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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Sanger Mouse Resources Portal Resource Report Resource Website 50+ mentions |
Sanger Mouse Resources Portal (RRID:SCR_006239) | Sanger Mouse Portal, WTSI Mouse Resources Portal, WTSI Mouse Resource Portal | biomaterial supply resource, material resource | Database of mouse research resources at Sanger: BACs, targeting vectors, targeted ES cells, mutant mouse lines, and phenotypic data generated from the Institute''''s primary screen. The Wellcome Trust Sanger Institute generates, characterizes, and uses a variety of reagents for mouse genetics research. It also aims to facilitate the distribution of these resources to the external scientific community. Here, you will find unified access to the different resources available from the Institute or its collaborators. The resources include: 129S7 and C57BL6/J bacterial artificial chromosomes (BACs), MICER gene targeting vectors, knock-out first conditional-ready gene targeting vectors, embryonic stem (ES) cells with gene targeted mutations or with retroviral gene trap insertions, mutant mouse lines, and phenotypic data generated from the Institute''''s primary screen. | bacterial artificial chromosome, vector, embryonic stem cell, mutant mouse line, phenotype, gene, knockout, gene expression, genetics, chromosome, mutant, mouse line, mammal, marker symbol |
is listed by: One Mind Biospecimen Bank Listing is related to: Ensembl has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Wellcome Trust 079643; Wellcome Trust 098051; NHGRI UO1-HG004080; NCRR 1-U42RR033192; European Union LSHG-CT-2006-037188; European Union 227490; European Union 312325; European Union 261492 |
For the scientific community | nlx_151819 | SCR_006239 | Mouse Resources Portal, Wellcome Trust Sanger Institute Mouse Resources Portal | 2026-02-14 02:07:08 | 51 | ||||||
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ShapeWorks Resource Report Resource Website 1+ mentions |
ShapeWorks (RRID:SCR_000424) | ShapeWorks | software resource, software application | THIS RESOURCE IS NO LONGER IN SERVICE.Documented on September 2, 2022. Software that is an open-source distribution of a new method for constructing compact statistical point-based models of ensembles of similar shapes that does not rely on any specific surface parameterization. The method requires very little preprocessing or parameter tuning, and is applicable to a wide range of shape analysis problems, including nonmanifold surfaces and objects of arbitrary topology. The proposed correspondence point optimization uses an entropy-based minimization that balances the simplicity of the model (compactness) with the accuracy of the surface representations. The ShapeWorks software includes tools for preprocessing data, computing point-based shape models, and visualizing the results. | c++, console (text based), linux, macos, microsoft, magnetic resonance, posix/unix-like, rendering, shape analysis, surface rendering, visualization, win32 (ms windows), windows, workflow |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Utah; Utah; USA |
NCRR 5P41RR012553-15; NIGMS 8 P41 GM103545-15 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_155961 | http://www.nitrc.org/projects/shapeworks | SCR_000424 | 2026-02-14 02:06:58 | 1 | ||||||
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pRESTO Resource Report Resource Website 50+ mentions |
pRESTO (RRID:SCR_001782) | pRESTO | software resource, software toolkit | Software toolkit for processing raw reads from high-throughput sequencing of lymphocyte repertoires. | lymphocyte, high throughput sequencing, processing, raw reads, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Yale School of Medicine; Connecticut; USA |
EMD/Merck/Serono ; United States-Israel Binational Science Foundation 2009046; NCRR RR19895; NLM T15 LM07056; NIAAA U19AI089992; NIAAA U19AI050864 |
PMID:24618469 | Free, Freely available | SCR_001782 | REpertoire Sequencing TOolkit | 2026-02-14 02:06:31 | 70 | ||||||
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Primate Embryo Gene Expression Resource Resource Report Resource Website 1+ mentions |
Primate Embryo Gene Expression Resource (RRID:SCR_002765) | PREGER | biomaterial supply resource, material resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. Sample collection of oocytes obtained from various sized antral follicles, and embryos obtained through a variety of different protocols. The PREGER makes it possible to undertake quantitative gene-expression studies in rhesus monkey oocytes and embryos through simple and cost-effective hybridization-based methods. | primate, embryo, gene, expression, embryologist, microarray, rhesus, monkey, oocyte, embryo, cdna, library, molecular, analysis, stem cell, oocyte quality, preimplantation development, transcription |
is listed by: One Mind Biospecimen Bank Listing has parent organization: Temple University School of Medicine; Pennsylvania; USA |
NIH Office of the Director R24 OD012221; NCRR RR15253 |
PMID:14724133 PMID:17147927 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-24366 | https://orip.nih.gov/comparative-medicine/programs/genetic-biological-and-information-resources | SCR_002765 | PREGER Online, Preger.org | 2026-02-14 02:07:02 | 6 | ||||
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SRMAtlas Resource Report Resource Website 1+ mentions |
SRMAtlas (RRID:SCR_016996) | SRM Atlas, SRMatlas | data or information resource, atlas, database | Resource of targeted proteomics assays to detect and quantify proteins in complex proteome digests by mass spectrometry. Used to quantify the complete human proteome. | collection, proteomic, assay, detect, quantify, protein, mass, spectrometry, peptide | American Recovery and Reinvestment Act ; NHGRI RC2 HG005805; NIGMS R01 GM087221; NCRR S10 RR027584; NIGMS P50 GM076547; Luxembourg Centre for Systems Biomedicine University Luxembourg ; European Research Council ; Swiss National Science Foundation |
PMID:27453469 | Publicly available, Registration required | SCR_016996 | 2026-02-14 02:06:47 | 3 | ||||||||
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Nonhuman Primate Reagent Resource Resource Report Resource Website 100+ mentions |
Nonhuman Primate Reagent Resource (RRID:SCR_012986) | NHPRR | material resource, antibody supplier, reagent supplier | Center that facilitates the optimal use of nonhuman primate models in biomedical research by identifying, developing, characterizing and producing reagents for monitoring or modulating immune responses. They distribute non-human primate-specific antibodies for in vitro diagnostics, as well as develop and produce primate recombinant antibodies for in vivo cell depletion or modulating immune responses. | anti-ig, antibody, biomedical, cell, depletion, diagnostic, immune, immunoglobulin, in vitro, in vivo, macaque, monkey, nonhuman, primate, reagent, recombinant, research, response, specie | NIH Office of the Director R24 OD010976; NIH HHSN272200900037C; NIH HHSN286200400101C; NIH HHSN2722001300031C; NIAID AI126683; NCRR RR016001; NIAID AI040101; NIH 272200900037C; NIH 286200400101C; NIH AI-126683; NIH OD-010976; NIH RR-016001; NIH 2722001300031C; NIH 272201300031C; NIH AI-040101; NIH NHPRR |
nif-0000-24368 | https://orip.nih.gov/comparative-medicine/programs/vertebrate-models http://www.nhpreagents.org/NHP/contact.aspx |
http://nhpreagents.bidmc.harvard.edu/NHP/default.aspx | SCR_012986 | nhp reagents, Nonhuman Primate Reagent Resources, Non-human primate repository, Non human Primate Reagent Resources, NHP Reagent Resource, nhpreagents, NIH Nonhuman Primate Reagent Resource, NHP Reagent, nhpreagent, Non-human Primate Reagent Resources | 2026-02-14 02:05:32 | 221 | ||||||
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Homer2 Resource Report Resource Website 100+ mentions |
Homer2 (RRID:SCR_009586) | software resource, image analysis software, data processing software, software application | Software matlab scripts used for analyzing fNIRS data to obtain estimates and maps of brain activation. Graphical user interface (GUI) for visualization and analysis of functional near-infrared spectroscopy (fNIRS) data. | Analysis, optical, imaging, fnirs, map, brain, activation, BRAIN Initiative |
is recommended by: BRAIN Initiative is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: NIRx2nirs: A NIRx to .nirs data converter |
NIBIB EB025145; NIBIB R01 EB006385; NCRR P41 RR14075 |
Free, Available for download, Freely available | nlx_155773 | http://www.nitrc.org/projects/homer2 https://homer-fnirs.org/ |
SCR_009586 | HOMER1, Photon Migration Imaging toolbox | 2026-02-14 02:05:30 | 223 | ||||||
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TRACULA Resource Report Resource Website 10+ mentions |
TRACULA (RRID:SCR_013152) | TRACULA | software resource, data processing software, software application | Software tool developed for automatically reconstructing a set of major white matter pathways in the brain from diffusion weighted images using probabilistic tractography. This method utilizes prior information on the anatomy of the pathways from a set of training subjects. By incorporating this prior knowledge in the reconstruction procedure, our method obviates the need for manual intervention with the tract solutions at a later stage and thus facilitates the application of tractography to large studies. The trac-all script is used to preprocess raw diffusion data (correcting for eddy current distortion and B0 field inhomogenities), register them to common spaces, model and reconstruct major white matter pathways (included in the atlas) without any manual intervention. trac-all may be used to execute all the above steps or parts of it depending on the dataset and user''''s preference for analyzing diffusion data. Alternatively, scripts exist to execute chunks of each processing pipeline, and individual commands may be run to execute a single processing step. To explore all the options in running trac-all please refer to the trac-all wiki. In order to use this script to reconstruct tracts in Diffusion images, all the subjects in the dataset must have Freesurfer Recons. | tractography, white matter tract, white matter pathway, diffusion weighted image, diffusion magnetic resonance imaging, white matter, brain, reconstruct, diffusion tensor imaging |
is related to: FreeSurfer has parent organization: Harvard Medical School; Massachusetts; USA |
Aging | NIH Blueprint for Neuroscience Research ; Ellison Medical Foundation ; NIBIB EB008129; NIMH U01-MH093765; NCRR P41-RR14075; NCRR U24-RR021382; NIBIB R01-EB006758; NIA R01-AG022381; National Center for Complementary and Alternative Medicine RC1-AT005728; NINDS R01-NS052585; NINDS R21-NS072652; NINDS R01-NS070963 |
PMID:22016733 | nlx_143919 | SCR_013152 | TRACULA - TRActs Constrained by UnderLying Anatomy, TRACULA: TRActs Constrained by UnderLying Anatomy, TRActs Constrained by UnderLying Anatomy | 2026-02-14 02:05:32 | 17 | |||||
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CAWorks Resource Report Resource Website 1+ mentions |
CAWorks (RRID:SCR_014185) | software resource, image analysis software, data processing software, software application | A software application developed to support computational anatomy and shape analysis. The capabilities of CAWorks include: interactive landmark placement to create segmentation (mask) of desired region of interest; specialized landmark placement plugins for subcortical structures such as hippocampus and amygdala; support for multiple Medical Imaging data formats, such as Nifti, Analyze, Freesurfer, DICOM and landmark data; Quadra Planar view visualization; and shape analysis plugin modules, such as Large Deformation Diffeomorphic Metric Mapping (LDDMM). Specific plugins are available for landmark placement of the hippocampus, amygdala and entorhinal cortex regions, as well as a browser plugin module for the Extensible Neuroimaging Archive Toolkit. | image analysis software, computational anatomy, shape analysis, plugin, subcortex, landmark placement |
is used by: Northwestern University Schizophrenia Data and Software Tool (NUSDAST) is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Johns Hopkins University; Maryland; USA |
NIMH 1R01 MH084803; NIBIB R01 EB008171; NIA 5U01AG033655; NCRR P41 RR015241; NIBIB R01 EB000975 |
Available to the research community | http://www.cis.jhu.edu/software/caworks/ | SCR_014185 | Computational Anatomy Works | 2026-02-14 02:05:31 | 1 | |||||||
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TiltPicker Resource Report Resource Website |
TiltPicker (RRID:SCR_016674) | software resource, data processing software, software application | Software tool to facilitate particle selection in single particle electron microscopy. An interactive graphical interface application designed to streamline the selection of particle pairs from tilted-pair datasets. Designed to work with existing software tools for image processing. | particle, selection, single, electron, microscopy, interactive, graphical, interface, tilted, pair, dataset, image, processing | is listed by: OMICtools | NCRR RR23093; NCRR RR17573 |
PMID:19374019 | Free, Available for download, Freely available | http://emg.nysbc.org/redmine/projects/appion/wiki/Appion_Home | SCR_016674 | 2026-02-14 02:05:34 | 0 | |||||||
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Slingshot Resource Report Resource Website 50+ mentions |
Slingshot (RRID:SCR_017012) | software resource, data processing software, software application | Software R package for identifying and characterizing continuous developmental trajectories in single cell data. Cell lineage and pseudotime inference for single-cell transcriptomics. | identify, characterize, continuous, developmental, trajectory, single, cell, data, lineage, pseudotime, inference, transcriptomic | is used by: Totem | NIMH U01 MH105979; NIDCD R01 DC007235; NCRR S10 RR029668; Siebel Foundation ; NIA K01 AG045344; NHGRI T32 HG000047; California Institute of Regenerative Medicine |
PMID:29914354 | Free, Available for download, Freely available | SCR_017012 | 2026-02-14 02:05:34 | 84 | ||||||||
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DOAF Resource Report Resource Website 1+ mentions |
DOAF (RRID:SCR_015666) | DOAF | data or information resource, portal, database, project portal | Project portal for a collaborative database aiming to provide a comprehensive annotation to human genome.It uses the computable, controlled vocabulary of Disease Ontology (DO) and NCBI Gene Reference Into Function (GeneRIF). | disease ontology, annotation, collaboration, collaborative project, java, perl, rubby |
uses: Human Disease Ontology is related to: NUgene Project is related to: Gene Ontology is related to: OBO has parent organization: Northwestern University; Illinois; USA |
NCRR 1R01RR025342; CTSA UL1RR025741 |
PMID:23251346 | Public, Available for download, Tutorial Available | SCR_015666 | Disease Ontology Annotation Framework, Disease Ontology Annotation Framework (DOAF) | 2026-02-14 02:05:34 | 1 | ||||||
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SPAdes Resource Report Resource Website 100+ mentions |
SPAdes (RRID:SCR_000131) | SPAdes | software resource, software toolkit | Software package for assembling single cell genomes and mini metagenomes. Uses short read sets as input. Used for genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. Works with Illumina or IonTorrent reads and can provide hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Intended for small genomes like bacterial or fungal., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | assembler, single, cell, small, genome, short, read, data |
is used by: shovill is listed by: OMICtools is listed by: Debian is listed by: SoftCite is related to: rnaSPAdes is related to: rnaQUAST has parent organization: Saint Petersburg Academic University; Saint Petersburg; Russia works with: Illumina iSeq 100 Sequencing System |
Government of the Russian Federation ; NCRR P41 RR024851 |
PMID:24093227 PMID:22506599 DOI:10.1089/cmb.2012.0021 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01502 | https://sources.debian.org/src/spades/ | http://bioinf.spbau.ru/spades/ | SCR_000131 | SPAdes Genome Assembler | 2026-02-14 02:04:59 | 101 | |||
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ToppCluster Resource Report Resource Website 100+ mentions |
ToppCluster (RRID:SCR_001503) | ToppCluster | data analysis service, analysis service resource, resource, production service resource, service resource | A tool for performing multi-cluster gene functional enrichment analyses on large scale data (microarray experiments with many time-points, cell-types, tissue-types, etc.). It facilitates co-analysis of multiple gene lists and yields as output a rich functional map showing the shared and list-specific functional features. The output can be visualized in tabular, heatmap or network formats using built-in options as well as third-party software. It uses the hypergeometric test to obtain functional enrichment achieved via the gene list enrichment analysis option available in ToppGene. | term enrichment, gene, analysis, gene enrichment analysis, connectivity, heatmap, ortholog, microarray, function, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: GenitoUrinary Development Molecular Anatomy Project is related to: ToppGene Suite |
NIDDK 1U01DK70219; NIDDK P30DK078392; NCRR U54 RR025216; NIDCR U01DE020049 |
PMID:20484371 | Free | OMICS_02225, nlx_152801, biotools:toppcluster | https://bio.tools/toppcluster | SCR_001503 | ToppCluster: A multiple gene list feature analyzer for the dissection of biological systems | 2026-02-14 02:04:27 | 144 | ||||
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DoG picker Resource Report Resource Website 10+ mentions |
DoG picker (RRID:SCR_016655) | DoG picker | image processing software, software resource, data processing software, software application | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 18,2023. Software tool for general particle picking in the single-particle processing of unknown macromolecules. Reference free particle picker with ability to sort particles based on size or it can be used to bootstrap the creation of templates or training datasets for other particle pickers. Used to facilitate particle selection in single particle electron microscopy., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | general, single, particle, picking, macromolecule, size, selection, electron, microscopy, image, transform | is listed by: OMICtools | NCRR RR23093; NCRR RR17573 |
PMID:19374019 | THIS RESOURCE IS NO LONGER IN SERVICE | http://emg.nysbc.org/redmine/projects/appion/wiki/Appion_Home | SCR_016655 | Difference of Gaussians (DoG) picker, Difference of Gaussians Picker, Difference of Gaussians picker | 2026-02-14 02:04:52 | 21 | |||||
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SerialEM Resource Report Resource Website 100+ mentions |
SerialEM (RRID:SCR_017293) | software resource, data processing software, data acquisition software, software application | Software tool for automated EM data acquisition. Used for efficient tilt series acquisition and interface for image capture, display, and storage and for control of some aspects of microscope function. | automated, data, acquisition, tilt, image, capture, display, storage, microscope | NCRR RR00592; NIGMS P01 GM61306 |
PMID:16182563 | Restricted | SCR_017293 | 2026-02-14 02:03:23 | 213 | |||||||||
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BinPacker Resource Report Resource Website 10+ mentions |
BinPacker (RRID:SCR_017038) | data analysis software, software resource, data processing software, software application | Software tool as de novo trascriptome assembler for RNA-Seq data. Used to assemble full length transcripts by remodeling problem as tracking set of trajectories of items over splicing graph. Input RNA-Seq reads in fasta or fastq format, and ouput all assembled candidate transcripts in fasta format. Operating system Unix/Linux. | de novo, transcriptome, assembler, RNAseq, data, full, length, transcript, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
National Natural Science Foundation of China ; NSF 1553680; NCRR P20 RR01 6460; NIGMS P20 GM103429 |
PMID:26894997 | Free, Available for download, Freely available | OMICS_11199, biotools:binpacker | http://sourceforge.net/projects/transcriptomeassembly/files/BinPacker_1.0.tar.gz/download http://sourceforge.net/projects/transcriptomeassembly/files/BinPacker_binary.tar.gz/download https://bio.tools/binpacker |
SCR_017038 | 2026-02-14 02:03:07 | 10 | ||||||
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Appion Package Resource Report Resource Website 10+ mentions |
Appion Package (RRID:SCR_016734) | Appion | data processing software, software application, image processing software, software resource, image analysis software | Software package for processing and analysis of EM images. Appion is integrated with Leginon data acquisition but can also be used stand-alone after uploading images (either digital or scanned micrographs) or particle stacks using a set of provided tools. | processing, analysis, electron, microscope, image | NCRR RR17573; NCRR RR023093; ARCS |
PMID:19263523 | Free, Available for download, Freely available | http://www.appion.org | SCR_016734 | 2026-02-14 02:03:09 | 16 | |||||||
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University of Nebraska Medical Center Advanced Microscopy Core Facility Resource Report Resource Website 10+ mentions |
University of Nebraska Medical Center Advanced Microscopy Core Facility (RRID:SCR_022467) | core facility, access service resource, service resource | Facility houses imaging technologies ranging from super resolution (~ 0.120 um to 0.020 um) to microscopic (~ 0.300 um) to mesoscopic (~ 1 um) biomedical imaging. Imaging specialists provide training and/or actively assist researchers collecting images across imaging instrumentation. Instrumentation includes Zeiss ELYRA PS.1 is inverted microscope for super resolution (SR) structured illumination microscopy (SIM) and single molecule localization microscopy (SMLM) including, PhotoActivated Localization Microscopy (PALM) using photo switchable/convertible fluorescent proteins, Total Internal Reflection Fluorescence (TIRF) and STochastic Optical Reconstruction Microscopy (STORM);Zeiss 800 CLSM with Airyscan is an inverted microscope dramatically increasing conventional confocal image resolution to ~180 nm using Airyscan technology; Zeiss 710 LSM is inverted microscope supporting most basic imaging applications, multi channel and spectral, co localization, live cell, 3D, and time series imaging; Zeiss Celldiscoverer 7 is widefield imaging system for automated, time lapse imaging of live samples; Zeiss Axioscan 7 is high performance whole slide scanning system for fluorescence, brightfield, and polarization imaging;Miltenyi Biotec Ultramicroscope II Light Sheet fluorescence microscope (LSFM) extends fluorescent imaging into true 3D, large scale volumetric imaging of intact tissues, organs, and small organisms. AMCF also houses several high-end data analysis workstations with premier image analysis software including HALO (Indica Labs) and IMARIS (Oxford Instruments) facilitating data rendering, analyses, and presentation options. | USEDit, ABRF, biomedical imaging, microscopy |
is listed by: ABRF CoreMarketplace is related to: USEDit has parent organization: University of Nebraska; Nebraska; USA |
NIGMS GM103427; NIGMS GM106397; NCI CA036727; NCRR RR027301; NIH Office of the Director OD030486 |
open | ABRF_1375 | https://coremarketplace.org/?FacilityID=1375&citation=1 | SCR_022467 | UNMC Advanced Microscopy Core Facility | 2026-02-14 02:08:44 | 18 | ||||||
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University of Texas Southwestern Medical Center Quantitative Light Microscopy Core Facility Resource Report Resource Website 1+ mentions |
University of Texas Southwestern Medical Center Quantitative Light Microscopy Core Facility (RRID:SCR_022605) | QLMC | core facility, access service resource, service resource | Provides access to variety of microscope modalities including laser scanning and spinning disk confocal, multiphoton, wide field deconvolution, CFP/YFP FRET, TIRF, single molecule imaging, and more. Offers customized microscopy training, advise and help with sample preparation, image quantification, and offer basic microscope maintenance. Can streamline your data handling and image visualization as well as automate your image analysis workflow through customized Fiji macros. | Light microscopy, laser scanning and spinning disk confocal, multiphoton, wide field deconvolution, CFP/YFP FRET, TIRF, single molecule imaging, ABRF, USEDit |
is related to: USEDit has parent organization: University of Texas Southwestern Medical Center; Texas; USA |
NCRR 1S10 RR029731; NIH Office of the Director 1S10 OD021684; NIH Office of the Director 1S10OD028630; NCI 1P30 CA142543 |
Restricted | SCR_022605 | Quantitative Light Microscopy Core | 2026-02-14 02:08:28 | 2 |
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