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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Human Reference Protein Interactome Project Resource Report Resource Website 10+ mentions |
Human Reference Protein Interactome Project (RRID:SCR_015670) | HuRI | data or information resource, database, portal, project portal, software resource, web application | Project portal for the Human Reference Protein Interactome Project, which aims generate a first reference map of the human protein-protein interactome network by identifying binary protein-protein interactions (PPIs). It achieves this by systematically interrogating all pairwise combinations of predicted human protein-coding genes using proteome-scale technologies. | protein interactome, protein-protein interaction, ppi, pairwise combination, proteome, human reference | NHGRI R01/U01HG001715; NHGRI P50HG004233; NHLBI U01HL098166; NHLBI U01HL108630; NCI U54CA112962; NCI R33CA132073; NIH RC4HG006066; NICHD ARRA R01HD065288; NICHD ARRA R21MH104766; NICHD ARRA R01MH105524; NIMH R01MH091350; NSF CCF-1219007; NSERC RGPIN-2014-03892 |
PMID:25416956 | Freely Available, Free, Available for download | SCR_015670 | HuRI: The Human Reference Protein Interactome Mapping Project | 2026-09-03 04:58:24 | 20 | |||||||
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Seurat Resource Report Resource Website 10000+ mentions |
Seurat (RRID:SCR_016341) | data analysis software, data processing software, software application, software resource, software toolkit | Software R package designed for QC, analysis, and exploration of single cell RNA-seq data. Enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. Used for quality control, analysis, and exploration of single-cell RNA sequencing (scRNA-seq) data. | single, cell, genomic, RNA-seq, data, QC, analysis, source, heterogeneity, transcriptomic, measurement, integrate, diverse |
is used by: Stardust is used by: Seurat MapQuery is used by: scSidekick is related to: DoubletFinder is related to: Azimuth works with: SeuratWrappers works with: Connectome |
NHGRI 1DP2HG009623; NIMH 5R01MH071679; NSF |
PMID:29608179 | Free, Available for download, Freely available | https://satijalab.org/seurat/get_started.html | SCR_016341 | 2026-09-03 04:58:09 | 11480 | |||||||
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CytoMAP Resource Report Resource Website 10+ mentions |
CytoMAP (RRID:SCR_021227) | data analysis software, data analytics software, data processing software, software application, software resource, software toolkit | Software tool as spatial analysis software for whole tissue sections.Utilizes information on cell type and position to phenotype local neighborhoods and reveal how their spatial distribution leads to generation of global tissue architecture.Used to make advanced data analytic techniques accessible for single cell data with position information. | Histo cytometric multidimensional, analysis pipeline, whole tissue sections, spatial analysis, single cell data with position information, phenotype local neighborhoods, global tissue architecture | has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA | NIAID R01 AI076327; NIAID R01 AI134246; NIAID R01 AI134713; NIAID R21 AI142667; NIAID T32 AI10667; NIAID U19 AI135976; NICHD T32 HD007233; NIGMS T32 GM007270; NSF DGE 1762114 |
PMID:32320656 | Free, Available for download, Freely available | SCR_021227 | Histo-Cytometric Multidimensional Analysis Pipeline | 2026-09-03 04:58:28 | 23 | |||||||
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Computational Analysis of gene Family Evolution Resource Report Resource Website 10+ mentions |
Computational Analysis of gene Family Evolution (RRID:SCR_018924) | CAFE | data analysis software, data processing software, software application, software resource | Software tool for computational analysis of gene family evolution. Used for statistical analysis of evolution gene family sizes. Models evolution of gene family sizes over phylogeny. | Computational analysis, gene family evolution, evolution statistical analysis, gene family size, gene evolution, phylogeny | has parent organization: Indiana University; Indiana; USA | Lilly Endowment ; Inc ; METACyt Initiative of Indiana University ; NHGRI R33 HG003070; NSF MCB 0528465 |
PMID:16543274 | SCR_018924 | CAFE v2.0, CAFE v4.0, CAFE v3.0, CAFE v5.0, Computational Analysis of gene Family Evolution | 2026-09-03 04:58:33 | 17 | |||||||
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SuperSegger Resource Report Resource Website 1+ mentions |
SuperSegger (RRID:SCR_018532) | data processing software, image analysis software, software application, software resource, software toolkit | Software package as automated MATLAB based trainable image cell segmentation, fluorescence quantification and analysis suite. Used for high throughput time lapse fluorescence microscopy of in vivo bacterial cells. Robust image segmentation, analysis and lineage tracking of bacterial cells. | Image cell segmentation, fluorescence quantification, data analysis, high throughput, time lapse, fluorescence microscopy, bacteria cell, image segmentation |
is related to: MATLAB has parent organization: University of Washington; Seattle; USA |
Danish National Research Foundation ; NSF MCB‐1151043‐CAREER; NSF PHY‐084845; Sloan BR2011‐110; University of Washington Royalty Research Fund |
PMID:27569113 | Free, Available for download, Freely available | https://github.com/wiggins-lab/SuperSegger | SCR_018532 | 2026-09-03 04:58:30 | 3 | |||||||
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Drop-seq tools Resource Report Resource Website 100+ mentions |
Drop-seq tools (RRID:SCR_018142) | data analysis software, data processing software, software application, software resource | Software Java tools for analyzing Drop-seq data. Used to analyze gene expression from thousands of individual cells simultaneously. Analyzes mRNA transcripts while remembering origin cell transcript. | Simultaneous analysis, Drop-seq data, gene expression, thousands individual cells |
is listed by: Debian has parent organization: Broad Institute |
Klarman Cell Observatory ; MGH Psychiatry Residency Research Program ; NHGRI P50 HG006193; NICHD F32 HD075541; NIMH R25 MH094612; NIMH U01 MH105960; NSF DMR 1310266; NSF DMR 1420570; NSF ECS 0335765; Simons Foundation ; Stanley Center for Psychiatric Research ; Stanley-MGH Fellowship in Psychiatric Neuroscience ; Stewart Trust Fellows Award |
PMID:26000488 | https://sources.debian.org/src/drop-seq-tools/ | SCR_018142 | Droplet sequencing tools, Droplet sequencing data analysis software tools | 2026-09-03 04:58:31 | 112 | |||||||
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MITE-Hunter Resource Report Resource Website 1+ mentions |
MITE-Hunter (RRID:SCR_020946) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software pipeline to identify MITEs as well as other small Class 2 non autonomous Transposable Elements from genomic DNA data sets. Used for discovering miniature inverted repeat transposable elements from genomic sequences. Can search large genomic data sets including whole genome sequences. | Class 2 non-autonomous transposable element, genes non-coding regions, genome evolution, coding sequence, genomic DNA data sets, | NSF 0607123 | PMID:20880995 | Free, Available for download, Freely available | https://github.com/jburnette/MITE-Hunter | SCR_020946 | Miniature Inverted repeat Transposable Elements Hunter | 2026-09-03 04:57:18 | 7 | |||||||
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runBioSimulations Resource Report Resource Website 1+ mentions |
runBioSimulations (RRID:SCR_019110) | software resource, web application | Web tool for executing broad range of modeling studies and visualizing their results. Provides web interface for reusing any model. Models, simulations, and visualizations are available under licenses specified for each resource. | Executing modeling studies, visualization, model reusing, simulation, bio.tools |
uses: BioSimulators is listed by: bio.tools is listed by: Debian |
Center for Reproducible Biomodeling Modeling ; National Institute of Bioimaging and Bioengineering ; National Institute of General Medical Sciences ; NIH ; NSF |
Free, Freely available | biotools:runbiosimulations | https://bio.tools/runbiosimulations | SCR_019110 | 2026-09-03 04:55:39 | 3 | |||||||
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HDBIG Resource Report Resource Website |
HDBIG (RRID:SCR_014120) | data processing software, image analysis software, software application, software resource, software toolkit | A collection of software tools for high dimensional brain imaging genomics. These tools are designed to perform comprehensive joint analysis of heterogeneous imaging genomics data. HDBIG-SR is an HDBIG toolkit for sparse regression while HDBIG-SCCA is an HDBIG toolkit for sparse association. | image analysis software, genomics, imaging, joint analysis, toolkit, sparse association, sparse regression |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Indiana University; Indiana; USA |
NLM R01 LM011360; NSF IIS-1117335 |
http://www.iu.edu/~hdbig/ | SCR_014120 | High Dimensional Brain Imaging Genomics Toolkit | 2026-09-03 04:52:34 | 0 | ||||||||
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Wisconsin Cortical Thickness Analysis (CTA) Toolbox Resource Report Resource Website |
Wisconsin Cortical Thickness Analysis (CTA) Toolbox (RRID:SCR_014180) | data analysis software, data processing software, software application, software resource, software toolkit | A Matlab tool to perform statistical analysis on cortical thickness signals on brain surfaces obtained from Freesurfer. It is used for multi-resolutional analysis of such cortical thickness signals and detecting group differences. It is based on the Spectral Graph Wavelet Transform (SGWT) toolbox and provides plug and play methods for deriving Wavelet Multiscale Descriptor (WMD), cortical thickness smoothing using SGWT, Multivariate General Linear Model (MGLM), and False Discovery Rate (FDR). | matlab, software toolkit, cortical thickness signal, data analysis software |
uses: FreeSurfer is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) |
Wisconsin Partnership Program ; NIA R01AG040396; NIA R01AG021155; NSF RI 1116584; NSF CAREER 1252725; UW ADRC NIA P50 AG033514; UW ICTR NCRR 1UL1RR025011; NIA P30 AG010129; NIA K01 AG030514 |
http://pages.cs.wisc.edu/~wonhwa/code/CTA_toolbox.html, http://pages.cs.wisc.edu/~wonhwa/project/ctdiscrim.html | SCR_014180 | 2026-09-03 04:52:26 | 0 | |||||||||
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ALCHEMY Resource Report Resource Website 1+ mentions |
ALCHEMY (RRID:SCR_005761) | ALCHEMY | software resource, source code | ALCHEMY is a genotype calling algorithm for Affymetrix and Illumina products which is not based on clustering methods. Features include explicit handling of reduced heterozygosity due to inbreeding and accurate results with small sample sizes. ALCHEMY is a method for automated calling of diploid genotypes from raw intensity data produced by various high-throughput multiplexed SNP genotyping methods. It has been developed for and tested on Affymetrix GeneChip Arrays, Illumina GoldenGate, and Illumina Infinium based assays. Primary motivations for ALCHEMY''s development was the lack of available genotype calling methods which can perform well in the absence of heterozygous samples (due to panels of inbred lines being genotyped) or provide accurate calls with small sample batches. ALCHEMY differs from other genotype calling methods in that genotype inference is based on a parametric Bayesian model of the raw intensity data rather than a generalized clustering approach and the model incorporates population genetic principles such as Hardy-Weinberg equilibrium adjusted for inbreeding levels. ALCHEMY can simultaneously estimate individual sample inbreeding coefficients from the data and use them to improve statistical inference of diploid genotypes at individual SNPs. The main documentation for ALCHEMY is maintained on the sourceforge-hosted MediaWiki system. Features * Population genetic model based SNP genotype calling * Simultaneous estimation of per-sample inbreeding coefficients, allele frequencies, and genotypes * Bayesian model provides posterior probabilities of genotype correctness as quality measures * Growing number of scripts and supporting programs for validation of genotypes against control data and output reformating needs * Multithreaded program for parallel execution on multi-CPU/core systems * Non-clustering based methods can handle small sample sets for empirical optimization of sample preparation techniques and accurate calling of SNPs missing genotype classes ALCHEMY is written in C and developed on the GNU/Linux platform. It should compile on any current GNU/Linux distribution with the development packages for the GNU Scientific Library (gsl) and other development packages for standard system libraries. It may also compile and run on Mac OS X if gsl is installed. | diploid, genotype, snp, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: SourceForge has parent organization: Cornell University; New York; USA |
NSF 0606461 | PMID:20926420 | GNU General Public License | biotools:alchemy, nlx_149227 | https://bio.tools/alchemy | SCR_005761 | ALCHEMY - An automated population genetic model driven SNP genotype calling method | 2026-09-03 05:06:15 | 5 | ||||
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Sol Genomics Network - Bulk download Resource Report Resource Website |
Sol Genomics Network - Bulk download (RRID:SCR_007161) | data or information resource, data set | Allows users to download Unigene or BAC information using a list of identifiers or complete datasets with FTP., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | database, dataset, unigene, gene, bac, genomics, clone, array spot, unigene id, bac ends |
is related to: SGN has parent organization: Boyce Thompson Institute for Plant Research |
NSF 0820612; USDA CSREES |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30227 | SCR_007161 | SGN bulk download | 2026-09-03 05:06:02 | 0 | |||||||
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Early Indicators of Later Work Levels Disease and Death (EI) - Union Army Samples Public Health and Ecological Datasets Resource Report Resource Website 1+ mentions |
Early Indicators of Later Work Levels Disease and Death (EI) - Union Army Samples Public Health and Ecological Datasets (RRID:SCR_008921) | Early Indicators of Later Work Levels Disease and Death, EI project | data or information resource, data set | A dataset to advance the study of life-cycle interactions of biomedical and socioeconomic factors in the aging process. The EI project has assembled a variety of large datasets covering the life histories of approximately 39,616 white male volunteers (drawn from a random sample of 331 companies) who served in the Union Army (UA), and of about 6,000 African-American veterans from 51 randomly selected United States Colored Troops companies (USCT). Their military records were linked to pension and medical records that detailed the soldiers������?? health status and socioeconomic and family characteristics. Each soldier was searched for in the US decennial census for the years in which they were most likely to be found alive (1850, 1860, 1880, 1900, 1910). In addition, a sample consisting of 70,000 men examined for service in the Union Army between September 1864 and April 1865 has been assembled and linked only to census records. These records will be useful for life-cycle comparisons of those accepted and rejected for service. Military Data: The military service and wartime medical histories of the UA and USCT men were collected from the Union Army and United States Colored Troops military service records, carded medical records, and other wartime documents. Pension Data: Wherever possible, the UA and USCT samples have been linked to pension records, including surgeon''''s certificates. About 70% of men in the Union Army sample have a pension. These records provide the bulk of the socioeconomic and demographic information on these men from the late 1800s through the early 1900s, including family structure and employment information. In addition, the surgeon''''s certificates provide rich medical histories, with an average of 5 examinations per linked recruit for the UA, and about 2.5 exams per USCT recruit. Census Data: Both early and late-age familial and socioeconomic information is collected from the manuscript schedules of the federal censuses of 1850, 1860, 1870 (incomplete), 1880, 1900, and 1910. Data Availability: All of the datasets (Military Union Army; linked Census; Surgeon''''s Certificates; Examination Records, and supporting ecological and environmental variables) are publicly available from ICPSR. In addition, copies on CD-ROM may be obtained from the CPE, which also maintains an interactive Internet Data Archive and Documentation Library, which can be accessed on the Project Website. * Dates of Study: 1850-1910 * Study Features: Longitudinal, Minority Oversamples * Sample Size: ** Union Army: 35,747 ** Colored Troops: 6,187 ** Examination Sample: 70,800 ICPSR Link: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/06836 | late adult human, male, caucasian, african-american, veteran, military, medical, socioeconomic, civil war, american civil war, cause of death, census data, demographic, disease, health status, labor force, medical record, midlife, military pension, pension, military recruitment, military service, mortality rate, nineteenth century, nutrition, socioeconomic status, twentieth century, union army, census |
is related to: National Archive of Computerized Data on Aging (NACDA) has parent organization: University of Chicago; Illinois; USA |
Aging | NIA PO1 AG10120; NSF SBR 9114981 |
Publicly available from ICPSR; copies on CD-ROM may be obtained from the CPE, Which also maintains an interactive Internet Data Archive and Documentation Library. | nlx_151822 | http://www.cpe.uchicago.edu/ | SCR_008921 | Public Health and Ecological Datasets, Aging of Veterans of the Union Army, Early Indicators of Later Work Levels Disease and Death ������?? Union Army Samples | 2026-09-03 05:06:11 | 1 | ||||
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Montana State University Functional Genomics Core Facility Resource Report Resource Website |
Montana State University Functional Genomics Core Facility (RRID:SCR_009939) | access service resource, core facility, service resource | Core provides instrumentation and support for academic investigators throughout Montana and Rocky Mountain west. For most instrumentation, facility provides instruction and supervision followed by independent user access. For those doing Affymetrix microarrays, facility can also accept RNA samples and provides full service processing. Assists with experimental planning and grantmanship phases. | affymetrix array, nucleic acid isolation, nucleic acid microarray assay, gene expression analysis assay, transcription profiling assay |
is listed by: Eagle I has parent organization: Montana State University |
MJ Murdock Charitable Trust ; MT INBRE ; NSF |
Restricted | nlx_156407 | http://bugserv2.core.montana.edu/index.php?page=functional-genomics-core-facility http://cores.montana.edu/genomics | http://montana.eagle-i.net/i/0000012a-2502-57bb-f94c-e32480000000 | SCR_009939 | MSU Functional Genomics Core Facility | 2026-09-03 05:06:46 | 0 | |||||
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Efficient Permutation Testing Resource Report Resource Website |
Efficient Permutation Testing (RRID:SCR_014104) | software resource, source code | A Matlab implementation for efficient permutation testing by using matrix completion. | permutation, nueroimaging, source code, fast, matlab |
uses: MATLAB is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Wisconsin-Madison; Wisconsin; USA |
Wisconsin Partnership Fund ; NIA R01 AG040396; NSF CAREER 1252725; NSF RI 1116584; UW ADRC NIA P50 AG033514; UW ICTR NCRR 1UL1RR025011; Veterans Administration Merit Review I01CX000165 |
Available for download, Acknowledgement requested | http://pages.cs.wisc.edu/~vamsi/pt_fast.html | SCR_014104 | Speeding Up Permutation Testing in Neuroimaging | 2026-09-03 05:07:52 | 0 | |||||||
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National High Magnetic Field Laboratory High B/T Core Facility Resource Report Resource Website |
National High Magnetic Field Laboratory High B/T Core Facility (RRID:SCR_017360) | B/T | access service resource, core facility, service resource | Facility to conduct experiments in high magnetic fields up to 15 tesla and at very low temperatures down to 0.4 mK simultaneously. Located at University of Florida in Gainesville, it is operated as part of Physics Department Microkelvin Laboratory. | Magnetic, field, temperature | is related to: University of Florida; Florida; USA | Department of Defense ; Department of Energy ; Florida State ; NIH ; NSF DMR-1644779 |
Restricted | SCR_017360 | NHMF Laboratory High B/T Facility, High B/T (magnetic field / temperature) Facility, High B/T Facility | 2026-09-03 05:08:18 | 0 | |||||||
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National MagLab University of Florida McKnight Brain Institute Advanced Magnetic Resonance Imaging and Spectroscopy AMRIS Core Facility Resource Report Resource Website 500+ mentions |
National MagLab University of Florida McKnight Brain Institute Advanced Magnetic Resonance Imaging and Spectroscopy AMRIS Core Facility (RRID:SCR_017362) | AMRIS | access service resource, core facility, service resource | National High Magnetic Field Laboratory (MagLab) site. It provides researchers with advanced NMR, MRI, and spectroscopy tools (human/animal imaging) for biomedical studies, specializing in high-field magnetic resonance technology. Hosts spectrometers and scanners, including high-field NMR (up to 1.5 GHz), MR microscopy, and human/animal MRI systems (e.g., 3T and 900 MHz). Offers expertise in high-resolution solution NMR, solid-state NMR, and specialized imaging for in vivo animal models and humans.Features an RF coil lab that designs, builds, and tests custom MRI/NMR coils to optimize data collection. Supports research into Alzheimer's, cancer, metabolism, and brain development. | Nuclear Magnetic Resonance, Magnetic Resonance Imaging, spectroscopy, magnetic resonans, scanner, magnet |
has parent organization: National High Magnetic Field Laboratory has parent organization: University of Florida; Florida; USA |
Department of Defense ; Department of Energy ; NSF DMR-1157490; NSF DMR-1644779; NSF DMR-2128556; State of Florida |
Restricted | SCR_017363 | https://nationalmaglab.org/user-facilities/nmr-mri, https://nationalmaglab.org | SCR_017362 | , Advanced Magnetic Resonance Imaging and Spectroscopy AMRIS Facility | 2026-09-03 05:08:23 | 859 | |||||
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SpikeHunter Resource Report Resource Website 1+ mentions |
SpikeHunter (RRID:SCR_024831) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software deep learning tool for identifying phage tailspike proteins. Used to identify phage tailspike proteins. | identifying phage tailspike proteins, phage tailspike protein, deplolymerase, right-handed beta-helix, | NLM ; NSF |
PMID:37503040 | Free, Available for download, Freely available | SCR_024831 | 2026-09-03 05:09:06 | 1 | |||||||||
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Guided Sparse Factor Analysis Resource Report Resource Website 1+ mentions |
Guided Sparse Factor Analysis (RRID:SCR_025023) | GSFA | software resource, software toolkit | Software R package that performs sparse factor analysis and differential gene expression discovery simultaneously on single cell CRISPR screening data. | sparse factor analysis, differential gene expression, discovery simultaneously, single cell CRISPR screening data, | NHGRI R01 HG011883; NHGRI R01HG010773; NIGMS R01 GM126553; NIMH R01MH110531; NIMH R01MH116281; NSF ; Sloan Research Fellowship |
PMID:37770710 | Free, Available for download, Freely available | SCR_025023 | 2026-09-03 05:09:12 | 1 | ||||||||
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PyContact Resource Report Resource Website 1+ mentions |
PyContact (RRID:SCR_025066) | data analysis software, data processing software, software application, software resource | Software tool for analysis of non-covalent interactions in molecular dynamics trajectories. Implemented in Python and is universally applicable to any kind of MD trajectory supported by MDAnalysis package. | non-covalent interactions, molecular dynamics trajectories, | is related to: MDAnalysis | German Research Foundation ; NIGMS P41 GM104601; NSF |
PMID:29414703 | Free, Available for download, Freely available, | https://github.com/maxscheurer/pycontact | SCR_025066 | 2026-09-03 05:09:18 | 3 |
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