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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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nelpy Resource Report Resource Website 1+ mentions |
nelpy (RRID:SCR_016209) | data processing software, software resource, data analysis software, software toolkit, data visualization software, software application | 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) | 2025-04-27 10:39:48 | 2 | ||||||||
|
UTHSCSA ImageTool Resource Report Resource Website 1+ mentions |
UTHSCSA ImageTool (RRID:SCR_016208) | IT | data processing software, software resource, image analysis software, software application, image processing 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) | 2025-04-27 10:39:47 | 5 | |||||||
|
CATNAP Resource Report Resource Website 10+ mentions |
CATNAP (RRID:SCR_016170) | data processing software, data analysis software, software application, software resource | 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 | database, analysis, | PMID:26044712 | SCR_016170 | CATNAP - Compile Analyze and Tally Neutralizing Antibody Panels | 2025-04-27 10:39:46 | 44 | ||||||||||
|
star-for-criu Resource Report Resource Website 1+ mentions |
star-for-criu (RRID:SCR_016294) | data processing software, software resource, image analysis software, alignment software, software application | 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 | 2025-04-27 10:39:52 | 1 | ||||||||
|
GoldWave Resource Report Resource Website 50+ mentions |
GoldWave (RRID:SCR_016189) | data processing software, data analysis software, software application, software resource | 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 | 2025-04-27 10:39:46 | 83 | |||||||||||
|
Lifebit Deploit Resource Report Resource Website 1+ mentions |
Lifebit Deploit (RRID:SCR_016428) | production service resource, data management software, software resource, data analysis service, service resource, analysis service resource, software application | 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 | 2025-04-27 10:39:58 | 2 | |||||||
|
GOTrack Resource Report Resource Website 1+ mentions |
GOTrack (RRID:SCR_016399) | software resource, data access protocol, database, data or information resource, web service | 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 | 2025-04-27 10:39:56 | 1 | |||||||
|
FCS Express Resource Report Resource Website 100+ mentions |
FCS Express (RRID:SCR_016431) | data processing software, data analysis software, software application, software resource | Software tool for flow and image cytometry data analysis by De Novo Software company. | flow, image, analysis, data, cytometry, De Novo Software, research, clinical, laboratory | is listed by: SoftCite | Commercially available, Tutorial available | SCR_016431 | 2025-04-27 10:39:58 | 453 | ||||||||||
|
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 | 2025-04-27 10:39:56 | 8 | |||||||||||
|
OmicsBean Resource Report Resource Website 100+ mentions |
OmicsBean (RRID:SCR_016322) | data processing software, software resource, data analysis software, software application, 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 | 2025-04-27 10:39:53 | 139 | |||||||||||
|
ANNOgesic Resource Report Resource Website 10+ mentions |
ANNOgesic (RRID:SCR_016326) | data processing software, software resource, data analysis software, software toolkit, standalone software, software application | 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 | 2025-04-27 10:39:53 | 10 | ||||||||||
|
MxPro QPCR Resource Report Resource Website 500+ mentions |
MxPro QPCR (RRID:SCR_016375) | data processing software, data analysis software, software application, software resource | Software that performs data analysis algorithms for QPCR data. The software is included with the purchase of the Agilent MxPro QPCR System. | pcr, qpcr, polymerase, qualitative, analysis, nucleic, acid, gene | Commercially available, Available for purchase, Purchase in bundle | SCR_016375 | MxPro QPCR Software | 2025-04-27 10:39:56 | 535 | ||||||||||
|
MetaCyto Resource Report Resource Website 1+ mentions |
MetaCyto (RRID:SCR_016415) | data processing software, software resource, data analysis software, software toolkit, software application | Software tool for automated meta-analysis of mass and flow cytometry data. Provides functions for preprocessing, automated gating and meta-analysis of cytometry data and collection of cytometry data from the ImmPort database. | automated, analysis, meta, flow, cytometry, data, bio.tools |
is listed by: Bioconductor is listed by: NIDDK Information Network (dkNET) is listed by: bio.tools is listed by: Debian is related to: The Immunology Database and Analysis Portal (ImmPort) |
the National Institute of Allergy and Infectious Diseases HHSN272201200028C | Free, Available for download, Freely available | biotools:metacyto | https://bio.tools/metacyto | SCR_016415 | 2025-04-27 10:39:57 | 5 | |||||||
|
Deeptools Resource Report Resource Website 1000+ mentions |
Deeptools (RRID:SCR_016366) | data processing software, software resource, data analysis software, software toolkit, data visualization software, software application | 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 | 2025-04-27 10:39:55 | 1881 | |||||||
|
SMAGEXP Resource Report Resource Website 1+ mentions |
SMAGEXP (RRID:SCR_016360) | SMAGEXP | data processing software, software resource, data analysis software, software toolkit, software application | 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 | 2025-04-27 10:39:55 | 2 | |||||
|
migec Resource Report Resource Website 1+ mentions |
migec (RRID:SCR_016337) | MIGEC | data processing software, software resource, data analysis software, software toolkit, software application | 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 | 2025-04-27 10:39:54 | 8 | |||||||
|
FLIR tools Resource Report Resource Website 10+ mentions |
FLIR tools (RRID:SCR_016330) | data processing software, software resource, data analysis software, image analysis software, software application | 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 | 2025-04-27 10:39:53 | 13 | |||||||||||
|
UAMH Centre for Global Microfungal Biodiversity Resource Report Resource Website 1+ mentions |
UAMH Centre for Global Microfungal Biodiversity (RRID:SCR_016466) | biomaterial supply resource, material resource, organism supplier | Repository of microbial in Canada. Culture collection, preservation, analysis, identification of fungi living strains. Backed up by herbarium dried colonies. A reference and training centre for the identification of human and animal pathogens and allied taxa.Provides advice or assistance to projects involving fungi. | microbial, repository, collection, preservation, analysis, identification, fungi | is related to: University of Toronto; Ontario; Canada | SCR_016466 | 2025-04-27 10:40:00 | 4 | |||||||||||
|
masked ICA (mICA) Toolbox Resource Report Resource Website 1+ mentions |
masked ICA (mICA) Toolbox (RRID:SCR_016349) | mICA | data processing software, software resource, data analysis software, software toolkit, software application | 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 | 2025-04-27 10:39:55 | 1 | ||||||
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Global Catalogue of Microorganisms Resource Report Resource Website 1+ mentions |
Global Catalogue of Microorganisms (RRID:SCR_016460) | GCM | organism-related portal, database, topical portal, data or information resource, portal | Database and information retrieval, analysis, and visualization system for microbial resources to help culture collections to manage, disseminate and share the information related to their holdings. Provides an interface for the scientific and industrial communities to access the microbial resource information. | research, deep, mining, genomic, data, retrival, analysis, visualisation, , microbial, resource, | the Strategic Priority Research Program of the Chinese Academy of Sciences ; the Bureau of International Cooperation of the Chinese Academy of Sciences ; the National Key Research Program of China ; the 13th Five-year Informatization Plan of the Chinese Academy of Sciences ; the National Science Foundation for Young Scientists of China |
PMID:29718202 | Free, Available to the scientific and industrial communities | SCR_016460 | GCM:Global Catalogue of Microorganisms | 2025-04-27 10:40:00 | 5 |
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