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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Willoughby–Hoye Python Scripts A-D Resource Report Resource Website 1+ mentions Issue |
Willoughby–Hoye Python Scripts A-D (RRID:SCR_017562) | software application, software resource, data analysis software, data processing software | Software tool as scripts for calculating NMR chemical shifts. Warning - this group of Python scripts used to process NMR data, described in Willoughby et al, 2014, has been found to contain bug. Please see PMID:31591889. | Python, NMR, script, caluclating, chemical, shift, data | NIA R01 AG039468 | PMID:24556787 PMID:31591889 |
Free, Freely available | SCR_017562 | 2026-07-28 09:44:35 | 1 | |||||||||
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ISB Cancer Genomics Cloud Resource Report Resource Website 1+ mentions |
ISB Cancer Genomics Cloud (RRID:SCR_017681) | ISB-CGC | service resource, web application, data repository, software resource, storage service resource | Web tool as flexible cloud-based platform for cancer genomics research. Platform that serves as large-scale repository and provides computational infrastructure necessary to carry out cancer genomics research at unprecedented scales. ISB-CGC is providing access to TCGA data and computation on Google Cloud Platform. | Cancer, genomics, repository, data | National Cancer Institute ; National Institutes of Health |
PMID:29092928 | Restricted | SCR_017681 | ISB Cancer Genomics Cloud, Institute for Systems Biology Cancer Genomics Cloud | 2026-07-28 09:44:36 | 9 | |||||||
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GADMA Resource Report Resource Website 1+ mentions |
GADMA (RRID:SCR_017680) | GADMA | software application, software resource, data analysis software, data processing software | Software tool to implement methods for automatic inferring joint demographic history of multiple populations from genetic data. Genetic algorithm for inferring demographic history of multiple populations from allele frequency spectrum data. | Inferring, demographic, history, population, genetic, data, allele, frequency, spectrum, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
DOI:10.1101/407734 | Free, Available for download, Freely available | biotools:GADMA | https://bio.tools/GADMA | SCR_017680 | Genetic Algorithm for Demographic Model Analysis | 2026-07-28 09:44:32 | 3 | |||||
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shinyGEO Resource Report Resource Website |
shinyGEO (RRID:SCR_017605) | service resource, web application, software resource, production service resource, analysis service resource | Web based tool to download gene expression datasets from GEO in order to perform differential expression and survival analysis for gene of interest. Produces publication ready graphics and generates R code ensuring that all analyses are reproducible. Web based application for analyzing gene expression omnibus datasets. | Gene, expression, dataset, GEO, differencial, analysis, gene, graphic, omnibus, data, bio.tools |
uses: Shiny is listed by: Debian is listed by: bio.tools has parent organization: Eastern Connecticut State University; Connecticut; United States works with: Gene Expression Omnibus (GEO) |
Google Summer of Code | PMID:27503226 | Free, Available for download, Freely available | biotools:shinygeo | https://gdancik.github.io/shinyGEO/, https://bio.tools/shinygeo | SCR_017605 | 2026-07-28 09:44:31 | 0 | ||||||
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SciGraph Resource Report Resource Website 1+ mentions |
SciGraph (RRID:SCR_017576) | software application, software resource, data processing software, data visualization software, standalone software | Software tool to represent ontologies and data described using ontologies as Neo4j graph. Ontology serving middleware tool using Neo4J as base server, able to ingest ttl files, and serve them to quickly create services that can underpin autocomplete, term lookup and tree traversal. | Ontology, data, Neo4j graph, server, ttl, file |
is used by: SPARC Portal is used by: SciCrunch is used by: CINERGI is used by: Human Brain Project |
Free, Available for download, Freely available | SCR_017576 | 2026-07-28 09:44:31 | 3 | ||||||||||
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PoloPlus USB Drive software Resource Report Resource Website 10+ mentions |
PoloPlus USB Drive software (RRID:SCR_017614) | software application, software resource, data analysis software, data processing software | Software to perform Probit and Logit analsis with grouped data. Original Polo Software available through USB Drive. Able to work on all versions of Windows as all files are kept on USB. | LeOra Software LLC, grouped, data, analysis, USB, drive, probit, logit | Restricted | SCR_017614 | Probit Or LOgit Plus USB Drive, PoloPlus USB Drive | 2026-07-28 09:44:31 | 35 | ||||||||||
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StatPackets Resource Report Resource Website |
StatPackets (RRID:SCR_017613) | data or information resource, narrative resource, standard specification | Standardized method to export statistical data, associated with KOMP project. Standard way to keep data and results of analyzing that data together. | Standardized, method, export, statistical, data, KOMP, result, analysis, together | is related to: Knockout Mouse Project | Free, Freely available | SCR_017613 | 2026-07-28 09:44:39 | 0 | ||||||||||
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EBRAINS Knowledge Graph Resource Report Resource Website 1+ mentions |
EBRAINS Knowledge Graph (RRID:SCR_017612) | software application, service resource, data or information resource, database, software resource, data management software | Metadata management system built for EBRAINS. Multi modal metadata store which brings together information from different areas of Human Brain Project as well as from external partners. Graph database tracks linkage between experimental data and neuroscientific data science supporting more extensive data reuse and complex computational research.Supports rich terminologies, ontologies and controlled vocabularies. Built by design to support iterative elaborations of common standards and supports these by probabilistic suggestion and review systems. | Metadata, managing, system, neuroscience, experimental, data, human, brain, graph, database, terminology, ontology |
is related to: Human Brain Project is related to: MarmotGraph |
European Union’s Horizon 2020 Framework Programme for Research and Innovation 720270; European Union’s Horizon 2020 Framework Programme for Research and Innovation 785907 |
Free, Freely available | https://kg.humanbrainproject.eu/ | SCR_017612 | New Enabling Infrastructure for Neuroscience Knowledge Graph, EBRAINS Knowledge Graph (KG), HBP Knowledge Graph | 2026-07-28 09:44:35 | 8 | |||||||
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Project DARE Resource Report Resource Website |
Project DARE (RRID:SCR_017538) | DARE | project portal, data or information resource, organization portal, consortium, portal | EU data infrastructure with workflow connectivity layer. Common Workflow Language. Project pioneers methodologies and integrated set of supporting technologies that will transform European RIs productivity and rate of innovation when three challenges – extreme data, extreme computation and extreme complexity – are faced simultaneously. | European Union, infrastructure, workflow, connectivity, layer, methodology, integrated, data, Agile | European Union | SCR_017538 | project-dare, Delivering Agile Research Excellence on European e-Infrastructures | 2026-07-28 09:44:31 | 0 | |||||||||
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Worm Lab Resource Report Resource Website 1+ mentions |
Worm Lab (RRID:SCR_017669) | software application, software resource, data analysis software, data processing software | Software tool for imaging, tracking, and analyzing C. elegans and other nematodes. It has user friendly software interface with patented model specific tracking algorithm that collects data about single worm or multiple worms, even through omega bends, coiling, reversals, and entanglements. Provides quantitative analysis of locomotory behavior with user configurable metrics for crawling and swimming assays. | MBF Bioscience, imaging, tracking, analysis, C.elegans, nematode, collect, data, worm, omega, bend, coiling, reversal, entanglement, locomotry, behavior, crawling, swimming, assay | Restricted | SCR_017669 | 2026-07-28 09:44:39 | 8 | |||||||||||
|
Single Cell Developmental Database Resource Report Resource Website 1+ mentions |
Single Cell Developmental Database (RRID:SCR_017546) | SCDevDB | service resource, data set, data or information resource, data repository, database, storage service resource | Database for insights into single cell gene expression profiles during human developmental processes. Interactive database provides DE gene lists in each developmental pathway, t-SNE map, and GO and KEGG enrichment analysis based on these differential genes. | Single, cell, gene, expression, profile, human, development, process, data | RGC General Research Fund ; GRF Research Project |
DOI:10.3389/fgene.2019.00903 | Free, Available for download, Freely available | SCR_017546 | Single-Cell Developmental Database | 2026-07-28 09:44:35 | 2 | |||||||
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Transcriptive Resource Report Resource Website |
Transcriptive (RRID:SCR_017545) | software application, data analysis software, software resource, data processing software, software toolkit | Software tool as bioinformatics analysis pipeline used for RNA sequencing data. Workflow processes raw data from FastQ inputs, aligns reads, generates gene and transcript counts, and performs quality control on results. | Analysis, pipeline, RNA, sequencing, data, raw, FastQ, input, align, read, gene, transcript, count, quality, control | Free, Available for download, Freely available | SCR_017545 | 2026-07-28 09:44:31 | 0 | |||||||||||
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fineSTRUCTURE Resource Report Resource Website 10+ mentions |
fineSTRUCTURE (RRID:SCR_018170) | software application, software resource, data analysis software, data processing software | Software tool as algorithm for identifying population structure using dense sequencing data. Can perform model based Bayesian clustering on large datasets, including full resequencing data. | Identifying population structure, dense sequencing data, Bayesian clustering, large dataset, data, analysis, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:finestructure | https://bio.tools/finestructure | SCR_018170 | FineSTRUCTURE version 2 | 2026-07-28 09:44:51 | 23 | |||||||
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ChiCMaxima Resource Report Resource Website 1+ mentions |
ChiCMaxima (RRID:SCR_018178) | service resource, data access protocol, software resource, production service resource, web service, analysis service resource | Pipeline for analyzing and identificantion of chromatin loops in CHi-C promoters data. Used to capture Hi-C visualization and interaction calling. | Chromatin loop, CHi-C promoter, data, Hi-C visualization, interaction calling, data, analysis, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:31118054 | Free, Freely available | biotools:ChiCMaxima | https://bio.tools/ChiCMaxima | SCR_018178 | 2026-07-28 09:44:38 | 2 | |||||||
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SpydrPick Resource Report Resource Website 1+ mentions |
SpydrPick (RRID:SCR_018176) | software application, software resource, data analysis software, data processing software | Software command line tool for performing direct coupling analysis of aligned categorical datasets. Used for analysis at scale of pan genomes of many bacteria. Incorporates correction for population structure, which adjusts for phylogenetic signal in data without requiring explicit phylogenetic tree. | Direct coupling analysis, aligned categorical datasets, analysis, genome, bacteria, phylogenetic signal, correction, phylogenetic tree, data, bio.tools |
is listed by: Debian is listed by: bio.tools |
COIN Center of Excellence ; Academy of Finland ; Wellcome Trust ; European Research Council |
PMID:31361894 | Free, Available for download, Freely available | biotools:SpydrPick | https://anaconda.org/bioconda/spydrpick, https://bio.tools/SpydrPick | SCR_018176 | 2026-07-28 09:44:51 | 2 | ||||||
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MaxTRAQ Resource Report Resource Website 1+ mentions |
MaxTRAQ (RRID:SCR_018188) | software application, software resource, data analysis software, data processing software | Software package for motion capture analysis by Innovision Systems Inc. | Motion capture, analysis, data, data tracking, Innovision Systems Inc. | Restricted | SCR_018188 | Innovision Systems MaxTRAQ software | 2026-07-28 09:44:42 | 1 | ||||||||||
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NeMO Analytics Resource Report Resource Website 10+ mentions |
NeMO Analytics (RRID:SCR_018164) | service resource, data or information resource, data analysis service, production service resource, analysis service resource, topical portal, portal | Portal enabling web based visualization and analysis of multi omic data describing cell types in developing and adult brain, powered by gEAR and EpiViz. Release 1 on April 2019 includes single cell and bulk tissue RNAseq, ATACseq, and ChIPseq from fetal human prefrontal cortex, as well as from stem cell models of neural induction. Portal will expand to include multiple regions of developing and adult brain and additional analytical tools. | Visualization, analysis, multi omic data, cell type, developing brain, adult brain, RNAseq, ATACseq, CHIPseq, fetal human prefrontal cortex, stem cell, neural induction, brain, data |
is used by: BICCN is related to: NeMOarchive is related to: BRAIN Initiative is related to: Brainome portal is related to: BRAIN Initiative Cell Atlas Network |
Free, Freely available | SCR_018244 | SCR_018164 | Neuroscience Multi-Omic Analytics | 2026-07-28 09:44:42 | 13 | ||||||||
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Database of Immune Cell Epigenomes Resource Report Resource Website 50+ mentions |
Database of Immune Cell Epigenomes (RRID:SCR_018259) | DICE | data or information resource, database, data access protocol, software resource, web service | Database of Immune Cell Expression, Expression quantitative trait loci (eQTLs) and Epigenomics. Collection of identified cis-eQTLs for 12,254 unique genes, which represent 61% of all protein-coding genes expressed in human cell types. Datasets to help reveal effects of disease risk associated genetic polymorphisms on specific immune cell types, providing mechanistic insights into how they might influence pathogenesis. | Data set, immune cell expression, expression quantitative trait loci, epigenomics, data, cis-eQLC, gene, protein coding gene, human cell type, genetic polymorphism disease, immune cell, pathogenesis | has parent organization: La Jolla Institute for Immunology | William K. Bowes Jr Foundation ; NIAID R24 AI108564; NCRR S10 RR027366; NIH Office of the Director S10 OD016262 |
PMID:30449622 | Free, Freely available | SCR_018259 | Database of Immune Cell Expression, Expression quantitative trait loci (eQTLs) and Epigenomics | 2026-07-28 09:44:39 | 59 | ||||||
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syGlass Resource Report Resource Website 10+ mentions |
syGlass (RRID:SCR_017961) | software application, data analysis software, software resource, data processing software, data visualization software | Software visualization tool for direct volume rendering with no segmentation required. Enables users to view, annotate and analyze 3D data in VR. Data visualization and annotation system that allows rendering of large, volumetric data in its true, three- or four-dimensional form. | Direct, volume, rendering, no segmentation, view, analyze, annotate, 3D, data, large, volumetric, IstoVisio, Inc | Commercially available | SCR_017961 | 2026-07-28 09:44:36 | 16 | |||||||||||
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SonarCloud Vulnerable Code Prospector for C Resource Report Resource Website |
SonarCloud Vulnerable Code Prospector for C (RRID:SCR_018011) | SVCP4C | service resource, data set, data or information resource, data repository, storage service resource | Software tool to collect vulnerable source code from open-source repositories linked to SonarCloud. Dataset repository with tagged files with BufferOverflow features associated to source code repositories publicly available. | Repository, SonarCloud, data, dataset, BufferOverflow | DOI:10.3390/app10041270 | Free, Available for download, Freely available | SCR_018011 | SonarCloud Vulnerable Code Prospector for C, SVCP4CDataset | 2026-07-28 09:44:49 | 0 |
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