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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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DotDotGoose Resource Report Resource Website 1+ mentions |
DotDotGoose (RRID:SCR_025485) | software resource, source code | Software tool to assist with manually counting objects in images. Used for many conservation applications. | American Museum of Natural History, Center for Biodiversity and Conservation, manually counting objects in images, conservation applications, | Free, Available for download, Freely available | https://github.com/persts/DotDotGoose | SCR_025485 | 2026-08-12 10:53:27 | 1 | ||||||||||
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The Great Genoytper Resource Report Resource Website 1+ mentions |
The Great Genoytper (RRID:SCR_025487) | data processing software, software resource, software application | Software workflow begins by preprocessing short-read samples of raw data to create counting colored De Bruijn graph. Graph based method for population genotyping of small and structural variants. Population genotyping workflow. | Population genotyping, genotyping of small and structural variants, preprocessing short-read samples, raw data, create counting colored De Bruijn graph, | DOI:10.1101/2024.07.04.24309921 | Free, Available for download, Freely available, | SCR_025487 | 2026-08-12 10:53:31 | 1 | ||||||||||
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Incucyte Cell-By-Cell Analysis Software Module Resource Report Resource Website 1+ mentions |
Incucyte Cell-By-Cell Analysis Software Module (RRID:SCR_025367) | software resource, software application | Software for analysis to determine live versus dead cells – no fluorescent dyes needed. | determine live versus dead cells, no fluorescent dyes needed, analysis | Restricted | SCR_025367 | 2026-08-12 10:53:25 | 3 | |||||||||||
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DokuMate Resource Report Resource Website |
DokuMate (RRID:SCR_025402) | software resource, software application | DokuMate helps standardize and reuse documents, simplifies and speeds-up editing, and automates many tedious tasks. A docId” is one of the “magic” Content Control tag names. A docId is an alphanumerical ID (e.g., “R01-01-C00”, “R01-11-100”, “R01-11-410”, “R01-30-100”) that uniquely identifies and sorts documents (e.g., Schedule C, Exhibit 1, Attachment 4.1, Appendix 1) within a larger set of documents, e.g., all documents belonging to (a) a specific RFP or (b) the set of contracts between a first party and a second party. | automate documents, simplify editing, automate task, Content Control tag names, | Restricted | SCR_025402 | 2026-08-12 10:53:25 | 0 | |||||||||||
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SCOM Resource Report Resource Website 1+ mentions Rating or validation data |
SCOM (RRID:SCR_023738) | simulation software, software resource, software application | Software application to Pan-cancer characterization of ncRNA synergistic competition. Used to predict ncRNA synergistic competition network from gene expression data and predicted ncRNA-related ceRNA networks. | Pan-cancer characterization, ncRNA synergistic competition, predict ncRNA synergistic competition network, gene expression data, ncRNA-related ceRNA networks, | Free, Available for download, Freely available | SCR_023738 | Synergistic COMpetition | 2026-08-12 10:52:58 | 1 | ||||||||||
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MetaboSERV Resource Report Resource Website 1+ mentions |
MetaboSERV (RRID:SCR_025496) | service resource, computational service resource, data repository, storage service resource | Browser based platform for selecting, exchanging, and visualizing metabolomics data with controlled data access. Used to facilitate collaborative metabolomics research and to enable researchers to make their experimental data findable, accessible, interoperable, and re-usable as defined by the FAIR principles. | FAIR, FAIR data, metabolomics data, controlled data access, | German Federal Ministry of Education and Research (BMBF) 01ZX1912A; German Federal Ministry of Education and Research (BMBF) 01ZX1912C; German Federal Ministry of Education and Research (BMBF) 01ZX1912D |
Restricted | https://gitlab.gwdg.de/metaboserv2 (source code); https://metaboserv.ckdn.app (centralized instance) | SCR_025496 | 2026-08-12 10:53:24 | 1 | |||||||||
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FAE Resource Report Resource Website 50+ mentions |
FAE (RRID:SCR_025378) | FAE | software toolkit, software resource, source code | Open-source software Python package for developing and comparing radiomics models. Used to build radiomics models and evaluate them using independent testing dataset. It also provides easy model comparison and result visualization. | extract radiomcs feature, preprocess feature matrix, developing and comparing radiomics models, radiomics models, model comparison and result visualization, | National Key Research and Development Program of China ; Key Project of the National Natural ; Science Foundation of China ; Siemens Healthcare |
PMID:32804986 | Free, Available for download, Freely available | SCR_025378 | , FeAture Explorer (FAE), FeAture Explorer | 2026-08-12 10:53:23 | 55 | |||||||
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EventIDE Resource Report Resource Website 1+ mentions |
EventIDE (RRID:SCR_025412) | software resource, software application | Software for designing and running advanced behavioral experiments and neuroscientific studies. | Okazo lab, neuroscience, neuroscietific studies, visibility test, designing experiments, running experiments, behavioral experiments, | Restricted | SCR_025412 | 2026-08-12 10:53:23 | 1 | |||||||||||
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NWB Inspector Resource Report Resource Website 1+ mentions |
NWB Inspector (RRID:SCR_025465) | software resource, software application | Software Python-based package designed to asses quality of Neurodata Without Borders files and based on compliance with Best Practice. Meant as companion to PyNWB validator, which checks for strict schema compliance. Attempts to apply some commonsense rules and heuristics to find data components of file that pass validation, but are probably incorrect, or suboptimal, or deviate from best practices. In other words, while PyNWB validator focuses on compliance of structure of file with the schema, the inspector focuses on compliance of actual data with best practices. Meant as data review aid. It does not catch all best practice violations, and any warnings it does produce should be checked by knowledgeable reviewer. | data review aid, asses quality of Neurodata Without Borders files, compliance with Best Practice, companion to PyNWB validator, compliance of actual data with best practices, |
is related to: Neurodata Without Borders is related to: PyNWB |
Free, Freely available | SCR_025465 | 2026-08-12 10:53:27 | 1 | ||||||||||
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olsrr Resource Report Resource Website 1+ mentions |
olsrr (RRID:SCR_025511) | software toolkit, software resource, source code | Software tools for developing Ordinary Least Squares regression models. | Ordinary Least Squares, regression model, developing OLS, | Free, Available for download, Freely available, | SCR_025511 | 2026-08-12 10:53:24 | 2 | |||||||||||
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con/duct Resource Report Resource Website |
con/duct (RRID:SCR_025436) | software resource, source code | Software application as helper to run command, capture stdout/stderr and details about running. | run command helper, capture stdout/stderr, | Free, Available for download, Freely available | SCR_025436 | duct | 2026-08-12 10:53:26 | 0 | ||||||||||
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ColabFold Resource Report Resource Website 100+ mentions |
ColabFold (RRID:SCR_025453) | software resource, source code | Software application offers accelerated prediction of protein structures and complexes by combining homology search of MMseqs2 with AlphaFold2 or RoseTTAFold. Used for protein folding. | prediction of protein structures and complexes, protein folding, protein structure prediction, | Max Planck Society ; University of Göttingen ; National Research Foundation of Korea ; Seoul National University ; NIH Office of the Director DP5OD026389; NIAID R21AI156595; NSF |
PMID:35637307 | Free, Available for download, Freely available | https://github.com/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb | SCR_025453 | 2026-08-12 10:53:26 | 493 | ||||||||
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AlphaFold Resource Report Resource Website 100+ mentions |
AlphaFold (RRID:SCR_025454) | software toolkit, software resource, source code | Software package provides implementation of inference pipeline of AlphaFold v2. Incorporates physical and biological knowledge about protein structure, leveraging multi-sequence alignments, into design of deep learning algorithm. Used for protein structure prediction. | inference pipeline, protein structure prediction, protein structure, | is related to: AlphaFold Server | National Research Foundation of Korea ; Seoul National University |
PMID:34265844 | Free, Available for download, Freely available | SCR_025454 | , AlphaFold v2, AlphaFold2 | 2026-08-12 10:53:23 | 149 | |||||||
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pbmm2 Resource Report Resource Website 1+ mentions |
pbmm2 (RRID:SCR_025549) | software resource, source code | Software application as minimap2 frontend for PacBio native data formats. SMRT C++ wrapper for minimap2's C API. | minimap2, PacBio, native data formats, SMRT C++ wrapper, minimap2 C API, | Free, Available for download, Freely available, | SCR_025549 | 2026-08-12 10:53:29 | 7 | |||||||||||
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signed ks test Resource Report Resource Website 1+ mentions |
signed ks test (RRID:SCR_025636) | software resource, source code | Software tool as modified R ks.test to obtain sign and force exact p-value. | modified R ks.test, obtain sign and force exact p-value, p-value, | Free, Available for download, Freely available, | SCR_025636 | 2026-08-12 10:53:31 | 1 | |||||||||||
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scGBM Resource Report Resource Website 1+ mentions |
scGBM (RRID:SCR_025518) | software resource, source code | Software application for model-based dimensionality reduction of scRNA-seq data. Quantifies uncertainty in each cell's latent position and leverages these uncertainties to assess confidence associated with given cell clustering. On real and simulated single-cell data produces low-dimensional embeddings that better capture relevant biological information while removing unwanted variation. Used for model-based dimensionality reduction for single-cell RNA-seq with generalized bilinear models. | Generalized bilinear models, model-based dimensionality reduction, scRNA-seq data, removing unwanted variation, | NCI T32CA009337; NCI R01CA240299 |
PMID:37162914 | Free, Available for download, Freely available, | SCR_025518 | 2026-08-12 10:53:24 | 3 | |||||||||
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GPU-assisted Distance Estimation Software Resource Report Resource Website |
GPU-assisted Distance Estimation Software (RRID:SCR_025519) | GADES | software toolkit, software resource, source code | Software package to compute distance matrices in sparse or dense mode with GPU or CPU. | compute distance matrices, sparse mode, dense mode, GPU, CPU | Free, Available for download, Freely available, | SCR_025519 | GPU-Assisted Distance Estimation Software | 2026-08-12 10:53:32 | 0 | |||||||||
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SomaticSignatures Resource Report Resource Website 1+ mentions |
SomaticSignatures (RRID:SCR_025620) | software toolkit, software resource, source code | Software R package for identifying mutational signatures of single nucleotide variants (SNVs) from high-throughput experiments. | R, identifying mutational signatures, single nucleotide variants, high-throughput experiments, | NSF | PMID:26163694 | Free, Available for download, Freely available, | https://github.com/juliangehring/SomaticSignatures | SCR_025620 | 2026-08-12 10:53:31 | 7 | ||||||||
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2s-LCA Resource Report Resource Website 1+ mentions |
2s-LCA (RRID:SCR_025613) | software resource, software application | Software for multi-omic data integration. Used to jointly decompose multiple biologically related experimental data sets with biological and technological relationships that can be structured into the decomposition. | multi-omic data integration, two-stage linked component analysis, jointly decompose biologically related experimental data sets, decomposition, | PMID:35358296 | https://github.com/CHuanSite/SJD | SCR_025613 | two-stage Linked Component Analysis | 2026-08-12 10:53:34 | 1 | |||||||||
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GRNBoost2 Resource Report Resource Website 10+ mentions |
GRNBoost2 (RRID:SCR_025614) | software resource, software application | Algorithm for regulatory network inference using gradient boosting, based on GENIE3 architecture. Used for inference of gene regulatory networks. | GRN, Gene Regulatory Network, inference of gene regulatory networks, | PMID:30445495 | Free, Freely available | https://arboreto.readthedocs.io/en/latest/, https://github.com/aertslab/GRNBoost | SCR_025614 | GRNBoost, Gene Regulatory Network Boost | 2026-08-12 10:53:31 | 11 |
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