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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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fqtrim Resource Report Resource Website 10+ mentions |
fqtrim (RRID:SCR_028291) | source code, software application, software resource | Software tool for filtering and trimming next generation sequencing reads. | filtering, trimming, next generation sequencing reads, | Free, Available for download, Freely available | https://github.com/gpertea/fqtrim/tree/v0.9.7, https://zenodo.org/records/1185412 | SCR_028291 | 2026-08-14 09:30:03 | 10 | ||||||||||
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VitroVivo Biotech Resource Report Resource Website 1+ mentions |
VitroVivo Biotech (RRID:SCR_028175) | commercial organization, production service resource, reagent manufacture, material service resource, service resource | Specialized biotechnology company that provides histology services, molecular pathology services, and specialized research reagents to accelerate biomedical research. They assist scientists in academia and industry with tissue preparation, immunostaining, 3D cell culture processing, and laser capture microdissection (LCM) for cancer, neuroscience, and drug development studies. | histology services, molecular pathology services, specialized research reagents, tissue preparation, immunostaining, 3D cell culture processing, laser capture microdissection, | SCR_028175 | VitroVivo Biotech - Histological Products and Services | 2026-08-14 09:29:41 | 1 | |||||||||||
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iRegulon Resource Report Resource Website 1+ mentions |
iRegulon (RRID:SCR_028223) | source code, software application, software resource | Software tool to reverse-engineer transcriptional regulatory networks from co-expressed gene sets by identifying master transcription factors (TFs) and their direct target genes. It operates by scanning for enriched TF binding motifs in promoter regions, utilizing over 10,000 position weight matrices (PWMs) for human, mouse, and Drosophila. Used to enable gene regulatory network mapping directly based on motif enrichment in co-expressed gene set. | reverse-engineer transcriptional regulatory networks, co-expressed gene sets, identifying master transcription factors and their direct target genes, |
has parent organization: Catholic University of Leuven; Flemish Brabant; Belgium is a plug in for: Cytoscape |
PMID:25058159 | Free, Available for download, Freely available | https://github.com/aertslab/iRegulon | SCR_028223 | 2026-08-14 09:29:41 | 9 | ||||||||
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SciNetX Resource Report Resource Website 1+ mentions |
SciNetX (RRID:SCR_028186) | data processing software, knowledge graph, web application, software application, software resource, knowledge resource | Local desktop and cloud-based bibliometric and network analysis platform offered through a licensed access model.Supports literature-centered bibliometric and scientometric workflows, and it can also be applied to custom datasets with or without associated literature papers, including broader general network analysis use cases. | bibliometrics; scientometrics; network analysis; PubMed; OpenAlex | has parent organization: University of Colorado; Colorado; USA | University of Colorado Anschutz Department of Orthopedics | Restricted | https://github.com/madavid-research/SciNetX | SCR_028186 | 2026-08-14 09:30:02 | 1 | ||||||||
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CPSM:Cancer Patient Survival Model Resource Report Resource Website 1+ mentions |
CPSM:Cancer Patient Survival Model (RRID:SCR_028188) | software toolkit, source code, software resource | Software R package that provides comprehensive computational pipeline for predicting survival probabilities and risk groups in cancer patients. Includes dedicated modules to perform key steps such as data preprocessing, training/test splitting, and normalization. | predicting survival probabilities, risk groups, cancer patients, data preprocessing, training, test splitting, normalization | DOI:10.1101/2024.11.14.623597 | Free, Available for download, Freely available | https://www.bioconductor.org/packages/devel/bioc/html/CPSM.html | SCR_028188 | , Cancer Patient Survival Model, CPSM:Cancer Patient Survival Model | 2026-08-14 09:29:41 | 1 | ||||||||
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Tokyo Chemical Industry Resource Report Resource Website 1+ mentions |
Tokyo Chemical Industry (RRID:SCR_028220) | commercial organization, production service resource, reagent supplier, reagent manufacture, material service resource, service resource, material resource | Tokyo Chemical Industry Co., Ltd. (TCI) is a leading global manufacturer of specialty organic chemicals, founded in 1946. They produce over 30,000 research chemicals, including laboratory chemicals, reagents, and functional materials. TCI also acts as a supplier, offering custom synthesis and bulk production from milligrams to tons. | organic chemicals, laboratory chemicals, reagents, functional materials, custom synthesis, bulk production | SCR_028220 | , Tokyo Chemical Industry Co Ltd, Ltd. (TCI), Tokyo Chemical Industry Co. | 2026-08-14 09:30:02 | 1 | |||||||||||
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OncoDB Resource Report Resource Website 50+ mentions |
OncoDB (RRID:SCR_028340) | database, data or information resource | Database offers integrated multi-omic data for patients across 33 cancer types. It encompasses gene expression, DNA methylation, somatic mutations, proteomic profiles, and chromatin accessibility, drawing from TCGA, GTEx, and CPTAC projects. Users can compare gene expression, DNA methylation, and protein levels between tumor and normal tissues, identifying differentially expressed genes and proteins, and examining gene-to-gene correlations. Provides oncogene mutation profiles and allows for survival analysis based on gene expression and methylation, linked to clinical parameters. Facilitates exploration of multi-omic correlations, such as gene expression with DNA methylation, and their variations with mutation status. Extends its analytical capabilities to include six major oncoviruses, offering insights into their impact on gene expression, methylation, and patient survival. | cancer patients data, gene expression, DNA methylation, somatic mutations, proteomic profiles, chromatin accessibility, | NIDCR R01DE026471; NIGMS R35GM141535; NCI R01CA287778 |
PMID:34718715 PMID:40995640 |
Free, Freely available, | SCR_028340 | OncoDB2.0 | 2026-08-14 09:30:03 | 84 | ||||||||
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University of Tennessee KnoxvilleAdvanced Microscopy and Imaging Center AMIC Core Facility Resource Report Resource Website 1+ mentions |
University of Tennessee KnoxvilleAdvanced Microscopy and Imaging Center AMIC Core Facility (RRID:SCR_028273) | service resource, access service resource, core facility | Multi-user, multi-disciplinary facility that provides microscopy and imaging services. It houses instrumentation for optical microscopy including laser scanning confocal microscopy and total internal reflection microscopy (TIRF), scanning as well as transmission electron microscopy, MALDI mass spectrometry imaging, and an X-ray MicroCT. Offers complete technical support, individual training and courses that cover both the practical applications and physical principles of microscopy. Provides consultations for development of microscopy projects for inclusion in grant proposals. | ABRF, microscopy and imaging services, optical microscopy, laser scanning confocal microscopy, total internal reflection microscopy, scanning and transmission electron microscopy, MALDI mass spectrometry imaging, X-ray MicroCT, |
is listed by: ABRF CoreMarketplace has parent organization: University of Tennessee; Tennessee; USA |
Open | ABRF_5857 | https://coremarketplace.org/RRID:SCR_028273/?citation=1 | SCR_028273 | Advanced Microscopy and Imaging Center (AMIC) | 2026-08-14 09:29:58 | 1 | |||||||
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Yale Center for Molecular Discovery YCMD Core Facility Resource Report Resource Website 1+ mentions |
Yale Center for Molecular Discovery YCMD Core Facility (RRID:SCR_028309) | service resource, access service resource, core facility | Full-service core facility specializing in high throughput assay development and screening of chemical and genomic probes. | ABRF, high throughput assay development, screening of chemical and genomic probes, molecular discovery services, |
is listed by: ABRF CoreMarketplace has parent organization: Yale University; Connecticut; USA |
ABRF_5884 | https://coremarketplace.org/RRID:SCR_028309/?citation=1 | SCR_028309 | Yale Center for Molecular Discovery (YCMD) | 2026-08-14 09:30:03 | 7 | ||||||||
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BoneMarrowMap Resource Report Resource Website 1+ mentions |
BoneMarrowMap (RRID:SCR_028324) | software toolkit, source code, software resource | Software R package to enable rapid reference mapping and annotation of new scRNA-seq data across the spectrum of normal and malignant hematopoietic contexts. Single cell RNA-seq reference map of human hematopoietic development in the bone marrow, with balanced representation of hematopoietic stem and progenitor cells and differentiated populations. | bone marrow AML acute myeloid leukemia scRNA-seq, reference mapping and annotation, scRNA-seq data, hematopoietic context, reference map, human hematopoietic development, bone marrow, | NCI P30 CA021765; NCI R35 CA197695 |
PMID:40294241 | Free, Available for download, Freely available | SCR_028324 | 2026-08-14 09:29:59 | 5 | |||||||||
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SNFtool Resource Report Resource Website 1+ mentions |
SNFtool (RRID:SCR_028497) | software toolkit, source code, software resource | Software R package for constructing networks of samples (e.g., patients) for each available data type and then efficiently fuses these into one network that represents the full spectrum of underlying data. Used to taking multiple views of a network and merging them into a combined view. | taking multiple views of network, full spectrum of underlying data, merging views into combined view, | Government of Canada | PMID:24464287 | Free, Available for download, Freely available | SCR_028497 | Similarity Network Fusion (SNF) tool | 2026-08-14 09:30:02 | 5 | ||||||||
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CoolBox Resource Report Resource Website 1+ mentions |
CoolBox (RRID:SCR_028427) | software toolkit, source code, software resource | Software Jupyter notebook based genomic data visualization toolkit. | Jupyter notebook, genomic data, data visualization, | Free, Available for download, Freely available | SCR_028427 | 2026-08-14 09:30:01 | 8 | |||||||||||
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MOFA2 Resource Report Resource Website 10+ mentions |
MOFA2 (RRID:SCR_028488) | source code, software application, software resource | Software statistical framework for comprehensive integration of multi-modal single-cell data. Used for integration of multi-omic data sets in unsupervised fashion. | reconstructs low-dimensional representation, variational inference, flexible sparsity constraints, jointly model variation, multiple sample groups and data modalities, | PMID:32393329 | Free, Available for download, Freely available | SCR_028488 | , MOFA+, Multi-Omics Factor Analysis v2 | 2026-08-14 09:30:05 | 18 | |||||||||
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MoNETA Resource Report Resource Website 1+ mentions |
MoNETA (RRID:SCR_028485) | software toolkit, source code, software resource | Software R package to compress multi-omic data into a single matrix of reduced size. Used for fast and scalable identification of relevant multi-omics relationships between biological entities at the bulk and single-cells level. | compress multi-omic data, single matrix of reduced size, identification of relevant multi-omics relationships, | PMID:39416887 | Free, Available for download, Freely available | SCR_028485 | MultiOmics Network Embedding for subType Analysis | 2026-08-14 09:30:05 | 2 | |||||||||
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influential Resource Report Resource Website 1+ mentions |
influential (RRID:SCR_028517) | software toolkit, source code, software resource | Software R package for identifying and ranking influential nodes in biological and other complex networks. Implements the Integrated Value of Influence (IVI), Experimental data-based Integrative Ranking (ExIR), SIRIR, and numerous network centrality measures, enabling network topology analysis, influential node detection, feature prioritization, and candidate biomarker discovery. Provides functions for network reconstruction, centrality assessment, visualization, and analysis of relationships between centrality measures. Used for identification and classification of the most influential nodes. | identification and classification of influential nodes, network reconstruction, centrality assessment, visualization, analysis of relationships between centrality measures, | PMID:33205118 | Free, Available for download, Freely available | https://cran.r-project.org/package=influential | SCR_028517 | 2026-08-14 09:30:02 | 1 | |||||||||
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University of Washington Histology and Imaging Core Facility Resource Report Resource Website 1+ mentions |
University of Washington Histology and Imaging Core Facility (RRID:SCR_028435) | service resource, access service resource, core facility | Core provides histology, immunohistochemistry, imaging, quantitative image analysis, and pathology consultation services. Offers experience, expertise and instrumentation across all platforms. Through the partnership with the Comparative Pathology Program (CPP), we have board certifies veterinary pathologists on staff who are available for research consultation and collaboration. | ABRF, histology, immunohistochemistry, imaging, quantitative image analysis, pathology consultation services, |
is listed by: ABRF CoreMarketplace has parent organization: University of Washington; Seattle; USA |
ABRF_5945 | https://https://coremarketplace.org/?FacilityID=5945&citation=1 | SCR_028435 | HIC - Histology and Imaging Core | 2026-08-14 09:30:01 | 1 | ||||||||
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Bokeh Resource Report Resource Website 1+ mentions |
Bokeh (RRID:SCR_028392) | software toolkit, software resource, source code, software library | Software Python package for interactive and static data visualization.Interactive visualization library for modern web browsers. Provides concise construction of graphics and affords high-performance interactivity across large or streaming datasets. | Interactive data visualization, interactive and static data visualization, | Free, Available for download, Freely available | https://github.com/bokeh/bokeh | SCR_028392 | 2026-08-14 09:30:04 | 3 | ||||||||||
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GlycoShape Resource Report Resource Website 1+ mentions |
GlycoShape (RRID:SCR_028443) | database, data or information resource | Database of glycans 3D structural data and information that can be downloaded or used with Re-Glyco to rebuild glycoproteins from the RCSB PDB or EMBL-EBI AlphaFold repositories. Glycan structure database and toolbox designed to restore glycoproteins to their native and functional form. | glycans 3D structural data, glycans information, glycan structure, restore glycoproteins to their native and functional form, | PMID:39402214 | Free, Freely available, | SCR_028443 | 2026-08-14 09:30:01 | 5 | ||||||||||
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GATK VariantFiltration Resource Report Resource Website 1+ mentions |
GATK VariantFiltration (RRID:SCR_028441) | software application, software resource | Software command-line tool designed for hard-filtering variant callsets (VCF files) by applying user-defined criteria to annotate, rather than remove, low-quality variants. It marks fails in the FILTER field (e.g., using JEXL expressions to filter by DP, QD, or FS), making it essential for filtering small datasets, non-model organisms, or whenever Variant Quality Score Recalibration (VQSR) is not feasible | hard-filtering variant callsets, annotate low-quality variants, |
is related to: GATK is organization facet of: Broad Institute |
Free, Freely available | https://gatk.broadinstitute.org/hc/en-us | SCR_028441 | 2026-08-14 09:29:43 | 1 | |||||||||
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bedGraphToBigWig Resource Report Resource Website 1+ mentions |
bedGraphToBigWig (RRID:SCR_028439) | software application, software resource | Command-line utility provided by the UCSC Genome Browser to convert text-based bedGraph files into indexed binary bigWig files. It is specifically used in bioinformatics to transform dense, continuous genome coverage data into a format that enables fast visualization and remote viewing in genome browsers like IGV or the UCSC Genome Browser. | Convert bedGraph file to bigWig format, convert text-based bedGraph files, indexed binary bigWig files, transform genome coverage data, |
is related to: BigWig and BigBed works with: UCSC Genome Browser |
DOI:10.1093/bioinformatics/btq351 | Free, Freely available, | SCR_028439 | 2026-08-14 09:30:04 | 3 |
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