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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Astrophysics Source Code Library Resource Report Resource Website 1+ mentions |
Astrophysics Source Code Library (RRID:SCR_017604) | ASCL | software repository, software resource | Registry for source codes of interest to astronomers and astrophysicists, including solar system astronomers, and lists codes that have been used in research that has appeared in, or been submitted to, peer-reviewed publications. ASCL is indexed by SAO/NASA Astrophysics Data System (ADS) and Web of Science and is citable by using unique ascl ID assigned to each code. The ascl ID can be used to link to the code entry by prefacing the number with ascl.net . | Sorce, code, astronomer, astrophysicist, data, list, publication | Free, Freely available | SCR_017604 | 2026-09-19 12:58:16 | 2 | ||||||||||
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BVA import/export EEGLAB plugin Resource Report Resource Website 1+ mentions |
BVA import/export EEGLAB plugin (RRID:SCR_016333) | bva-io | software application, software resource, software toolkit | Software package for interfacing the Brain Vision Analyser data files (load/save) for ongoing development of Matlab routines . This package is also compatible with the EEGLAB software, and may be uncompressed in the plugin folder of this software. | interfacing, brain, vision, analyser, data, file, load, save, Matlab, routine, compatible, EEGLAB |
is related to: SourceForge is related to: EEGLAB is related to: MATLAB |
Free, Available for download, Freely available | SCR_016333 | Brain Vision Analyser | 2026-09-19 12:58:14 | 4 | ||||||||
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Scrattch.Hicat Resource Report Resource Website 10+ mentions |
Scrattch.Hicat (RRID:SCR_018099) | data analytics software, software application, software resource | Software R package as hierarchical, iterative clustering for analysis of transcriptomics data.Used for single cell RNA-seq analysis for transcriptomic type characterization from Allen Institute. | Hierarchical, iterative clustering, analysis, transcriptomics, data, single cell RNAseq, Allen Institute | has parent organization: Allen Institute | Free, Available for download, Freely available | SCR_018099 | Scrattch Hierarchical, Iterative Clustering for Analysis of Transcriptomics | 2026-09-19 12:58:16 | 32 | |||||||||
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clustLasso Resource Report Resource Website 1+ mentions |
clustLasso (RRID:SCR_018820) | software resource, software toolkit | Software R package to build predictive signatures of microbial phenotypes. Software package implementing cluster lasso approach. | Predictive signatures, microbial phenotype, cluster lasso approach, build predictive signature, phenotype, data, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Freely available | biotools:clustlasso | https://bio.tools/clustlasso | SCR_018820 | 2026-09-19 12:58:17 | 1 | ||||||||
|
ODDPub Resource Report Resource Website 1+ mentions |
ODDPub (RRID:SCR_018385) | algorithm resource, software resource | Text mining algorithm to screen biomedical publications to find data sharing statements. Algorithm that parses set of publications and detects which publications disseminated Open Data or Open Code together with publication. Tailored towards biomedical literature. | Text mining, biomedical publication screening, data sharing statement detection, open data, open code, publication, data, biomedical literature, Berlin Institute of Health, ASWG | is used by: rtransparent | Free, Available for download, Freely available | SCR_018385 | 2026-09-19 12:58:16 | 6 | ||||||||||
|
SCENIC Resource Report Resource Website 100+ mentions |
SCENIC (RRID:SCR_017247) | data processing software, software application, software resource | Software R package as single cell regulatory network inference and clustering. Used for simultaneous gene regulatory network reconstruction and cell state identification from single cell RNA-seq data. | single, cell, regulatory, network, inference, clustering, simultaneous, gene, reconstruction, single, RNA-seq, data | ERC Consolidator Grant ; Foundation Against Cancer ; Special Research Fund (BOF) KU Leuven ; The Research Foundation - Flanders |
PMID:28991892 | Free, Available for download, Freely available | https://aertslab.org/#scenic | SCR_017247 | 2026-09-19 12:56:07 | 161 | ||||||||
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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) | 2026-09-19 12:56:07 | 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 | 2026-09-19 12:56:06 | 14 | |||||||||||
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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 | 2026-09-19 12:56:06 | 2 | |||||||||||
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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 | 2026-09-19 12:56:07 | 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 | 2026-09-19 12:56:07 | 26 | ||||||
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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 | 2026-09-19 12:56:06 | 1 | |||||||||
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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 | 2026-09-19 12:56:06 | 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 | 2026-09-19 12:56:06 | 88 | ||||||||||
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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 | 2026-09-19 12:56:06 | 4 | ||||||
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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 | 2026-09-19 12:56:05 | 1 | |||||||
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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 | 2026-09-19 12:56:06 | 1 | ||||||||||
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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 | 2026-09-19 12:56:05 | 4 | |||||||||
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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 | 2026-09-19 12:56:06 | 9 | ||||||||
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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 | 2026-09-19 12:56:06 | 11 |
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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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