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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Kourami Resource Report Resource Website 1+ mentions |
Kourami (RRID:SCR_022280) | data processing software, software application, software resource | Software graph guided assembly for novel human leukocyte antigen allele discovery. Graph guided assembly for HLA haplotypes covering typing exons using high coverage whole genome sequencing data.Implemented in Java and supported on Linux and Mac OS X. | graph guided assembly, novel human leukocyte antigen allele discovery, HLA alleles, HLA alleles assembly | Gordon and Betty Moore Foundation ; NHGRI R01HG007104; NSF CCF1256087; NSF CCF1319998 |
PMID:29415772 | Free, Available for download, Freely available | SCR_022280 | 2026-09-05 06:31:00 | 4 | |||||||||
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iSamples Resource Report Resource Website 1+ mentions |
iSamples (RRID:SCR_021750) | data or information resource, portal, project portal | Project to align physical sample identifiers. Used to design, develop, and promote service infrastructure to uniquely, consistently, and conveniently identify material samples, record metadata about them, and persistently link them to other samples and derived digital content, including images, data, and publications. | Align physical sample identifiers, physical sample identifiers, align identifiers | NSF 2004562; NSF 2004642; NSF 2004815; NSF 2004839 |
DOI:10.1093/gigascience/giab028 | Free, Freely available | https://zenodo.org/communities/isamples?page=1&size=20 | SCR_021750 | internet of Samples | 2026-09-05 06:30:59 | 1 | |||||||
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Rascaf Resource Report Resource Website 1+ mentions |
Rascaf (RRID:SCR_022014) | data processing software, software application, software resource | Software tool for scaffolding with RNA-seq read alignments. Used for improving genome assembly with RNA sequencing data. | Scaffolding, RNA-seq data, scaffolding with RNAseq read alignments, improving genome assembly, RNA sequencing data | NSF IOS1339134 | DOI:10.3835/plantgenome2016.03.0027 | Free, Available for download, Freely available | SCR_022014 | 2026-09-05 06:30:59 | 3 | |||||||||
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OmicsGAN Resource Report Resource Website 1+ mentions |
OmicsGAN (RRID:SCR_022976) | software application, software resource | Software generative adversarial network to integrate two omics data and their interaction network to generate one synthetic data corresponding to each omics profile that can result in better phenotype prediction. Used to capture information from interaction network as well as two omics datasets and fuse them to generate synthetic data with better predictive signals. | integrate two omics data, interaction network, generate one synthetic data corresponding to each omics profile, phenotype prediction | NIDA DK097771; NIGMS R01GM113952; NSF III1755761 |
PMID:34415323 | Free, Available for download, Freely available | SCR_022976 | Omics Generative Adversarial Network | 2026-09-05 06:33:12 | 1 | ||||||||
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VirusDetect Resource Report Resource Website 10+ mentions |
VirusDetect (RRID:SCR_023669) | software resource, software toolkit | Software package to efficiently and exhaustively analyze large scale sRNA datasets for virus identification. Automated pipeline for virus discovery using deep sequencing of small RNAs. | Virus discovery, analyze large scale sRNA datasets, virus identification, deep sequencing of small RNAs, sequencing, small RNAs | NSF | PMID:27825033 | Free, Available for download, Freely available | https://github.com/kentnf/VirusDetect | SCR_023669 | 2026-09-05 06:33:15 | 18 | ||||||||
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rockd Resource Report Resource Website |
rockd (RRID:SCR_024431) | data or information resource, database | Map database allows to record your geological observations and uses your location to provide spatially informed suggestions for nearby geologic units, time intervals, and fossils. | Map database, record geological observations, | NSF ; UW Geoscience |
Free, Freely available | SCR_024431 | 2026-09-05 06:33:18 | 0 | ||||||||||
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Lamont-Doherty Core Repository Resource Report Resource Website |
Lamont-Doherty Core Repository (RRID:SCR_002216) | LDEO-DSSR, LDCR | access service resource, core facility, service resource | Core repository and one of the world's most unique and important collections of scientific samples from the deep sea. Sediment cores from every major ocean and sea are archived at the Core Repository. The collection contains approximately 72,000 meters of core composed of 9,700 piston cores; 7,000 trigger weight cores; and 2,000 other cores such as box, kasten, and large diameter gravity cores. They also hold 4,000 dredge and grab samples, including a large collection of manganese nodules, many of which were recovered by submersibles. Over 100,000 residues are stored and are available for sampling where core material is expended. In addition to physical samples, a database of the Lamont core collection has been maintained for nearly 50 years and contains information on the geographic location of each collection site, core length, mineralogy and paleontology, lithology, and structure, and more recently, the full text of megascopic descriptions. Samples from cores and dredges, as well as descriptions of cores and dredges (including digital images and other cruise information), are provided to scientific investigators upon request. Materials for educational purposes and museum displays may also be made available in limited quantities when requests are adequately justified. Various services and data analyses, including core archiving, carbonate analyses, grain size analyses, and RGB line scan imaging, GRAPE, P-wave velocity and magnetic susceptibility runs, can also be provided at cost. The Repository operates a number of labs and instruments dedicated to making fundamental measurements on material entering the repository including several non-destructive methods. Instruments for conducting and/or assisting with analyses of deep-sea sediments include a GeoTek Multi-Sensor Core Logger, a UIC coulometer, a Micromeritics sedigraph, Vane Shear, X-radiograph, Sonic Sifter, freeze dryer, as well as a variety of microscopes, sieves, and sampling tools. They also make these instruments available to the scientific community for conducting analyses of deep-sea sediments. If you are interested in borrowing any field equipment, please contact the Repository Curator. | deep sea, sediment, ocean, sea, geoscience, metadata |
is listed by: CINERGI is listed by: DataCite is listed by: re3data.org has parent organization: Columbia University; New York; USA |
NSF ; Lamont -Doherty Earth Observatory |
Free, Freely available | DOI:10.26022, DOI:10.17616/R3PV10, nlx_154738 | https://doi.org/10.17616/R3PV10, https://doi.org/10.17616/r3pv10, https://doi.org/10.26022/, https://dx.doi.org/10.26022/ | SCR_002216 | LDEO-Deep Sea Sample Repository, LDEO Core Repository, Lamont -Doherty Earth Observatory | 2026-09-05 06:33:22 | 0 | |||||
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National Lacustrine Core Facility Resource Report Resource Website |
National Lacustrine Core Facility (RRID:SCR_002215) | LacCore | access service resource, core facility, service resource | Archive of almost 20,000 meters of high quality sediment cores from large and small expeditions to lakes all around the world. LacCore advocates for, coordinates, and facilitates core-based research on Earth's continents through collaborative support for logistics, field and laboratory, and data and sample curation and dissemination. They provide a wide variety of fee-based analytical services, as well as offer training and instrument time to lab visitors. They also develop Standard Operating Procedures (SOPs) for local training and adoption by individuals at other labs. | lacustrine, lake, sediment, climate, environment, biota, microscopic, microscopy, marine, mineral, mineraloid, metadata |
is listed by: CINERGI has parent organization: University of Minnesota Twin Cities; Minnesota; USA |
NSF EAR-1226265 | Free, Freely available | nlx_154737 | SCR_002215 | Limnological Research Center LacCore Facility, LRC LacCore Facility | 2026-09-05 06:33:22 | 0 | ||||||
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Fungal Genome Initiative Resource Report Resource Website 10+ mentions |
Fungal Genome Initiative (RRID:SCR_003169) | FGI | data or information resource, data set | Produces and analyzes sequence data from fungal organisms that are important to medicine, agriculture and industry. The FGI is a partnership between the Broad Institute and the wider fungal research community, with the selection of target genomes governed by a steering committee of fungal scientists. Organisms are selected for sequencing as part of a cohesive strategy that considers the value of data from each organism, given their role in basic research, health, agriculture and industry, as well as their value in comparative genomics. | sequence, fungi, gene annotation, genome |
is listed by: 3DVC has parent organization: Broad Institute |
NHGRI ; NSF ; NIAID ; USDA |
Free, Freely available | nif-0000-30591 | SCR_003169 | 2026-09-05 06:33:23 | 18 | |||||||
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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 | 2026-09-05 06:33:26 | 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 | 2026-09-05 06:33:28 | 0 | |||||||
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PyNWB Resource Report Resource Website 1+ mentions |
PyNWB (RRID:SCR_017452) | software application, software resource | Software Python package for working with Neurodata stored in Neurodata Without Borders files. Software providing API allowing users to read and create NWB formatted HDF5 files. Developed in support to NWB project with aim of spreading standardized data format for cellular based neurophysiology information. | Neurodata, stored, NWB, file, share, standardized, data, format, neurophysiology, BRAIN Initiative |
uses: Hierarchical Data Modeling Framework is used by: NWB Explorer is recommended by: BRAIN Initiative is listed by: OMICtools is listed by: Neurodata Without Borders is related to: Neurodata Extensions Catalog is related to: HDMF Common Schema is related to: NWB Inspector |
Allen Institute for Brain Science ; General Electric ; Howard Hughes Medical Institute ; International Neuroinformatics Coordinating Facility ; Kavli Foundation ; NIH BRAIN Initiative R24 MH116922; NSF 0855272 |
PMID:26590340 | Free, Available for downloading, Freely available | https://github.com/NeurodataWithoutBorders/pynwb | https://github.com/AllenInstitute/nwb-api | SCR_017452 | 2026-09-05 06:33:03 | 4 | ||||||
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CellChat Resource Report Resource Website 500+ mentions |
CellChat (RRID:SCR_021946) | software resource, software toolkit | Software R toolkit for inference, visualization and analysis of cell-cell communication from single cell data.Quantitatively infers and analyzes intercellular communication networks from single-cell RNA-sequencing data. Predicts major signaling inputs and outputs for cells and how those cells and signals coordinate for functions using network analysis and pattern recognition approaches. Classifies signaling pathways and delineates conserved and context specific pathways across different datasets. | inference, visualization, analysis, cell-cell communication, single cell data, intercellular communication networks, single-cell RNA-sequencing data | Howard Hughes Medical Institute ; LEO Foundation ; NIGMS R01 GM123731; NIH P30 AR07504; NIH U01 AR073159; NSF DMS1763272; Pew Charitable Trust ; Simons Foundation ; UC Irvine |
PMID:33597522 | Free, Available for download, Freely available | http://www.cellchat.org/ | SCR_021946 | 2026-09-05 06:33:09 | 753 | ||||||||
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simplePHENOTYPES Resource Report Resource Website 1+ mentions |
simplePHENOTYPES (RRID:SCR_022523) | software resource, software toolkit | Software R package that simulates pleiotropy, partial pleiotropy, and spurious pleiotropy in wide range of genetic architectures, including additive, dominance and epistatic models. Used to simulate multiple traits controlled by loci with varying degrees of pleiotropy. | Multiple traits simulation, pleiotropy, partial pleiotropy, spurious pleiotropy, causal mutations affecting multiple traits |
is related to: CRAN is related to: R Project for Statistical Computing |
NSF 1733606 | PMID:33129253 | Free, Available for download, Freely available | https://github.com/samuelbfernandes/simplePHENOTYPES | SCR_022523 | Simulation of Pleiotropic, Linked and Epistatic Phenotypes | 2026-09-05 06:33:10 | 2 | ||||||
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SYGNAL Resource Report Resource Website 1+ mentions |
SYGNAL (RRID:SCR_023080) | software resource, software toolkit | Software pipeline to integrate correlative, causal and mechanistic inference approaches into unified framework that systematically infers causal flow of information from mutations to TFs and miRNAs to perturbed gene expression patterns across patients. Used to decipher transcriptional regulatory networks from multi-omic and clinical patient data. Applicable for integrating genomic and transcriptomic measurements from human cohorts. | Integrating genomic and transcriptomic measurements, human cohorts, transcriptional regulatory networks, integrate correlative, causal and mechanistic inference, unified framework, infers causal flow of information, mutations to TFs, miRNAs to perturbed gene expression patterns across patients, | American Cancer Society Research Scholar Grant ; NCI U24CA143835; NIGMS P50GM076547; NIGMS R01GM077398; NSF ABI NSF-1262637; NSF DBI-0640950 |
PMID:27426982 | Free, Available for download, Freely available | SCR_023080 | SYstems Genetic Network AnaLysis | 2026-09-05 06:33:13 | 1 | ||||||||
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Automated Fiber Quantification in Python Resource Report Resource Website 10+ mentions |
Automated Fiber Quantification in Python (RRID:SCR_023366) | pyAFQ | software resource, software toolkit | Software package focused on automated delineation of major fiber tracts in individual human brains, and quantification of tissue properties within the tracts.Software for automated processing and analysis of diffusion MRI data. Automates tractometry. | Automates tractometry, automated delineation of major fiber tracts, individual human brains, quantification of tissue properties, tissue properties within fiber tracts, diffusion MRI data, | Alfred P. Sloan Foundation ; Gordon and Betty Moore Foundation ; NIBIB R01EB027585; NIMH 1RF1MH121868; NSF 1551330; The BRAIN Initiative |
PMID:35079748 | Free, Available for download, Freely available | SCR_023366 | 2026-09-05 06:33:14 | 12 | ||||||||
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MaAsLin2 Resource Report Resource Website 100+ mentions |
MaAsLin2 (RRID:SCR_023241) | software resource, software toolkit | SoftwareR package that identifies microbial taxa correlated with factors of interest using generalized linear models and mixed models.Used for efficiently determining multivariable association between clinical metadata and microbial meta'omic features. | Microbiome Multivariable Associations with Linear Models, | NHGRI R01HG005220; NIAID U19AI110820; NIDDK R24DK110499; NIDDK U54DK102557; NSF DEB-2028280 |
DOI:10.1371/journal.pcbi.1009442 | Free, Available for download, Freely available | https://huttenhower.sph.harvard.edu/maaslin/ | SCR_023241 | 2026-09-05 06:33:13 | 212 | ||||||||
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AmpliconArchitect Resource Report Resource Website 50+ mentions |
AmpliconArchitect (RRID:SCR_023150) | software resource, software toolkit | Software package designed to call circular DNA from short read WGS data.Used to identify one or more connected genomic regions which have simultaneous copy number amplification and elucidates architecture of amplicon.Used to reconstruct structure of focally amplified regions using whole genome sequencing and validate it extensively on multiple simulated and real datasets, across wide range of coverage and copy numbers. | call circular DNA, short read WGS data, connected genomic regions identification, simultaneous copy number amplification, amplicon | NHGRI HG010149; NIGMS R01GM114362; NSF NSF-DBI-1458557 |
DOI:10.1038/s41467-018-08200-y | SCR_023150 | 2026-09-05 06:33:13 | 53 | ||||||||||
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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 | 2026-09-05 06:33:29 | 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 | 2026-09-05 06:33:37 | 0 |
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