTB (RRID:SCR_026929) | software toolkit, source code, software resource | Software semiempirical extended tight-binding program package. Provides userfriendly interface for performing geometry optimizations, vibrational frequency calculations, and Molecular Dynamics simulations. | performing geometry optimizations, vibrational frequency calculations, Molecular Dynamics simulations, | DOI:10.1002/wcms.1493 | Free, Available for download, Freely available | https://xtb-docs.readthedocs.io/en/latest/ | SCR_026929 | , eXtended TB (xTB), eXtended TB, extended Tight Binding | 2026-08-14 09:29:26 | 4 | ||||||||
|
QCxMS Resource Report Resource Website 1+ mentions |
QCxMS (RRID:SCR_026928) | source code, software application, software resource | Software application as quantum chemical based program that enables users to calculate mass spectra using Born-Oppenheimer Molecular Dynamics. Quantum mechanic mass spectrometry calculation program. | Quantum mechanic mass spectrometry calculation, calculate mass spectra, Born-Oppenheimer Molecular Dynamics, | PMID:23630109 | Free, Available for download, Freely available, | SCR_026928 | 2026-08-14 09:29:35 | 1 | ||||||||||
|
OpenTOPAS Resource Report Resource Website 1+ mentions |
OpenTOPAS (RRID:SCR_026927) | source code, software application, software resource | 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 | 2026-08-14 09:29:50 | 2 | |||||||
|
IFOM ETS Cogentech GU Genomics Core Facility Resource Report Resource Website 1+ mentions |
IFOM ETS Cogentech GU Genomics Core Facility (RRID:SCR_026935) | service resource, access service resource, core facility | Cogentech's Genomic Core Facility (GU) provides professional support for workflow of research projects, from counseling on experimental design to functional interpretation of results. Support includes identification of the most suitable methodology to achieve the experimental aim, quality control of nucleic acid, generation of indexed fragment library, sequencing according to experimental needs and bioinformatic support for selected applications. Customized protocols can be set-up as well. Sequencing data are delivered using a password protected user-friendly web interface. The laboratory is ISO9001 certified. | ABRF, counseling on experimental design, functional interpretation of results, research projects support, |
is listed by: ABRF CoreMarketplace has parent organization: IFOM ETS - The AIRC Institute of Molecular Oncology; Milan; Italy |
ABRF_3216 | https://coremarketplace.org/?FacilityID=3216&citation=1 | https://www.cogentech.it/ngs.php | SCR_026935 | , Cogentech GU Genomics, Cogentech GU - Genomics Core Facility | 2026-08-14 09:29:35 | 1 | |||||||
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IFOM ETS Cogentech HP Histopathology Core Facility Resource Report Resource Website 1+ mentions |
IFOM ETS Cogentech HP Histopathology Core Facility (RRID:SCR_026934) | service resource, access service resource, core facility | Cogentech's Histopathology (HP) Core Facility provides services including consultation, tissue trimming and embedding, cutting, staining, photographic documentation for the evaluation and characterization of normal and pathological tissues. Provides Optimization of protocols for new stains or biological specimen.The laboratory is ISO9001 certified. | ABRF, tissue, trimming and embedding, cutting, staining, photographic documentation, |
is listed by: ABRF CoreMarketplace has parent organization: IFOM ETS - The AIRC Institute of Molecular Oncology; Milan; Italy |
ABRF_3213 | https://coremarketplace.org/?FacilityID=3213&citation=1 | SCR_026934 | , Cogentech HP- Histopathology Core Facility, Cogentech HP Histopathology | 2026-08-14 09:29:51 | 1 | ||||||||
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McLaughlin Research Institute Gene Editing and Mouse Models Assessment Core Facility Resource Report Resource Website 1+ mentions |
McLaughlin Research Institute Gene Editing and Mouse Models Assessment Core Facility (RRID:SCR_027045) | service resource, access service resource, core facility | GEMMA Core offers transgenic and genotyping services needed for experiments, phenotyping and behavioral services, and mouse colony management services to COBRE faculty. Consultation and training for lab staff is also available. | transgenic and genotyping services, phenotyping and behavioral services, mouse colony management services, |
is listed by: ABRF CoreMarketplace has parent organization: McLaughlin Research Institute |
Open | ABRF_3261 | https://coremarketplace.org/RRID:SCR_027045/?citation=1 | SCR_027045 | , GEMMA Core, Gene Editing and Mouse Models Assessment (GEMMA) Core | 2026-08-14 09:29:51 | 5 | |||||||
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Augusta University GCC Small Animal Imaging Core Facility Resource Report Resource Website 1+ mentions |
Augusta University GCC Small Animal Imaging Core Facility (RRID:SCR_027047) | service resource, access service resource, core facility | Core provides preclinical imaging and radiation treatment resources for animal research. | preclinical imaging, radiation treatment, animal research, |
is listed by: ABRF CoreMarketplace has parent organization: Augusta University; Georgia; USA |
ABRF_3262 | https://coremarketplace.org/RRID:SCR_027047/?citation=1 | SCR_027047 | , GCC Small Animal Imaging Core, Augusta University GCC Small Animal Imaging Core, Small Animal Imaging Resource | 2026-08-14 09:29:37 | 2 | ||||||||
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OBiO Technology Resource Report Resource Website 1+ mentions |
OBiO Technology (RRID:SCR_027205) | service resource, commercial organization | Established in 2013, OBiO Technology（Shanghai）Corp.,Ltd. is Contract Research Organization and Contract Development and Manufacturing Organization in cell and gene therapy. Provides technical services for the field of Regenerative Medicine and Anti-aging, including cell preparation, production of recombinant proteins/exosomes, and cell storage. | Contract Research Organization, Contract Development and Manufacturing Organization, cell and gene therapy, cell preparation, production of recombinant proteins, exosomes, cell storage, | SCR_027205 | 2026-08-14 09:29:52 | 1 | ||||||||||||
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GevaertLab_DUNE Resource Report Resource Website 1+ mentions |
GevaertLab_DUNE (RRID:SCR_027208) | DUNE | source code, software application, software resource | Software tool to extract low-dimensional deep features from multisequence brain MRI data using unsupervised autoencoders. | extract low-dimensional deep features, multisequence brain MRI data, unsupervised autoencoders, | Free, Available for download, Freely available | SCR_027208 | Deep feature extraction by UNet-based Neuroimaging-oriented autoEncoder | 2026-08-14 09:29:30 | 1 | |||||||||
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slow5 format Resource Report Resource Website 1+ mentions |
slow5 format (RRID:SCR_027155) | SLOW5 | standard specification, data or information resource, narrative resource | File format for storing signal data from Oxford Nanopore Technologies sequencing devices. SLOW5 can be encoded in human-readable ASCII format, or more compact and efficient binary format (BLOW5) - this is analogous to the seminal SAM/BAM format for storing DNA sequence alignments. | File format, storing signal data, Oxford Nanopore Technologies, sequencing devices, | PMID:34980914 | Free, Freely available | SCR_027155 | 2026-08-14 09:29:29 | 1 | |||||||||
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f5c Resource Report Resource Website 1+ mentions |
f5c (RRID:SCR_027158) | image analysis software, data processing software, software application, software resource, source code, alignment software | Software ultra-fast methylation calling and event alignment tool for nanopore sequencing data (supports CUDA acceleration). | methylation calling, event alignment, nanopore sequencing data, | Government of Ontario ; Government of Canada |
PMID:32758139 | Free, Available for download, Freely available | SCR_027158 | 2026-08-14 09:29:38 | 2 | |||||||||
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gGnome Resource Report Resource Website 1+ mentions |
gGnome (RRID:SCR_027150) | software toolkit, source code, software resource | Software package provides flexible, queriable R interface to graphs and walks of reference genomic intervals. gGnome is written in R6 object oriented standard and built around GenomicRanges, data.table, and igraph backend, and thus supports agile interaction with graphs consisting of hundreds of thousands of nodes and edges. | queriable R interface to graphs and walks, reference genomic intervals, R6 object oriented standard, | Free, Available for download, Freely available | SCR_027150 | 2026-08-14 09:29:52 | 1 |
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