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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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AutoDockTools Resource Report Resource Website 1000+ mentions |
AutoDockTools (RRID:SCR_026401) | ADT | software application, software resource | Software graphical user interface to help to set up which bonds will treated as rotatable in the ligand and to analyze dockings. Used for automated docking with selective receptor flexibility. Designed to predict how small molecules, such as substrates or drug candidates, bind to receptor of known 3D structure. | automated docking, selective receptor flexibility, predict binding, bind to receptor of known 3D structure, ligand, analyze dockings | NIGMS RO1 GM069832 | PMID:19399780 | Free, Available for download, Freely available | https://autodock.scripps.edu/ | SCR_026401 | AutoDockTools: the Graphical User Interface for AutoDock | 2026-08-09 09:09:05 | 2063 | ||||||
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NucleAIzer Resource Report Resource Website 1+ mentions |
NucleAIzer (RRID:SCR_026500) | source code, software resource | Software tool as parameter-free deep learning framework for nucleus segmentation using image style transfer. Cell segmentation tool. | nucleus segmentation, image style transfer, | NIGMS R35 GM122547; European Regional Development Funds ; Academy of Finland ; Swedish Research Council |
DOI:10.1016/j.cels.2020.04.003 | Free, Available for download, Freely available | SCR_026500 | 2026-08-09 09:09:09 | 4 | |||||||||
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Eastern Cooperative Oncology Group Performance Status Scale Resource Report Resource Website 1+ mentions |
Eastern Cooperative Oncology Group Performance Status Scale (RRID:SCR_026432) | data or information resource, organization portal, narrative resource, portal, standard specification | ECOG Performance Scale describes patient’s level of functioning in terms of their ability to care for themself, daily activity, and physical ability (walking, working, etc.). Standard criteria for measuring how the disease impacts patient’s daily living abilities. Used to assess the functional status of patient. | ECOG-ACRIN Cancer Research Group, patient’s performance status, assess patient functional status, conduct clinical trials, | NCI | Free, Freely available | SCR_026432 | ECOG Performance Status Scale | 2026-08-09 09:09:07 | 5 | |||||||||
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timeROC Resource Report Resource Website 10+ mentions |
timeROC (RRID:SCR_026444) | software toolkit, software resource | Software R package for estimation of time-dependent ROC curve and area under time dependent ROC curve in the presence of censored data, with or without competing risks. Confidence intervals of AUCs and tests for comparing AUCs of two rival markers measured on the same subjects can be computed, using the iid-representation of the AUC estimator. | estimation of time-dependent ROC curve and area, presence of censored data, | Free, Available for download, Freely available | SCR_026444 | 2026-08-09 09:09:07 | 19 | |||||||||||
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hdf5r Resource Report Resource Website 1+ mentions |
hdf5r (RRID:SCR_026447) | software toolkit, software resource | Software R package as data model, library and file format for storing and managing large amounts of data. | data model, library, file format, storing and managing large amounts of data, | Free, Available for download, Freely available | https://github.com/hhoeflin/hdf5r/ | SCR_026447 | 2026-08-09 09:09:07 | 1 | ||||||||||
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Liftoff Resource Report Resource Website 10+ mentions |
Liftoff (RRID:SCR_026535) | source code, software resource | Software genome annotation lift-over tool capable of mapping genes between two assemblies of the same or closely related species. Aligns genes from reference genome to target genome and finds the mapping that maximizes sequence identity while preserving the structure of each exon, transcript and gene. Used for accurate mapping of gene annotations. | Aligns genes, reference genome to target genome alignment, mapping of gene annotations, genome annotation lift-over, mapping genes between two assemblies of species, mapping genes, same or closely related species, | NHGRI R01 HG006677; NIGMS R35 GM130151 |
PMID:33320174 | Free, Available for download, Freely available | SCR_026535 | 2026-08-09 09:09:27 | 10 | |||||||||
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SpheroidSegDeDeb Resource Report Resource Website 1+ mentions |
SpheroidSegDeDeb (RRID:SCR_026409) | software application, software resource | Software minimal tool for segmentation of irradiated tumor spheroids using optimized U-Net. | segmentation of irradiated tumor spheroids, segmentation, irradiated tumor spheroids, tumor spheroids, | Free, Available for download, Freely available, | SCR_026409 | 2026-08-09 09:09:06 | 1 | |||||||||||
|
modeltest Resource Report Resource Website 100+ mentions |
modeltest (RRID:SCR_026633) | software application, software resource | Software tool for selecting the best-fit model of evolution for DNA and protein alignments. Used for selection of DNA and Protein evolutionary models. | selecting the best-fit model of evolution, DNA and protein alignments, selection of DNA and Protein evolutionary models, | Ministry of Economy and Competitiveness of Spain ; FEDER funds of the EU ; Galician Government ; Klaus Tschira Foundation |
PMID:31432070 | Free, Available for download, Freely available | SCR_026633 | ModelTest-NG | 2026-08-09 09:09:30 | 160 | ||||||||
|
ssGSEA 2.0 Resource Report Resource Website 10+ mentions |
ssGSEA 2.0 (RRID:SCR_026610) | source code, software resource | Software application as updated version of original ssGSEA R-implementation. Depending on the input dataset and chosen database (gene sets or PTM signatures), the software performs either ssGSEA or PTM-SEA, respectively. | Single sample Gene Set Enrichment analysis, PTM Enrichment Analysis, | Free, Available for download, Freely available | SCR_026610 | ssGSEA2.0/PTM-SEA, Single sample Gene Set Enrichment analysis (ssGSEA) and PTM Enrichment Analysis (PTM-SEA) | 2026-08-09 09:09:13 | 30 | ||||||||||
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Mutect2 Resource Report Resource Website 1000+ mentions |
Mutect2 (RRID:SCR_026692) | software application, software resource | Software tool to call somatic short mutations via local assembly of haplotypes. Somatic variant caller that uses local assembly and realignment to detect SNVs and indels. | Somatic variant caller, call somatic short mutations, detect SNVs and indels, | DOI:10.1101/861054 | SCR_026692 | 2026-08-09 09:09:28 | 1271 | |||||||||||
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statannotations Resource Report Resource Website 1+ mentions |
statannotations (RRID:SCR_026623) | software toolkit, software resource | Software Python package to optionally compute statistical test and add statistical annotations on plots generated with seaborn. Used to add statistical significance or custom annotations on seaborn plots. | compute statistical test, add statistical annotations on plots, add statistical significance, add custom annotations, seaborn plots, | Free, Available for download, Freely available | SCR_026623 | 2026-08-09 09:09:27 | 2 | |||||||||||
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BIGapp Resource Report Resource Website 1+ mentions |
BIGapp (RRID:SCR_026676) | BIGapp | web application, source code, software resource | Species-agnostic web-based application for processing genotypic data in no-code RShiny user-friendly interface. Allows users without coding experience to process genetic data in all genome ploidy ranges and for multiallelic data, starting from number of input formats (including VCF). Also allows to perform downstream QC analyses (e.g., PCA) and run genomic analysis (e.g., Linkage mapping, QTL analysis, genome-wide association studies (GWAS), and genomic selection (GS). | processing genotypic data in no-code RShiny, process genetic data, genome ploidy ranges, multiallelic data, | USDA-ARS 8062-21000-043-004-A; USDA-ARS 8062-21000-052-002-A; USDA-ARS 8062-21000-052-003-A |
Free, Available for download, Freely available | https://github.com/Breeding-Insight | SCR_026676 | Breeding Insight Genomics App | 2026-08-09 09:09:30 | 1 | |||||||
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bi-web Resource Report Resource Website 1+ mentions |
bi-web (RRID:SCR_026678) | software application, source code, software resource | Breeding-Insight/bi-web development. | Breeding-Insight, bi-web development, | Free, Available for download, Freely available | SCR_026678 | breeding insight-web | 2026-08-09 09:09:28 | 1 | ||||||||||
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phenoimager2mc Resource Report Resource Website 1+ mentions |
phenoimager2mc (RRID:SCR_026561) | software application, source code, software resource | Software tool for formatting PhenoImager TIFF/OME-TIFF metadata for compatibility with MCMICRO workflow. | formatting PhenoImager TIFF/OME-TIFF metadata, compatibility with MCMICRO workflow, | Free, Available for download, Freely available | SCR_026561 | 2026-08-09 09:09:29 | 1 | |||||||||||
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HiGlass Resource Report Resource Website 10+ mentions |
HiGlass (RRID:SCR_026687) | web application, source code, software resource | Web-based visual exploration and analysis of genome interaction maps. | visual exploration and analysis, genome interaction maps, | NCI U01CA200059; NHGRI R00 HG007583; NHGRI U54 HG007963 |
PMID:30143029 | Free, Available for download, Freely available | SCR_026687 | 2026-08-09 09:09:16 | 45 | |||||||||
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Automated Projection Pursuit Resource Report Resource Website 1+ mentions |
Automated Projection Pursuit (RRID:SCR_026560) | APP | software application, source code, software resource | Software tool for automated projection pursuit clustering. Alternative clustering approach that alleviates the curse of dimensionality by sequentially projecting high-dimensional data into a low-dimensional representation. | automated projection pursuit clustering, projecting high-dimensional data, low-dimensional representation, | Free, Available for download, Freely available | SCR_026560 | 2026-08-09 09:09:11 | 1 | ||||||||||
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rrvgo Resource Report Resource Website 1+ mentions |
rrvgo (RRID:SCR_026680) | software toolkit, software resource | Software R package to reduce and visualize Gene Ontology terms. Used for interpreting lists of Gene Ontology terms. | interpreting lists of Gene Ontology terms, Gene Ontology terms, | German Research Foundation | PMID:37151216 | Free, Available for download, Freely available | SCR_026680 | 2026-08-09 09:09:31 | 3 | |||||||||
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NeuroDevTime Resource Report Resource Website 1+ mentions |
NeuroDevTime (RRID:SCR_026651) | source code, software resource | Software code for age prediction in fetal brain and organoid single cell data. This repository contains cell type agnostic models to predict the developmental age of brain cell types from single cell RNAseq data. Code contains 4 jupyter notebooks, which apply pretrained models to predict neurodevelopmental age of cell types in new human fetal brain and organoid datasets. | age prediction, fetal brain, organoid single cell data, developmental age of brain cell types, single cell RNAseq data, | DOI:10.1101/2025.02.24.639936v1.full | Free, Available for download, Freely available | SCR_026651 | 2026-08-09 09:09:15 | 2 | ||||||||||
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WebWarp Resource Report Resource Website 1+ mentions |
WebWarp (RRID:SCR_026759) | web application, source code, software resource | Web application for nonlinear refinement of image registration after WebAlign. | Nonlinear refinement, 2D, 3D, registration, quantitative analysis, image registration, | is related to: SeriesZoom | H2020-EU FPA 650003 | DOI:10.3389/fninf.2025.1629388 | Free, Available for download, Freely available | https://webwarp.readthedocs.io/en/latest/index.html | SCR_026759 | 2026-08-09 09:09:32 | 1 | |||||||
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WebAlign Resource Report Resource Website 1+ mentions |
WebAlign (RRID:SCR_026758) | web application, source code, software resource | Web application for 2D image registration to 3D atlas. Used for user guided affine spatial registration (anchoring) of sectional image data, typically high resolution histological images, to 3D reference atlas space. Can generate user defined cut planes through atlas templates that match orientation of cutting plane of 2D experimental images (atlas maps). | 2D image registration, 3D atlas, affine spatial registration, sectional image data, histological images, 3D reference atlas space, | is related to: SeriesZoom | H2020-EU FPA 650003 | DOI:10.3389/fninf.2025.1629388 | https://webalign.readthedocs.io/en/latest/index.html | SCR_026758 | 2026-08-09 09:09:29 | 1 |
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