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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Duke University Medical Center Neuropsychiatric Imaging Research Laboratory Resource Report Resource Website 1+ mentions |
Duke University Medical Center Neuropsychiatric Imaging Research Laboratory (RRID:SCR_007124) | data or information resource, organization portal, portal | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. Neuropsychiatric Imaging Research Laboratory (NIRL) analyze magnetic resonance images to research numerous psychiatric disorders including depression, bipolar disorder, and post traumatic stress disorder. NIRL also develop new methods for MR image processing to improve quality and reliability of research in the field of neuroimaging. The laboratory computer resources include Sun MicroSystems SPARC workstations, Windows PCs, over 3 terabytes of online hard disk space, and a web server system. The lab has a site filtered anonymous ftp server system for data transfer. There are individual offices for visiting fellows and analysts for image processing as well as shared work-study rooms and conference facilities. | allele, antioxidant, apolipoprotein-e, biomedical, bipolar, child, cognitive, data, depression, disorder, geriatric, hard disk, hiv, imaging, impairment, infection, magnetic resonance, magnetic resonance image, marijuana, mri, neurobiology, neurofibromatosis, neurological, neuropsychiatric, neuroscience, post traumatic stress disorder, prognostic, psychiatric, ptsd, research, server, terabyte, vascular, neuroimaging | has parent organization: Duke University; North Carolina; USA | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10212 | http://nirlweb.mc.duke.edu/ | SCR_007124 | DMC NIRL | 2026-02-14 02:05:27 | 1 | |||||||
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Human Microbiome Project Resource Report Resource Website 100+ mentions |
Human Microbiome Project (RRID:SCR_012956) | HMP, NIH HMP, HMP1 | data or information resource, portal, project portal | NIH Project to generate resources to characterize the human microbiota and to analyze its role in human health and disease at several different sites on the human body, including nasal passages, oral cavities, skin, gastrointestinal tract, and urogenital tract using metagenomic and traditional approach to genomic DNA sequencing studies.HMP was supported by the Common Fund from 2007 to 2016. | generate, resource, human, body, microbiota, analyze, health, disease, metagenomic, DNA, sequesncing, data |
lists: Pathogen Portal lists: DNACLUST lists: QIIME lists: mothur lists: Greengenes lists: Ribosomal Database Project lists: DeconSeq lists: FragGeneScan lists: MetAMOS lists: MetaPhlAn lists: MetaPhyler lists: METAREP lists: PRINSEQ lists: TagCleaner lists: BioCyc lists: MG-RAST lists: Core Gene Evaluation Script lists: IMG System lists: RAST Server lists: GINGKO lists: inVUE lists: LEfSe lists: Metastats lists: MicrobiomeUtilities lists: Hypothesis Testing and Power Calculations for Comparing Metagenomic Samples from HMP lists: HMPTrees lists: Simrank lists: speciateIT lists: Unifrac lists: Fast-Unifrac lists: SitePainter lists: BMTagger lists: HUMAnN lists: Metapath lists: IMG System is related to: biobakery is related to: Integrative Human Microbiome Project is related to: MicrobiomeDB has parent organization: National Institutes of Health is parent organization of: HMP Data Analysis and Coordination Center |
NIH | nif-0000-25316 | https://www.hmpdacc.org/ihmp/ https://www.hmpdacc.org/hmp |
http://nihroadmap.nih.gov/hmp/ | SCR_012956 | Human Microbiome Project, NIH HMP, HMP1, HMP, NIH Human Microbiome Project | 2026-02-14 02:05:29 | 385 | |||||
|
Trimmomatic Resource Report Resource Website 10000+ mentions |
Trimmomatic (RRID:SCR_011848) | Trimmomatic | software resource, data processing software, software application | Software Java pipeline for trimming tasks for Illumina paired end and single ended data. Flexible Trimmer for Illumina Sequence Data. Pair aware preprocessing tool optimized for Illumina next generation sequencing data. Includes several processing steps for read trimming and filtering. Operating systems Unix/Linux, Mac OS, Windows. | trimming, task, paired, end, single, data, next, generation, sequencing, filtering, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: shovill |
BLE/BMELV Verbundprojekt ; BMBF |
PMID:24695404 DOI:10.1093/bioinformatics/btu170 |
biotools:trimmomatic, OMICS_01097 | https://omictools.com/trimmomatic-tool https://bio.tools/trimmomatic https://sources.debian.org/src/trimmomatic/ |
SCR_011848 | Trimmomatic v 0.32 | 2026-02-14 02:05:32 | 21028 | |||||
|
SCENIC Resource Report Resource Website 100+ mentions |
SCENIC (RRID:SCR_017247) | software resource, data processing software, software application | 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 | The Research Foundation - Flanders ; Special Research Fund (BOF) KU Leuven ; Foundation Against Cancer ; ERC Consolidator Grant |
PMID:28991892 | Free, Available for download, Freely available | https://aertslab.org/#scenic | SCR_017247 | 2026-02-14 02:05:15 | 134 | ||||||||
|
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) | 2026-02-14 02:05:41 | 10 | |||||||
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LipidView Software Resource Report Resource Website 10+ mentions |
LipidView Software (RRID:SCR_017003) | software resource, data processing software, software application | 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 | 2026-02-14 02:05:15 | 14 | |||||||||||
|
DamMet Resource Report Resource Website 1+ mentions |
DamMet (RRID:SCR_016959) | data processing software, software resource, service resource, software application | 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 | 2026-02-14 02:05:15 | 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 | 2026-02-14 02:05:41 | 1 | ||||||||||
|
BIDS Validator Resource Report Resource Website 10+ mentions |
BIDS Validator (RRID:SCR_017255) | software resource, data processing software, software application | 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 | 2026-02-14 02:05:38 | 20 | ||||||
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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) | software resource, data processing software, software application | 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 | 2026-02-14 02:05:40 | 1 | |||||||||
|
mirDIP Resource Report Resource Website 100+ mentions |
mirDIP (RRID:SCR_016770) | data or information resource, portal, database | 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 | Krembil Foundation ; Ontario Research Fund ; Canadian Cancer Society Research Institute ; Natural Sciences Research Council ; Canada Foundation for Innovation |
PMID:29194489 | Free, Download available, Freely available, email address required to download, Acknowledgement requested | SCR_016770 | mirDIP 4.1, mirDIP, microRNA Data Integration Portal | 2026-02-14 02:05:37 | 187 | ||||||||
|
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 | 2026-02-14 02:05:15 | 79 | ||||||||||
|
rnaQUAST Resource Report Resource Website 1+ mentions |
rnaQUAST (RRID:SCR_016994) | software resource, data processing software, software application | 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 | 2026-02-14 02:05:34 | 3 | ||||||
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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 | 2026-02-14 02:05:40 | 1 | |||||||
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datastorr Resource Report Resource Website 1+ mentions |
datastorr (RRID:SCR_017040) | software resource, data processing software, software application | 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 | 2026-02-14 02:05:38 | 1 | ||||||||||
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Open Knowledge Maps Resource Report Resource Website 1+ mentions |
Open Knowledge Maps (RRID:SCR_016470) | data or information resource, organization portal, portal, database | 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 Transport ; Innovation and Technology ; the Austrian Federal Ministry of Economy ; Family and Youth ; the State of Styria |
Free, Public, Freely available | https://github.com/OpenKnowledgeMaps/Headstart https://github.com/OpenKnowledgeMaps |
SCR_016470 | 2026-02-14 02:05:34 | 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 | software resource, data processing software, software application | 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 | 2026-02-14 02:05:40 | 6 | ||||||||
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tbl2asn Resource Report Resource Website 1+ mentions |
tbl2asn (RRID:SCR_016636) | software resource, data processing software, software application | 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 | 2026-02-14 02:05:34 | 8 | ||||||||||
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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 | 2026-02-14 02:05:36 | 12 | ||||||
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Oufti Resource Report Resource Website 10+ mentions |
Oufti (RRID:SCR_016244) | software resource, image analysis software, data processing software, software application | 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 | 2026-02-14 02:05:34 | 13 |
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