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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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CATNAP Resource Report Resource Website 10+ mentions |
CATNAP (RRID:SCR_016170) | software resource, software application, data analysis software, data processing software | Analyze a database of HIV-1 IC50 and IC80 neutralization data from publicly-available sources, in conjunction with HIV-1 Envelope sequences. Access to an extensive databases of information about neutralizing antibodies and viruses used in published neutralization studies. Tool interfaces also allow input and analysis of user data. PMID: 26044712, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | database, analysis, | PMID:26044712 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_016170 | CATNAP - Compile Analyze and Tally Neutralizing Antibody Panels | 2026-02-12 09:46:17 | 49 | |||||||||
|
GoldWave Resource Report Resource Website 50+ mentions |
GoldWave (RRID:SCR_016189) | software application, software resource, data analysis software, data processing software | Software that enables users to digitally edit audio files. GoldWave can record, edit, and analyze audio for research-related purposes. | audio, sound, analysis, acquisition, visualization, record, edit, analysis, auditory | Commercially available, Available for purchase | SCR_016189 | 2026-02-12 09:46:26 | 86 | |||||||||||
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Clonalframe Resource Report Resource Website 100+ mentions |
Clonalframe (RRID:SCR_016060) | sequence analysis software, software resource, software application, data analysis software, data processing software | Software package for the inference of bacterial microevolution using multilocus sequence data. It is used to identify the clonal relationships between the members of a sample, while also estimating the chromosomal position of homologous recombination events that have disrupted the clonal inheritance. | analysis, sequence, inference, bacteria, microevolution, multilocus, clonal, sample, chromosome, homologuous, recombination, disrupted, inheritance, DNA, genome |
is listed by: Debian is listed by: OMICtools is related to: Imperial College London; London; United Kingdom is related to: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Wellcome Trust | DOI:10.1534/genetics.106.063305 | Free, Available for download | OMICS_14623 | https://github.com/xavierdidelot/ClonalFrameML https://sources.debian.org/src/clonalframe/ |
SCR_016060 | ClonalFrameML | 2026-02-12 09:46:24 | 379 | |||||
|
GOTrack Resource Report Resource Website 1+ mentions |
GOTrack (RRID:SCR_016399) | data access protocol, software resource, web service, database, data or information resource | Open source web-based system and database that provides access to historical records and trends in the Gene Ontology (GO) and GO annotations (GOA). Used for monitoring changes in the Gene Ontology and their impact on genomic data analysis. | database, system, access, historical, monitor, record, gene, genomic, data, analysis, ontology, annotation, bioinformatics |
is listed by: OMICtools is related to: University of British Columbia; British Columbia; Canada |
NIH MH111099; NSERC Discovery Grant ; Canadian Foundation for Innovation infrastructure ; CIHR |
DOI:10.1101/320861 | Free, Available for download, Freely available | https://github.com/PavlidisLab/gotrack https://omictools.com/gotrack-tool |
SCR_016399 | 2026-02-12 09:46:32 | 1 | |||||||
|
RELION Resource Report Resource Website 100+ mentions |
RELION (RRID:SCR_016274) | standalone software, software resource, software application, data analysis software, data processing software | Software for determination of cryo-EM structures. It employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy. | cryo, cryogenic, cryo em, determination, analysis, bayesian, statistic, map, maximum a posteriori, electron, cryomicroscopy |
is listed by: Debian is listed by: OMICtools |
UK Medical Research Council | PMID:23000701 | Free, Available for download, Tutorial available | OMICS_15597 | https://sources.debian.org/src/relion-bin+mpi+gui/ | SCR_016274 | RELION, REgularised LIkelihood OptimisatioN, RELION-3 | 2026-02-12 09:46:30 | 408 | |||||
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Vensim Resource Report Resource Website 1+ mentions |
Vensim (RRID:SCR_016394) | simulation software, software application, software resource | Simulation software for improving the performance of real systems. Used for developing, analyzing, and packaging dynamic feedback models. | performance, system, Ventana Systems Inc, model, modelling, analysis | Commercially available, Available for purchase | SCR_016394 | 2026-02-12 09:46:19 | 8 | |||||||||||
|
OmicsBean Resource Report Resource Website 100+ mentions |
OmicsBean (RRID:SCR_016322) | software resource, software application, data analysis software, data processing software, data analytics software | Software tool for multi-omics data analysis that can perform complex and personalized analysis. Network regulation and molecular mechanism models can be customized according to the requirements of the users. | GeneForHealth Biotech Inc (GFK), data, analysis, genome, proteome, metabolome, network, molecular, mechanism, model, collect, store, analytic, multi, omic | Commercially available, Demo available | SCR_016322 | 2026-02-12 09:46:28 | 145 | |||||||||||
|
ANNOgesic Resource Report Resource Website 10+ mentions |
ANNOgesic (RRID:SCR_016326) | standalone software, software toolkit, software resource, software application, data analysis software, data processing software | Software tool for bacterial/archaeal RNA-Seq based genome annotations. Used for integrating, detecting, predicting, and grouping RNA-Seq data. | bacterial, archaeal, RNA, sequencing, data, analysis, genome, annotation, statistic, visualization, protein, interaction, prediction, grouping, go, ontology, gene, differential, circular |
is related to: Infernal is related to: Vienna RNA is related to: Biopython is related to: MEME Suite - Motif-based sequence analysis tools is related to: Segemehl |
Free, Freely available, Available for download | SCR_016326 | 2026-02-12 09:46:31 | 10 | ||||||||||
|
MxPro QPCR Resource Report Resource Website 500+ mentions |
MxPro QPCR (RRID:SCR_016375) | software resource, software application, data analysis software, data processing software | Software that performs data analysis algorithms for QPCR data. The software is included with the purchase of the Agilent MxPro QPCR System., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | pcr, qpcr, polymerase, qualitative, analysis, nucleic, acid, gene | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_016375 | MxPro QPCR Software | 2026-02-12 09:46:29 | 543 | ||||||||||
|
Mapping Population-based Structural Connectomes Resource Report Resource Website |
Mapping Population-based Structural Connectomes (RRID:SCR_016232) | software resource, software application, data analysis software, data processing software | Data analysis software that can simultaneously characterize a large number of white matter bundles within and across different subjects for group analysis. It has three major components: construction of the structural connectome for the whole brain, low-dimensional representation of streamlines in each connection, and multi-level connectome analysis. | dwi, t1, tractography, algorithm, white matter, bundle, gray matter, shape, analysis, network, workflow | NIMH MH086633; NIMH MH092335; NSF SES-1357666; NSF DMS-1407655; CPRIT RR150054; NSF DMS1127914 |
Free for non-commercial use, Available for download | SCR_016232 | 2026-02-12 09:46:27 | 0 | ||||||||||
|
OpenEx Resource Report Resource Website 100+ mentions |
OpenEx (RRID:SCR_016230) | software toolkit, software resource, software application, data analysis software, data processing software, data visualization software | Software toolkit that is designed for configuration and control of TDT hardware. It can also display and analyze neurophysiology data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | tdt, analysis, neurophysiology, hardware, companion software, control, configuration, neuroimaging, eeg, stimulation | has parent organization: Tucker-Davis Technologies | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_016230 | The OpenEx Software Suite, OpenEx suite | 2026-02-12 09:46:29 | 103 | |||||||||
|
Deeptools Resource Report Resource Website 1000+ mentions |
Deeptools (RRID:SCR_016366) | software toolkit, software resource, software application, data analysis software, data processing software, data visualization software | Python based tools to process, visualize and analyse high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq. Implemented within Galaxy framework. Used to perform complete bioinformatic workflows ranging from quality controls and normalizations of aligned reads to integrative analyses, including clustering and visualization approaches. | process, visualize, analysis, sequencing, data, ChIP-seq, RNA-seq, MNase-seq, quality, control, normalization, aligned, read, clustering, bioinformatic | works with: Galaxy | German Research Foundation SFB 992; German Epigenome Programme DEEP 01KU1216G |
PMID:27079975 | Free, Available for download, Freely available | http://deeptools.ie-freiburg.mpg.de/ | SCR_016366 | 2026-02-12 09:46:32 | 2418 | |||||||
|
SMAGEXP Resource Report Resource Website 1+ mentions |
SMAGEXP (RRID:SCR_016360) | SMAGEXP | software toolkit, software resource, software application, data analysis software, data processing software | Software toolkit for transcriptomics data meta-analysis. It integrates metaMA and metaRNAseq packages into Galaxy, carries out meta-analysis of gene expression data, handles microarray data from Gene Expression Omnibus (GEO) database, and more. | transcriptomics, data, meta, analysis, MicroArrays, RNA-Seq, Galaxy, gene, expression, next, generation, sequencing, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Galaxy is related to: Gene Expression Omnibus is related to: metaMA is related to: metaRNASeq |
PMID:30698691 | Free, Available for download, Freely available | biotools:SMAGEXP | https://bio.tools/SMAGEXP | SCR_016360 | Statistical Meta Analysis for Gene EXPression | 2026-02-12 09:46:48 | 2 | |||||
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nelpy Resource Report Resource Website 1+ mentions |
nelpy (RRID:SCR_016209) | software toolkit, software resource, software application, data analysis software, data processing software, data visualization software | Software toolkit for neuroelectrophysiology object modeling and data analysis in Python. Open source Python package for analysis of neuroelectrophysiology data. | model, modelling, python, neuroelectrophysiology, object, neuroimaging, analysis, neurophysiology, electrophysiology, BRAIN Initiative | is recommended by: BRAIN Initiative | NSF CBET-1351692; NSF IOS-1550994; Human Frontiers Science Program RGY0088 |
Free, Available for download, Freely available | SCR_016209 | Nelpy (Neuroelectrophysiology) | 2026-02-12 09:46:27 | 3 | ||||||||
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UTHSCSA ImageTool Resource Report Resource Website 100+ mentions |
UTHSCSA ImageTool (RRID:SCR_016208) | IT | software resource, software application, data processing software, image processing software, image analysis software | Image processing and analysis program for Windows 95 NT and has many of the same capabilities as NIH Image. ImageTool can acquire, display, edit, analyze, process, compress, save and print gray scale and color images. | image, analysis, processing, data, acquisition, compression, modification | has parent organization: University of Texas Health Science Center at San Antonio; Texas; USA | Free, Available for download, Runs on Windows | http://en.bio-soft.net/draw/ImageTool.html | SCR_016208 | UTHSCSA Image Tool, UTHSCSA ImageTool (IT) | 2026-02-12 09:46:17 | 120 | |||||||
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migec Resource Report Resource Website 1+ mentions |
migec (RRID:SCR_016337) | MIGEC | software toolkit, software resource, software application, data analysis software, data processing software | Software package for analysis of immune repertoire sequencing data. Used for recovery of T Cell Receptor ( TCR ) data from bulk population data.Used for high-throughput sequencing data analysis. Allows for error correction while preserving the natural diversity of complex immune repertoires. | high sequencing, molecular, identifier, guided, error, correction, data, analysis, immune, recovery, T cell receptor, | Molecular and Cell Biology program RAS ; Russian Foundation for Basic Research ; Russian President ; European Regional Development Fund |
PMID:24793455 | Free, Available for download, Freely available | SCR_016337 | Molecular Identifier Guided Error Correction | 2026-02-12 09:46:31 | 9 | |||||||
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FLIR tools Resource Report Resource Website 10+ mentions |
FLIR tools (RRID:SCR_016330) | software resource, software application, data analysis software, data processing software, image analysis software | Software application for thermography for FLIR Systems. It has a basic thermal image analysis function including color palette and image adjustment function. Used to analyse the thermographic measurement data. | thermography, FLIR Systems, image, data, measurement, analysis | Free, Available for download | SCR_016330 | 2026-02-12 09:46:29 | 14 | |||||||||||
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star-for-criu Resource Report Resource Website 1+ mentions |
star-for-criu (RRID:SCR_016294) | software resource, alignment software, software application, data processing software, image analysis software | Software as an Hot Start software container for STAR alignment using CRIU (Checkpoint Restore in Userspace) tool to freeze the running container. Can be deployed to align RNA sequencing data. Used in the processing of biomedical big data for better reproducibility and reliability. | hot, start, container, star, aligner, sequencing, data, processing, biomedical, cloud, reproducibility, RNA, analysis, computing, environment | is related to: Systems Transcriptional Activity Reconstruction | NHLBI U54 HL127624; AMEDD Advanced Medical Technology Initiative ; NIGMS R01 GM126019 |
Free, Freely available, Available for download | https://github.com/paizhang/Hotstarting-For-STAR-Alignment | SCR_016294 | 2026-02-12 09:46:46 | 1 | ||||||||
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masked ICA (mICA) Toolbox Resource Report Resource Website 1+ mentions |
masked ICA (mICA) Toolbox (RRID:SCR_016349) | mICA | software toolkit, software resource, software application, data analysis software, data processing software | Software toolbox based on FSL command line tools that performs masked independent component analysis and related analyses in an integrated way within a spatially restricted subregion of the brain. Used for investigating functional connectivity in functional magnetic resonance imaging data in the field of neuroimaging. | masked, independent, component, analysis, neuroimaging, restricted, subregion, brain, magnetic, resonance, imaging, data, |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: FSL has parent organization: Hannover Medical School; Lower Saxony; Germany |
Horst Görtz Foundation | PMID:27168407 | Free, Freely available, Available for download | SCR_016349 | masked Independent Component Analysis | 2026-02-12 09:46:31 | 1 | ||||||
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Lifebit Deploit Resource Report Resource Website 1+ mentions |
Lifebit Deploit (RRID:SCR_016428) | analysis service resource, software resource, service resource, production service resource, data management software, software application, data analysis service | Platform for computing management for data analysis on the cloud from the Lifebit company. Allows the computational analyses to be permanently linked to live analyses pipelines. | Lifebit, compute, management, data, analysis, cloud, integrate, data, reproduce, transparent, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:28398311 | Commercially available | biotools:nextflow | https://bio.tools/nextflow | SCR_016428 | 2026-02-12 09:46:49 | 2 |
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