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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Secure Access to Research Data and E-Infrastructure Resource Report Resource Website 10+ mentions |
Secure Access to Research Data and E-Infrastructure (RRID:SCR_017246) | SAFE | data or information resource, portal, project portal | Platform for Secure Access to Research Data and E-Infrastructure based on European Standards for Health Case information. Used for secure processing of sensitive personal data in research in health and care sector. | secure, access, data, Europe, processing, sensitive, personal, health, standard, e infrastructure | has parent organization: University of Bergen; Bergen; Norway | Restricted | https://it.uib.no/ithjelp/images/b/b2/SAFE_E_-_For_decision_makers.pdf | SCR_017246 | Safe, SAFE, Secure Access to Research Data and E-Infrastructure, Secure Access to Research Data and E-Infrastructure (EUROPE) | 2026-09-12 01:01:05 | 10 | |||||||
|
LipidView Software Resource Report Resource Website 10+ mentions |
LipidView Software (RRID:SCR_017003) | data processing software, software application, software resource | Software tool for molecular characterization and quantification of lipid species from electrospray mass spectrometry data. Enables lipid profiling by searching parent and fragment ion masses against lipid fragment database and reports numerical and graphical output for various lipid molecular species, lipid classes, fatty acids, and long chain bases. | SCIEX, molecular, characterization, quantification, lipid, electrospray, mass, spectrometry, data | Commercially available, Free trial available | SCR_017003 | 2026-09-12 01:01:05 | 14 | |||||||||||
|
DamMet Resource Report Resource Website 1+ mentions |
DamMet (RRID:SCR_016959) | data processing software, service resource, software application, software resource | Software tool as a full probabilistic model for mapping ancient methylomes using sequencing data underlying an ancient specimen. | mapping, sequencing, data, ancient, speciment, DNA, methylation | Free, Freely available, Tutorial available | SCR_016959 | 2026-09-12 01:01:05 | 2 | |||||||||||
|
stop-signal task resources Resource Report Resource Website 1+ mentions |
stop-signal task resources (RRID:SCR_017137) | data or information resource, portal, project portal | Open source resources to execute stop signal task and analyze resulting data. Simulation code is provided, and can be used in planning stage for investigation of response inhibition and impuls control. | stop, signal, task, analyze, data, response, inhibition, impuls, control | has parent organization: Ghent University; Ghent; Belgium | Free, Restricted | SCR_017137 | 2026-09-12 01:01:05 | 1 | ||||||||||
|
BIDS Validator Resource Report Resource Website 10+ mentions |
BIDS Validator (RRID:SCR_017255) | data processing software, software application, software resource | Software validation tool that checks submitted folder structure for compliance to BIDS data standard. Validates Brain Imaging Data Structure. | BIDS, NeuroImaging, Neuroscience, check, folder, structure, compliance, data, standard, brain, imaging | is listed by: OMICtools | Laura and John Arnold Foundation ; NIBIB R01 EB020740 |
PMID:28278228 | Free, Available for download, Freely available | http://bids-standard.github.io/bids-validator/ | SCR_017255 | Brain Imaging Data Structure (BIDS) Validator | 2026-09-12 01:01:05 | 26 | ||||||
|
Digital Expression Explorer 2 Docker Image Resource Report Resource Website 1+ mentions |
Digital Expression Explorer 2 Docker Image (RRID:SCR_016931) | data processing software, software application, software resource | Docker image that is used to process all of the data present in the Digital Expression Explorer 2 dataset. It can be freely used by anyone to process data on NCBI SRA or process their own RNA-seq fastq files. Used for bulk reprocessing of public RNA-seq data from SRA. The pipeline tallies the reads assigned to each gene or transcript. | transcriptome, pipeline, bulk, reprocess, public, RNAseq, data, SRA, gene, read |
is related to: Digital Expression Explorer 2 Project is related to: Digital Expression Explorer 2 Source Code |
DOI:10.5281/zenodo.1561840 | Free, Registration required | SCR_016931 | 2026-09-12 01:01:05 | 1 | |||||||||
|
mirDIP Resource Report Resource Website 100+ mentions |
mirDIP (RRID:SCR_016770) | data or information resource, database, portal | microRNA data integration portal to find microRNAs that target a gene, or genes targeted by a microRNA, in Homo sapiens. Software to integrate prediction databases to elucidate accurate microRNA:target relationships. Used for human microRNA prediction studies. | data, integral, portal, DIP, collect, predict, microRNA, gene, human | Canada Foundation for Innovation ; Canadian Cancer Society Research Institute ; Krembil Foundation ; Natural Sciences Research Council ; Ontario Research Fund |
PMID:29194489 | Free, Download available, Freely available, email address required to download, Acknowledgement requested | SCR_016770 | mirDIP 4.1, mirDIP, microRNA Data Integration Portal | 2026-09-12 01:01:04 | 229 | ||||||||
|
Maestro Resource Report Resource Website 50+ mentions |
Maestro (RRID:SCR_016748) | data or information resource, portal | Software tool for all purpose molecular modeling environment. Maestro is the portal to all of Schrödinger's computational technology. Helps researchers organize and analyze data. | molecular, modeling, environment, computation, data, analyze, organize |
is listed by: SoftCite has parent organization: Schrodinger |
Commercially available, Trial available | SCR_016748 | 2026-09-12 01:01:04 | 88 | ||||||||||
|
rnaQUAST Resource Report Resource Website 1+ mentions |
rnaQUAST (RRID:SCR_016994) | data processing software, software application, software resource | Software tool for evaluating RNA-Seq assembly quality and benchmarking transcriptome assemblers using reference genome and gene database. Capable to estimate gene database coverage by raw reads and de novo quality assessment using third party software. | evaluation, quality, RNA-Seq, assembly, data, transcriptome, assembler, reference, genome, gene, database, raw, read, , bio.tools |
uses: BUSCO is listed by: Debian is listed by: bio.tools is related to: rnaSPAdes is related to: Python Programming Language is related to: SPAdes |
EMC Research and Development Department ; St. Petersburg State University ; Russia |
PMID:27153654 | Free, Available for download, Freely available | biotools:rnaQUASt | https://bio.tools/rnaQUAST | SCR_016994 | 2026-09-12 01:01:05 | 4 | ||||||
|
brainlife.io Resource Report Resource Website 1+ mentions |
brainlife.io (RRID:SCR_016513) | data or information resource, portal | Platform for publishing reproducible code and datasets and providing access to national supercomputers, private clouds, and institutional high-performance computer systems to promote open software and data sharing to advance understanding of the human brain. | human, brain, life, data, application, technology, share, open, software, reproducible, code, dataset, |
has parent organization: Indiana University Bloomington; Indiana; USA works with: brainlife |
NSF BCS 1734853; NSF IIS 1636893 |
DOI:10.1038/s41597-019-0073-y | Public, Free, Freely available, Login required | https://github.com/brain-life | SCR_016513 | 2026-09-12 01:01:04 | 1 | |||||||
|
datastorr Resource Report Resource Website 1+ mentions |
datastorr (RRID:SCR_017040) | data processing software, software application, software resource | Software package for simple data retrieval and versioning. | simple, data, retrieval, versioning | Free, Available for download, Freely available | http://ropenscilabs.github.io/datastorr/ | SCR_017040 | 2026-09-12 01:01:05 | 1 | ||||||||||
|
Open Knowledge Maps Resource Report Resource Website 1+ mentions |
Open Knowledge Maps (RRID:SCR_016470) | data or information resource, database, organization portal, portal | Software tool as an open source knowledge mapping software that increases the visibility of research findings for science and society. Visual interface to the world's scientific knowledge. | knowledge, mapping, visual, interface, visibility, research, finding, data, science, public, explore, discover, digital, ecosystem | the Austrian Federal Ministry of Economy ; Family and Youth ; the Austrian Federal Ministry of Transport ; Innovation and Technology ; the State of Styria |
Free, Public, Freely available | https://github.com/OpenKnowledgeMaps/Headstart, https://github.com/OpenKnowledgeMaps | SCR_016470 | 2026-09-12 01:01:04 | 4 | |||||||||
|
Whole Genome Shotgun (WGS) Project Resource Report Resource Website 1+ mentions |
Whole Genome Shotgun (WGS) Project (RRID:SCR_016637) | WGS | data processing software, software application, software resource | Project for assemblies of incomplete genomes or incomplete chromosomes of prokaryotes or eukaryotes that are being sequenced by a whole genome shotgun strategy. WGS projects may be annotated, but annotation is not required. The nucleotide and protein data from all WGS projects go into the BLAST database. | assembly, incomplete, chromosome, prokaryote, eukaryote, sequenced, whole, genome, shot, gun, strategy, data |
has parent organization: NCBI works with: NCBI BLAST |
National Library of Medicine | SCR_016637 | Whole Genome Shotgun WGS Project, Whole Genome Shotgun WGS, WGS Projects, Whole Genome Shotgun | 2026-09-12 01:01:04 | 9 | ||||||||
|
tbl2asn Resource Report Resource Website 10+ mentions |
tbl2asn (RRID:SCR_016636) | data processing software, software application, software resource | Software tool as a command-line program that automates the creation of sequence records for submission to GenBank. Records need no additional manual editing before submission. | command, line, program, automate, creation, sequence, record, submit, data, GenBank | has parent organization: NCBI | Free, Freely available | SCR_016636 | 2026-09-12 01:01:04 | 11 | ||||||||||
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ReproNim: A Center for Reproducible Neuroimaging Computation Resource Report Resource Website 10+ mentions |
ReproNim: A Center for Reproducible Neuroimaging Computation (RRID:SCR_016001) | ReproNim | data or information resource, organization portal, portal | Center to help neuroimaging researchers to find and share data in FAIR fashion, to describe their data and analysis workflows in replicable fashion, to manage their computational resource options so that outcomes of neuroimaging research are more reproducible. | Neuroimaging, share, data, FAIR, analysis, manage, reproducible |
is related to: ABCD-ReproNim Course is related to: SVNTest is parent organization of: ReproIn: The ReproNim image input management system (featuring DataLad) |
NIBIB P41 EB019936 | Restricted | SCR_016005 | http://repronim.org | SCR_016001 | 2026-09-12 01:01:04 | 16 | ||||||
|
Oufti Resource Report Resource Website 10+ mentions |
Oufti (RRID:SCR_016244) | data processing software, image analysis software, software application, software resource | Software designed for analysis of microscopy data. It performs sub-pixel precision detection, quantification of cells and fluorescence signals, as well as other image analysis functions. | microscopy, data, imaging, image, analysis, pixel, fluorescent, bio.tools |
is listed by: Debian is listed by: bio.tools |
NIGMS R01 GM065835 | PMID:26538279 | biotools:oufti | https://bio.tools/oufti | SCR_016244 | outfi | 2026-09-12 01:01:04 | 15 | ||||||
|
Porechop Resource Report Resource Website 1000+ mentions |
Porechop (RRID:SCR_016967) | data processing software, software application, software resource | Software tool for finding and removing adapters from Oxford Nanopore reads. | finding, removing, adapter, Oxford Nanopore, read, sequencing, data |
is listed by: Debian is listed by: OMICtools |
Free, Available for download, Freely available | OMICS_17306 | https://sources.debian.org/src/porechop/ | SCR_016967 | 2026-09-12 01:01:05 | 1350 | ||||||||
|
PopMedNet Resource Report Resource Website 1+ mentions |
PopMedNet (RRID:SCR_016456) | PopMedNet | data or information resource, portal | Software as an open source informatics platform to facilitate the implementation and operation of distributed health data networks. Consists of a web-based portal for distributing requests and administering the network, and the DataMart Client. Designed by the Therapeutics Research and Infectious Disease Epidemiology (TIDE) group at the Department of Population Medicine (DPM) of the Harvard Pilgrim Health Care Institute (HPHCI) to enable creation, operation, and governance of distributed health data networks. | implement, distribute, health, data, network, research, coordinate, center, governance, | has parent organization: Harvard Medical School; Massachusetts; USA | NIH DRN ; the HHS Assistant Secretary for Planning and Evaluation ; The National Institutes of Health |
PMID:27141522 | Free, Available for download, Freely available | https://github.com/PopMedNet-Team/popmednet | SCR_016456 | Population Medicine Network | 2026-09-12 01:01:04 | 3 | |||||
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glmmADMB Resource Report Resource Website 1+ mentions |
glmmADMB (RRID:SCR_016859) | data processing software, software application, software resource | Software R package for fitting generalized linear mixed models (GLMMs) using AD Model Builder. Fits mixed-effects models to count data using Poisson or negative binomial response distributions. | generalized, linear, mixed, model, ADMB, count, data, Poisson, negative, binominal, distribution |
uses: AD Model Builder is related to: R Project for Statistical Computing |
Free, Available for download, Freely available | http://r-forge.r-project.org/projects/glmmadmb/ | SCR_016859 | glmm AD Model Builder, generalized linear mixed models using AD Model Builder, generalized linear mixed models using ADMB | 2026-09-12 01:01:04 | 3 | ||||||||
|
cryoSPARC Resource Report Resource Website 1000+ mentions |
cryoSPARC (RRID:SCR_016501) | data processing software, image analysis software, software application, software resource | Software integrated platform used for obtaining 3D structural information from single particle cryo-EM data. Enables automated, high quality and high-throughput structure discovery of proteins, viruses and molecular complexes for research and drug discovery. | Structura Biotechnology Inc., data, processing, analysis, image, single, particle, cryo-EM, structure, discovery, automated, protein, virus, molecular, complex | is related to: University of Toronto; Ontario; Canada | PMID:28165473 | Available free of charge for academic users with a valid institutional email address, Trail available | SCR_016501 | 2026-09-12 01:01:04 | 2939 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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