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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Genotate Resource Report Resource Website |
Genotate (RRID:SCR_016659) | data access protocol, data or information resource, database, software resource, web service | Platform as a web-based interactive environment to automatically identify, explore and visualize homology and functional annotations for assembled transcripts. | identify, explore, visualize, homology, functional, annotation, assemble, transcript, dataset |
works with: Ensembl works with: UniProt works with: NONCODE |
ANR | Free, Available for download, Freely available, | SCR_016659 | SciCrunch Registry | 2026-09-26 02:15:50 | 0 | |||||||||
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NetworkUnit Resource Report Resource Website 1+ mentions |
NetworkUnit (RRID:SCR_016543) | software library, software resource, software toolkit | Library of a test driven framework for formally validating scientific models against experimental data used for validation testing of spiking neuron network simulations on the network activity level. | validation, neuroscience, electrophysiology, spiking, neural, network, simulation |
uses: Neo uses: Elephant is related to: SciUnit is related to: NeuronUnit |
Free, Available for download, Freely available | SCR_016543 | SciCrunch Registry | 2026-09-26 02:15:48 | 6 | ||||||||||
|
XYalign Resource Report Resource Website 1+ mentions |
XYalign (RRID:SCR_016661) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool for identifying, understanding, and correcting technical biases on the sex chromosomes in next generation sequencing data. | correct, technical, bias, sex, chromosome, next, generation, sequencing, data | is listed by: OMICtools | NIGMS R35 GM124827 | DOI:10.1101/346940 | Free, Available for download, Freely available | SCR_016661 | SciCrunch Registry | 2026-09-26 02:15:50 | 1 | ||||||||
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HARP Resource Report Resource Website 1+ mentions |
HARP (RRID:SCR_016546) | 3d visualization software, data processing software, data visualization software, image processing software, software application, software resource, standalone software | Software as a cross platform application for automating the processing of μCT and OPT image data. Used for standarization of embryo images prior to export to the PhenoDCC. Capable of processing other image modalities and specimens. Can be download as a stand alone release. | MRC Harwell UK, automating, processing, uCT, OPT, image, data | is related to: International Mouse Phenotyping Consortium (IMPC) | Free, Available for download, Freely available | harp.exe | SCR_016546 | SciCrunch Registry | 2026-09-26 02:15:48 | 1 | |||||||||
|
VPV Resource Report Resource Website 1+ mentions |
VPV (RRID:SCR_016545) | VPV | 3d visualization software, data processing software, data visualization software, software application, software resource | Software tool as a desktop 3D volume viewer. Used for analysing results of automatic phenotype detection from the LAMA pipeline. Developed in Python using QT, and the PyQtGraph. | Phyton, desktop, 3D viewer, analysis, results, phenotype, detection, LAMA pipeline | is listed by: International Mouse Phenotyping Consortium (IMPC) | Free, Available for download, Freely available | SCR_016545 | SciCrunch Registry | Volume Phenotype Viewer, volume phenotype viewer | 2026-09-26 02:15:48 | 1 | ||||||||
|
LoomPy Resource Report Resource Website 10+ mentions |
LoomPy (RRID:SCR_016666) | LoomPy | data processing software, data storage software, software application, software library, software resource, software toolkit | Python implementation of the Loom file format to store and organize very large omics datasets, consisting of a main matrix, optional additional layers, a variable number of row and column annotations and sparse graph objects. Used to store single-cell gene expression data. Official Python library (API) used to create, read, and manipulate .loom files, supporting out-of-memory operations to handle datasets larger than RAM. | Python, Loom file, format, store, organize, omics, dataset, single, cell, expression, data, HDF5 |
is used by: BICCN works with: loom-viewer works with: Loom |
Free, Available for download, Freely available | https://linnarssonlab.org/loompy/, https://github.com/linnarsson-lab/loompy | SCR_016666 | SciCrunch Registry | Loompy v2.0, Loompy v2.0.14, Loom Python, LoomPy, LoomPython | 2026-09-26 02:15:50 | 40 | |||||||
|
DCC Resource Report Resource Website 1+ mentions |
DCC (RRID:SCR_016544) | DCC | data analysis software, data processing software, software application, software resource | Software tool as an annotation structure and user-hosted platform for sequencing experiment data, suitable for lab-internal documentation, collaborations and large-scale annotation efforts. | databases, sequencing experiments, sequencing annotation, data annotation | Free, Available for download, Freely available | SCR_016544 | SciCrunch Registry | Data Coordination Center | 2026-09-26 02:15:48 | 1 | |||||||||
|
Centrifuge Classifier Resource Report Resource Website 10+ mentions |
Centrifuge Classifier (RRID:SCR_016665) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software for rapid and sensitive classification of metagenomic sequences. Used for the classification of DNA sequences from microbial samples and analysis of large metagenomics data sets on conventional desktop computers. | classification, large, metagenomic, sequence, DNA, microbial, sample, analysis, data, desktop, computer, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools is related to: Pavian has parent organization: Center for Computational Biology at JHU |
NHGRI R01 HG006677; NIGMS R01 GM083873; NSF ABI1356078; U. S. Army Research Office W911NF1410490 |
DOI:10.1101/gr.210641.116 | Free, Available for download, Freely available | biotools:centrifuge, OMICS_12217 | https://github.com/infphilo/centrifuge, https://bio.tools/centrifuge, https://sources.debian.org/src/centrifuge/ | SCR_016665 | SciCrunch Registry | 2026-09-26 02:15:50 | 10 | ||||||
|
PaVE Resource Report Resource Website 100+ mentions |
PaVE (RRID:SCR_016599) | PaVE | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource, software resource, web application | Collection of curated papillomavirus genomic sequences, accompanied by web-based sequence analysis tools. Database and web applications support the storage, annotation, analysis, and exchange of information. | data, curated, papilloma, virus, genomic, sequence, analysis, storage, annotation, FASEB list | is listed by: NIAID | NIAID ZIA AI001071 | PMID:28053164 | Open source | SCR_016599 | SciCrunch Registry | PapillomaVirus Episteme, Papillomavirus Episteme | 2026-09-26 02:15:49 | 156 | ||||||
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transfer_ learning_ ccnn Resource Report Resource Website 1+ mentions |
transfer_ learning_ ccnn (RRID:SCR_016590) | ccnn | data analysis software, data processing software, software application, software resource | Software program to implement transfer learning for a connectome convolutional neural network trained to classify functional connectomes using Tensorflow. | transfer, learning, connectome, convolutional, neural, network, functional, connectome, Tensorflow | uses: tensorflow | Free, Available for download, Freely available | SCR_016590 | SciCrunch Registry | connectome convolutional neural network, Connectome Convolutional Neural Network, CCNN | 2026-09-26 02:15:49 | 1 | ||||||||
|
NAT/NCS2 Hound Resource Report Resource Website 1+ mentions |
NAT/NCS2 Hound (RRID:SCR_016473) | NAT, NCS2 | data analysis software, data processing software, sequence analysis software, software application, software resource, web application | Web server for the detection and evolutionary classification of prokaryotic and eukaryotic nucleobase-cation symporters of the NAT/NCS2 family. Used to scan, identify and evolutionary classify NAT/NCS2 nucleobase transporter proteins. | protein, sequence, scan, identify, evolutionary, classify, prokaryotic, nucleobase, transporter, protein, amino acid, conserved |
is listed by: OMICtools has parent organization: University of Thessaly; Thessaly; Greece |
DOI:10.1101/332452 | Free, Available to download, Freely available | SCR_016473 | SciCrunch Registry | Nucleobase Ascorbate Transporter, NCS2:Nucleobase Cation Symporter 2 | 2026-09-26 02:15:47 | 1 | |||||||
|
TB PORTALS Resource Report Resource Website 10+ mentions |
TB PORTALS (RRID:SCR_016594) | consortium, data or information resource, data repository, disease-related portal, organization portal, portal, service resource, storage service resource, topical portal | Web based open access platform for global drug resistant tuberculosis data sharing and analysis. The NIAID TB Portals program and consortium of clinicians and scientists from countries with a heavy burden of TB, especially drug resistant TB, to collect TB data. | collect, data, sharing, analysis, tuberculosis, global, bio.tools |
is listed by: NIAID is listed by: bio.tools is listed by: Debian |
tuberculosis | NIH | DOI:10.1128/JCM.01013-17 | Free, Freely available | r3d100013925, biotools:TB_Portals | https://bio.tools/TB_Portals, https://doi.org/10.17616/R31NJN8L | SCR_016594 | SciCrunch Registry | 2026-09-26 02:15:49 | 20 | |||||
|
MetaPGN Resource Report Resource Website 1+ mentions |
MetaPGN (RRID:SCR_016472) | MetaPGN | data analysis software, data processing software, data visualization software, network graph visualization software, software application, software resource, software toolkit | Pipeline for construction and graphical visualization of annotated pangenome networks from microbial genomes. With the ability to extract and visualize gene contents and gene-gene physical adjacencies of a specific taxon from large-scale metagenomic data provides pangenome analysis to uncultured microbial taxa., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | construct, graphical, visualization, annotated, pangenome, network, microbal, genome, metagenome | PMID:30277499 | THIS RESOURCE IS NO LONGER IN SERVICE | https://github.com/peng-ye/MetaPGN | SCR_016472 | SciCrunch Registry | Meta PanGeNome | 2026-09-26 02:15:47 | 2 | |||||||
|
NMRProcFlow Resource Report Resource Website 10+ mentions |
NMRProcFlow (RRID:SCR_016592) | data processing software, data visualization software, software application, software resource | Software as graphical and interactive tool dedicated to 1D spectra processing for NMR-based metabolomics. | NMR, metabolomics, data, viewer, spectra, processing, graphical, interface, bio.tools |
uses: R Project for Statistical Computing is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
French National Infrastructure in Metabolomics and Fluxomics | DOI:10.1007/s11306-017-1178-y | Free, Available for download, Freely available | biotools:nmrprocflow, SCR_022777 | https://github.com/INRA/NMRProcFlow, https://bio.tools/nmrprocflow, https://github.com/inra/nmrprocflow | SCR_016592 | SciCrunch Registry | Nuclear Magnetic Resonance PROcessing FLOW, Nuclear Magnetic Resonance Processing Flow | 2026-09-26 02:15:49 | 29 | |||||
|
PNNsMiceMachineVision Resource Report Resource Website 1+ mentions |
PNNsMiceMachineVision (RRID:SCR_016485) | PNNsMiceMachineVision | data or information resource, database, software application, software resource, source code | Data and code (Python) related to research paper: V. Javier Traver, Filiberto Pla, Marta Miquel, Maria Carbo-Gas, Isis Gil-Miravet, Julian Guarque-Chabrera "Cocaine-induced preference conditioning: a machine vision perspective". | data, code, Phyton, research, paper, probabilistic, neural, network | Free, Available for download, Freely available | SCR_016485 | SciCrunch Registry | Probabilistic Neural Networks MiceMachineVision | 2026-09-26 02:15:47 | 2 | |||||||||
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Drug Gene Budger Resource Report Resource Website |
Drug Gene Budger (RRID:SCR_016489) | DGB | data access protocol, service resource, software resource, web service | Web based application to assist researchers with identifying drugs and small molecules that are predicted to maximally influence expression of mammalian gene of interest. Used to identify drugs and small molecules to regulate expression of target genes for research purpose only. Application for ranking drugs to modulate specific gene based on transcriptomic signatures. | identify, drug, small, molecule, predict, influence, expression, mammalian, gene, regulate, target |
is related to: LINCS Project has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA works with: CMAP works with: Gene Expression Omnibus (GEO) |
BD2K-LINCS Data Coordination and Integration Center Mount Sinai Knowledge Management Center for IDG ; NCI U24 CA224260; NHLBI U54 HL127624 |
PMID:30169739 | Restricted | SCR_016489 | SciCrunch Registry | Drug Gene Budger | 2026-09-26 02:15:47 | 0 | ||||||
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MorphoJ Resource Report Resource Website 10+ mentions |
MorphoJ (RRID:SCR_016483) | data analysis software, data processing software, software application, software resource, software toolkit | Software package written in Java for geometric morphometric analysis for two- and three-dimensional landmark data. Offers user-friendly environment for standard multivariate analyses such as principal components, discriminant analysis and multivariate regression as well as specialized applications including phylogenetics, quantitative genetics and analyses of modularity in shape data. | geometric, morphometric, analyse, 2D, 3D, landmark, data, principal, component, discriminant, multivariate, regression, shape | has parent organization: University of Manchester; Manchester; United Kingdom | PMID:21429143 | Free, Available for download, Freely available | SCR_016483 | SciCrunch Registry | 2026-09-26 02:15:47 | 38 | |||||||||
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Dormed Hellas: Monica AN24 Resource Report Resource Website 1+ mentions |
Dormed Hellas: Monica AN24 (RRID:SCR_016455) | instrument resource | Monitors the electrical signals on the patient’s abdomen by using the abdominal fECG and mECG wave shape to uniquely identify and separate the maternal and fetal heart rates. | Instrument, monitor, electrical, signal, patient, abdoment, separate, maternal, fetal, heart, rate | It has been discontinued | https://drive.google.com/file/d/1Agh-RBIqoW5hWevf4o9B6_dCYEUBsNH_/view?usp=sharing | https://www.accessdata.fda.gov/cdrh_docs/pdf11/K112390.pdf | SCR_016455 | SciCrunch Registry | 2026-09-26 02:15:47 | 1 | |||||||||
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Apnea, Bariatric surgery, and CPAP study Resource Report Resource Website 1+ mentions |
Apnea, Bariatric surgery, and CPAP study (RRID:SCR_016575) | ABC study | data or information resource, disease-related portal, portal, topical portal | Portal for randomized controlled trial to compare effectiveness of bariatric surgery versus continuous positive airway pressure (CPAP) therapy for obstructive sleep apnea. Signals included in the polysomnography (PSG) montage are EEG, EMG, EOG, ECG, SpO2, airflow, CPAP pressure, CPAP flow, plethysmography, position, pulse, light, respiratory effort, snore. | dataset, bariatric, surgery, continuous, positive, airway, pressure, therapy, sleep, apnea, obesity II | is listed by: National Sleep Research Resource (NSRR) | class II obesity, obstructive sleep apnea | NHLBI K24 HL127307; NHLBI R01 HL106410 |
DOI:10.1164/rccm.201708-1637LE | Free, Available for public download, Registration required | SCR_016575 | SciCrunch Registry | and Cpap study, Bariatric surgery, Apnea | 2026-09-26 02:15:48 | 1 | |||||
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MutaGene Resource Report Resource Website 10+ mentions |
MutaGene (RRID:SCR_016574) | data analysis software, data processing software, software application, software resource | Software tool to explore and analyze mutagenic factors leading to tumors to decipher cancer genetic heterogeneity. | analyze, mutagenic, factor, turmor, decipher, cancer, genetic, heterogeneity | is listed by: OMICtools | National Library of Medicine ; NIH |
PMID:28472504 | Free, Available for download, Freely available | https://ncbiinsights.ncbi.nlm.nih.gov/tag/mutagene/ | SCR_016574 | SciCrunch Registry | 2026-09-26 02:15:49 | 10 |
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