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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Expyfun Resource Report Resource Website 1+ mentions |
Expyfun (RRID:SCR_019285) | software resource, software library, software toolkit | Auditory and visual stimulus delivery library for psychoacoustics in Python. | Auditory, visual stimulus, stimulus delivery, library, psychoacoustics, Python. | Free, Available for download | SCR_019285 | 2026-08-01 12:06:13 | 1 | |||||||||||
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gbs2ploidy Resource Report Resource Website |
gbs2ploidy (RRID:SCR_019290) | software toolkit, data analysis software, software application, software resource, data processing software | Software R package as functions for inference of ploidy from Genotyping By Sequencing data, including function to infer allelic ratios and allelic proportions in Bayesian framework. | Genotyping-by-sequencing data, GBS data, ploidy inference, allelic ratios infer, allelic proportions, Bayesian framework, ploidy level detection | is listed by: CRAN | PMID:28150424 | Free, Available for download, Freely available | SCR_019290 | 2026-08-01 12:06:13 | 0 | |||||||||
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BayesEpiModels Web App Resource Report Resource Website 1+ mentions |
BayesEpiModels Web App (RRID:SCR_019292) | web application, service resource, production service resource, software resource, analysis service resource | Web app to help assess both short- and long-term forecasts of COVID-19 across the United States at multiple levels. Done by implementing one time-series model (ARIMA), one compartmental models (basic SIR), and six classical growth models, which all yield satisfactory prediction results in the past and current pandemics at early stage. | COVID-19, SARS-CoV-2, stochastic growth model, stochastic SIR model, Bayesian inference, | Free, Freely available | SCR_019292 | 2026-08-01 12:06:30 | 1 | |||||||||||
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ChiRA Resource Report Resource Website 1+ mentions |
ChiRA (RRID:SCR_019219) | data or information resource, software toolkit, workflow, narrative resource, software application, data processing software, software resource, training material | Software tool suite to analyze RNA-RNA interactome experimental data such as CLASH, CLEAR-CLIP, PARIS, SPLASH, etc. | RNA-RNA interactome experimental data, experimental data analysis, miRNA, RNA-RNA interactome, RNA structurome, CLASH, CLEAR-CLIP, PARIS, SPLASH, chimeric read, read, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:chira | https://rna.usegalaxy.eu/, https://bio.tools/chira | SCR_019219 | Chimeric Read Analyzer | 2026-08-01 12:06:11 | 4 | |||||||
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ConPlot Resource Report Resource Website 1+ mentions |
ConPlot (RRID:SCR_019216) | data access protocol, service resource, production service resource, software resource, web service, analysis service resource | Web application for visualisation of information derived from residue contact predictions in combination with other sources of information, such as secondary structure predictions, transmembrane helical topology, sequence conservation.Provides interactive interface for researchers in field of protein bioinformatics that are interested in analysing data on given protein. | Residue contact predictions, protein, secondary structure predictions, transmembrane helical topology, sequence conservation, protein bioinformatics, analysing data |
is related to: CCP4 has parent organization: University of Liverpool; Liverpool; United Kingdom |
Restricted | SCR_019216 | 2026-08-01 12:06:29 | 2 | ||||||||||
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Trial Registration Number screener Resource Report Resource Website |
Trial Registration Number screener (RRID:SCR_019211) | TRNscreener | data processing software, data analysis software, software application, software resource | Software tool as R script to provide function that takes two arguments: path to folder of plain text files named by their DOI, and output filename. For each file in folder, it searches for trial identifiers based on regex matching and writes CSV that contains all trial registration numbers and in case of ClinicalTrials.gov entries, whether they correspond to registry entry on ClinicalTrials.gov. | ClinicalTrials.gov, plain text files, DOI named, output filename, trial identifiers searches, regex matching, trial registration numbers, ASWG | has parent organization: Charite - Universitatsmedizin Berlin; Berlin; Germany | Free, Available for download, Freely available | SCR_019211 | Trial Registration Number screener, Trial registration number screener | 2026-08-01 12:06:10 | 0 | ||||||||
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Agilent: 1290 Infinity II Online SPE System Resource Report Resource Website |
Agilent: 1290 Infinity II Online SPE System (RRID:SCR_019380) | instrument resource | Online SPE System automates solid phase extraction to enrich analytes, remove matrix components or lower detection limits. | Agilent, GPS/SEC System, Instrument Equipment, USEDit, | Commercially available | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_019380.pdf | Model_Number_1290 Infinity II Online SPE | SCR_019380 | 2026-08-01 12:06:17 | 0 | |||||||||
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Agilent: 240Z AA Atomic Absorption System Resource Report Resource Website |
Agilent: 240Z AA Atomic Absorption System (RRID:SCR_019385) | instrument resource | Atomic Absorption System is used for detection limits and analyzes difficult matrices. | Agilent, Atomic Absorption System, Instrument Equipment, USEDit, | Commercially available | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_019385.pdf | Model_Number_240Z_AA | SCR_019385 | 2026-08-01 12:06:31 | 0 | |||||||||
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Agilent: 1290 Infinity II Preparative LC/MSD System Resource Report Resource Website |
Agilent: 1290 Infinity II Preparative LC/MSD System (RRID:SCR_019381) | instrument resource | Preparative LC/MSD System enables high throughput purification and delivers high quality compounds. | Agilent, Preperative LC System, Instrument Equipment, USEDit, | Commercially available | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_019381.pdf | Model_Number_Infinity_II | SCR_019381 | 2026-08-01 12:06:31 | 0 | |||||||||
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DEAP - Data Exploration and Analysis Portal Resource Report Resource Website 10+ mentions |
DEAP - Data Exploration and Analysis Portal (RRID:SCR_016158) | DEAP | software resource, data access protocol, web service | Web service for data exploration and analysis of the ABCD Study - the largest long-term study of brain development and child health in the United States. | data, exploration, analysis, portal, brain, development, child, health, United, States, long, term, study | is related to: ABCD Study | Free, Available for download | SCR_016158 | DEAP: Data Exploration and Analysis Portal | 2026-08-01 12:05:29 | 18 | ||||||||
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Linear Fascicle Evaluation Resource Report Resource Website 1+ mentions |
Linear Fascicle Evaluation (RRID:SCR_016153) | data processing software, data analysis software, software application, software resource | Software that implements a framework to encode structural brain connectomes into multidimensional arrays (tensors). Encoding Connectomes provides an agile framework for computing over connectome edges and nodes. | connectome, encode, framework, neuroanatomy, tract, dissection, array, tensor, edge, node | requires: MATLAB | NSF IIS-1636893; NSF BCS-1734853; NCATS ULT TR001108; Indiana University Areas of Emergent Research initiative Learning: Brains ; Machines ; Children |
Free, Available for download, Demo available | SCR_016153 | 2026-08-01 12:05:36 | 1 | |||||||||
|
AMBER Resource Report Resource Website 1000+ mentions |
AMBER (RRID:SCR_016151) | AMBER | data visualization software, software toolkit, data analysis software, software application, software resource, data processing software | Software toolkit for the comparative assessment of genome reconstructions from metagenome benchmark datasets. It provides performance metrics, results rankings, and comparative visualizations for assessing multiple programs or parameter effects. | binning, metagenomics, benchmarking, biobox, evaluation, comparison, reconstruction, metric, |
is used by: CHARMM-GUI is listed by: SoftCite |
DOI:10.1101/239582 | Free, Available for download | SCR_016151 | AMBER: Assessment of Metagenome BinnERs | 2026-08-01 12:05:28 | 2204 | |||||||
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NeMOarchive Resource Report Resource Website 100+ mentions |
NeMOarchive (RRID:SCR_016152) | NeMO | data or information resource, data repository, storage service resource, database, service resource | Data repository specifically focused on storage and dissemination of omic data generated from BRAIN Initiative and related brain research projects. Data repository and archive for BCDC and BICCN project, among others. NeMO data include genomic regions associated with brain abnormalities and disease, transcription factor binding sites and other regulatory elements, transcription activity, levels of cytosine modification, histone modification profiles and chromatin accessibility. | omic, neuroscience, neurobiology, bcbc, biccn, nih, brain, genomic, region, abnormal, transcription, factor, binding, site, chromatin, regulatory, element, data |
is used by: BRAIN Initiative Cell Atlas Network is used by: BICCN is recommended by: BRAIN Initiative is related to: NeMO Analytics has parent organization: University of Maryland School of Medicine; Maryland; USA |
NIMH MH114788; BRAIN Initiative |
Free, Freely available | https://data.nemoarchive.org/ | SCR_016152 | NeMO Archive, Neuroscience Multi-omic Data Archive, The Neuroscience Multi-Omic Archive, Neuroscience Multi-Omic Archive | 2026-08-01 12:05:28 | 113 | ||||||
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HIRN Consortium on Targeting and Regeneration Resource Report Resource Website |
HIRN Consortium on Targeting and Regeneration (RRID:SCR_016201) | HIRN-CTAR, CTAR, CTR, HIRN-CTR | portal, consortium, data or information resource, organization portal | Consortium that is an independent research initiative of the Human Research Information Network (HIRN). It is investigating methods to increase or maintain functional beta cell mass in T1D through targeted manipulation of islet plasticity or engineered protection of beta cells from immune-mediated destruction. | plasticity, bioengineering, cell, beta, cell, death | is organization facet of: Human Islet Research Network (HIRN) | NIDDK ; NIDDK U01 DK104162; NIDDK UC4 DK104211; NIDDK UC4 DK104204; NIDDK UC4 DK104209; NIDDK UC4 DK104143; NIDDK UC4 DK104119; NIDDK UC4 DK116241; NIDDK UC4 DK116264; NIDDK UC4 DK116252; NIDDK UC4 DK116255; NIDDK UC4 DK116280 |
SCR_016201 | Consortium on Targeting and Regeneration (HIRN-CTAR) | 2026-08-01 12:05:31 | 0 | ||||||||
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HyPhy Resource Report Resource Website 1000+ mentions |
HyPhy (RRID:SCR_016162) | software toolkit, data analysis software, software application, software resource, sequence analysis software, data processing software | Open source software package for comparative sequence analysis using stochastic evolutionary models. Used for analysis of genetic sequence data in particular the inference of natural selection using techniques in phylogenetics, molecular evolution, and machine learning. | analysis, genetic, sequence, multiply, alignment, rate, pattern, data, evolution, platform, python, r, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
NSF DBI-0096033; NSF DEB-9996118; NIH R01 AI47745; NIH U01 AI43638; University of California Universitywide AIDS Research Program IS02-SD-701; University of California ; San Diego Center for AIDS Research/NIAID Developmental Award 2 P30 AI36214; NIGMS R01 |
PMID:15509596 | Free, Available for download, Freely available | SCR_016271, biotools:HyPhy, OMICS_04235 | https://sources.debian.org/src/hyphy-pt/, https://veg.github.io/hyphy-site/, https://github.com/veg/hyphy, https://bio.tools/HyPhy, | SCR_016162 | HyPhy:Hypothesis Testing using Phylogenies, Hyphy-pt | 2026-08-01 12:05:28 | 1497 | |||||
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Indelible Resource Report Resource Website 10+ mentions |
Indelible (RRID:SCR_016163) | software resource, software application, simulation software | Software that generates nucleotide, amino acid and codon sequence data by simulating insertions and deletions (indels) as well as substitutions. It is used for biological sequence simulation of multi-partitioned nucleotide, amino-acid, or codon data sets through the processes of insertion, deletion, and substitution in continuous time. | indel, insertion, deletion, biological, sequence, simulation, multi-partitioned, nucleotide, amio-acid, codon, data, set, insertion, deletion, substitution, continous, time, non-homogeneous, non-stationary, phylogeny, simulator, evolution |
is listed by: Debian is listed by: OMICtools |
EPSRC/MRC Doctoral Training Centre studentship ; BBSRC |
PMID:19423664 | Free, Available for download | OMICS_15369 | https://sources.debian.org/src/indelible/ | SCR_016163 | 2026-08-01 12:05:36 | 23 | ||||||
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zUMIs Resource Report Resource Website 100+ mentions |
zUMIs (RRID:SCR_016139) | data processing software, data analysis software, software application, software resource | Software pipeline to process RNA-seq data with UMIs. The input to this pipeline is paired-end fastq files, where one read contains the cDNA sequence and the other read contains UMI and Cell Barcode information. | single-cell, RNA-seq, UMI, Genomics, shell, r, perl, rna, cdna, cell, sequencing, bio.tools |
is listed by: bio.tools is listed by: Debian |
DOI:10.1101/153940 | Open source, Free, Available for download | biotools:zumis | https://bio.tools/zumis | SCR_016139 | zumi | 2026-08-01 12:05:28 | 118 | ||||||
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Microsoft Excel Resource Report Resource Website 10000+ mentions |
Microsoft Excel (RRID:SCR_016137) | data visualization software, data analysis software, software application, software resource, data processing software | Software application with data analysis tools and spreadsheet templates to track and visualize data. It is used to manage and process data. | data, process, manage, analyze, spreadsheet, template, track, visualize, graph |
is related to: XLSTAT is related to: Statcel3 has plug in: OVAL has plug in: easyGV |
Microsoft | Commercially available, Trial available | SCR_016137 | , MS Excel | 2026-08-01 12:05:28 | 81724 | ||||||||
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Fastml Resource Report Resource Website 100+ mentions |
Fastml (RRID:SCR_016092) | software resource, data access protocol, web application, web service | Web application for the reconstruction of ancestral sequences. It computes maximum likelihood ancestral sequence reconstruction based on the phylogenetic relations between homologous sequences. | ancestral, amino-acid, sequence, reconstruction, phylogenetic, relation, accurate, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
Israel Science Foundation 878/09; Bioinformatics Center at Tel-Aviv University |
PMID:22661579 | Free, Freely available | biotools:fastml, OMICS_08650 | https://bio.tools/fastml, https://sources.debian.org/src/fastml/ | SCR_016092 | The FastML Server | 2026-08-01 12:05:35 | 109 | |||||
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Gubbins Resource Report Resource Website 500+ mentions |
Gubbins (RRID:SCR_016131) | data analysis software, software application, software resource, sequence analysis software, data processing software | Software application as an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions. It is used for phylogenetic analysis of genome sequences and generating highly accurate reconstructions under realistic models of short-term bacterial evolution., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | rapid, phylogenetic, analysis, large, sample, recombinant, bacteria, whole, genome, sequence, loci, elevated, densities, base, substitiution, mutatiion, outside, region, evolution, alignment |
is listed by: Debian is listed by: OMICtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Wellcome Trust 098051 | PMID:25414349 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_14386 | https://sources.debian.org/src/gubbins/ | SCR_016131 | Gubbins: Genealogies Unbiased By recomBinations In Nucleotide Sequences | 2026-08-01 12:05:28 | 602 |
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Data set from Kravitz, Owen and Kretizer's 2012 paper "Optogenetic identification of striatal projection neuron subtypes during in vivo recordings."
