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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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BioMart Project Resource Report Resource Website 100+ mentions |
BioMart Project (RRID:SCR_002987) | project portal, data or information resource, data access protocol, software resource, web service, portal | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4,2023.Platform provides free software and data services to international scientific community in order to foster scientific collaboration and facilitate scientific discovery process. Project adheres to open source philosophy that promotes collaboration and code reuse. | biology, data, management, data mining, search, descriptive, graphical, application, perl, java, gold standard |
is used by: Blueprint Epigenome is related to: Mouse Genome Informatics (MGI) is related to: biomaRt has parent organization: Ontario Institute for Cancer Research has parent organization: European Bioinformatics Institute |
Wellcome Trust ; Spanish Government ; Sandra Ibarra Foundation for Cancer ; Breast Cancer Campaign Tissue Bank ; U.S. Department of Energy ; NSF NRF 2013M3A6A4043695; Center for Genome Regulation ; Center for Mathematical Modelling ; European Molecular Biology Laboratory |
PMID:21930506 PMID:19144180 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30184 | SCR_002987 | BioMart software | 2026-07-28 09:40:34 | 284 | ||||||
|
RNAmut Resource Report Resource Website |
RNAmut (RRID:SCR_026965) | source code, software toolkit, software resource | Software package for robust identification of somatic mutations in acute myeloid leukemia using RNA-sequencing. Detects clinically important somatic mutations from RNA-seq data on relatively small gene panel (typically less than 100 genes). | identification of somatic mutations, acute myeloid leukemia, RNA-sequencing, clinically important somatic mutations, RNA-seq data, small gene panel, | Wellcome Trust ; European Research Council ; European Union Horizon 2020 |
PMID:31649132 | Free, Available for download, Freely available | SCR_026965 | 2026-07-28 09:46:55 | 0 | |||||||||
|
ped-sim Resource Report Resource Website 1+ mentions |
ped-sim (RRID:SCR_026957) | software application, simulation software, source code, software resource | Software tool to simulate pedigree structures. Used for simulating relatives that can utilize either sex-specific or sex averaged genetic maps and also either model of crossover interference or traditional Poisson model for inter-crossover distances. | Pedigree simulator, simulate pedigree structures, simulating relatives, sex-specific, sex averaged, genetic maps, | NIGMS R35 GM133805; Alfred P. Sloan Research Fellowship ; United States-Israel Binational Science Foundation ; NHLBI R01 HL0113323; NHLBI P01 HL045222; NIDDK R01 DK047482; NIDDK R01 DK053889; NIGMS T32 GM007617; NIGMS T32 GM083937; Wellcome Trust |
PMID:31860654 | Free, Available for download, Freely available | SCR_026957 | Ped-sim | 2026-07-28 09:46:54 | 2 | ||||||||
|
TWOMBLI Resource Report Resource Website |
TWOMBLI (RRID:SCR_027217) | source code, software toolkit, software resource | Software pipeline includes metrics of matrix alignment, length, branching, end points, gaps, fractal dimension, curvature, and the distribution of fibre thickness. FIJI macro for quantifying pattern in extracellular matrix. | quantifying pattern in extracellular matrix, matrix alignment, length, branching, end points, gaps, fractal dimension, curvature, distribution of fibre thickness, | is a plug in for: Fiji | Cancer Research UK ; UK Medical Research Council ; Wellcome Trust ; Spanish Society for Medical Oncology |
PMID:33504622 | Free, Available for download, Freely available, | SCR_027217 | Workflow Of Matrix BioLogy Informatics, , Workflow Of Matrix BioLogy Informatics (TWOMBLI) | 2026-07-28 09:46:53 | 0 | |||||||
|
Brain Intensity AbNormality Classification Algorithm Resource Report Resource Website 1+ mentions |
Brain Intensity AbNormality Classification Algorithm (RRID:SCR_024928) | BIANCA | software application, software resource, data processing software, segmentation software, image analysis software | Software tool for automated segmentation of white matter hyperintensities. Classifies image’s voxels based on their intensity and spatial features, and the output image represents the probability per voxel of being WMH. Flexible in terms of MRI modalities to use and offers different options for weighting spatial information, local spatial intensity averaging, and different options for choice of number and location of training points. | images voxels classification, automated segmentation of white matter hyperintensities, white matter hyperintensities, | is a plug in for: FSL | Wellcome Trust ; Wolfson Foundation ; UK Stroke Association ; NIHR Oxford Biomedical Research Centre |
PMID:27402600 | Free, Freely available | SCR_024928 | BIANKA:Brain Intensity AbNormality Classification Algorithm | 2026-07-28 09:46:12 | 3 | ||||||
|
Vireo Resource Report Resource Website 1+ mentions |
Vireo (RRID:SCR_027463) | software application, source code, software resource | Software tool for Bayesian demultiplexing of pooled single-cell RNA-seq data without genotype reference. | Bayesian demultiplexing, pooled single-cell RNA-seq data, without genotype reference, | University of Cambridge ; EMBL-EBI ; National Health and Medical Research Council of Australia ; Wellcome Trust ; Medical Research Council |
PMID:31836005 | Free, Available for download, Freely available | SCR_027463 | 2026-07-28 09:46:57 | 1 | |||||||||
|
Cell Model Passports Resource Report Resource Website 1+ mentions |
Cell Model Passports (RRID:SCR_027682) | data or information resource, catalog, database | Hub for clinical, genetic and functional datasets of preclinical cancer models.Provides details of cell model relationships, patient and clinical information, as well as access to associated genetic and functional datasets. Passports database contains curated details and standardized annotation for cell models, including cancer organoid cultures. Users can navigate database via tissue, cancer-type, genetic feature and data availability to select model. REST-API provides programmatic data access and exploration. | clinical, genetic, functional, datasets, preclinical cancer models, | has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom | Wellcome Trust ; Wellcome Sanger Institute |
PMID:30260411 | Free, Freely available | SCR_027682 | 2026-07-28 09:47:15 | 2 | ||||||||
|
TryTripDB Resource Report Resource Website |
TryTripDB (RRID:SCR_028607) | data or information resource, database | Free online resource for data mining of genomic and functional data from these kinetoplastid parasites and is part of the VEuPathDB Bioinformatics Resource Center. Integrates functional genome scale datasets (e.g. transcript expression, protein expression, genetic variation data) and information predicted from automated bioinformatics pipelines and from manual curation. Provides a user friendly web interface and a number of tools and functions for users to conduct in silico experiments to ask questions and generate hypotheses. Researchers can also contribute their expertise via the User Comments form and Apollo annotation platform, and utilize cloud-based workspace to analyze their own data. | data mining, genomic data, functional data, kinetoplastid parasites, | NIAID ; Wellcome Trust |
PMID:36656904 | Free, Freely available | SCR_028607 | 2026-07-28 09:47:24 | 0 |
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Data set from Kravitz, Owen and Kretizer's 2012 paper "Optogenetic identification of striatal projection neuron subtypes during in vivo recordings."
