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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Template Based Rotation Resource Report Resource Website 1+ mentions |
Template Based Rotation (RRID:SCR_012157) | TBR | data processing software, image analysis software, software application, software resource | A tool for functional connectivity analysis of fcMRI data that maps functional data from individual sessions onto a priori spatial components from group level parcellations. | functional connectivity, analysis, fmri, fcmri, parcellation, map, template, resting state, matlab | Aging | NIA P01AG036694 | DOI:10.1016/j.neuroimage.2014.08.022 | GNU General Public License v3 | rid_000095 | http://nmr.mgh.harvard.edu/harvardagingbrain/People/AaronSchultz/Aarons_Scripts.html | SCR_012157 | Template Based Rotation (TBR) | 2026-09-05 06:30:47 | 1 | ||||
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Anvi'o Resource Report Resource Website 10+ mentions |
Anvi'o (RRID:SCR_021802) | data analysis software, data processing software, data visualization software, software application, software resource | Open source software analysis and visualization platform for microbial omics including genomics, metagenomics, metatranscriptomics, pangenomics, metapangenomics, phylogenomics, and microbial population genetics in integrated fashion through extensive interactive visualization capabilities. | analysis, visualization, integrated omics, metagenomics, pangenomics, phylogenomics, microbial omics | Alfred P. Sloan Foundation ; Helmholtz Institute for Functional Marine Biodiversity ; Marine Biological Laboratory ; Simons Foundation ; University of Chicago ; W. M. Keck Foundation |
Free, Available for download, Freely available | biotools:anvio | https://github.com/merenlab/anvio, https://bio.tools/anvio | SCR_021802 | Anvi’o | 2026-09-05 06:29:46 | 21 | |||||||
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LYSIS Resource Report Resource Website 50+ mentions |
LYSIS (RRID:SCR_001385) | LYSIS | data analysis software, data processing software, simulation software, software application, software resource, software toolkit, source code | Interactive software of a set of modular programs (each performing a specific task) that provide an integrated computing environment for data analysis and system modeling. Unique capabilities of LYSIS include input-output nonlinear system modeling and the novel methodology of Principal Dynamic Modes (PDMs). LYSIS is currently available in two versions: one for LYSIS 7.1 Windows and one for LYSIS 7.2 Matlab. Early versions are also available for UNIX environments, distributed as source code that can be compiled for each UNIX implementation (e.g., Solaris, HPUX, Linux). Specific features of LYSIS that cannot be found in commercially available packages include the efficient kernel estimation using Laguerre expansions and the use of Principal Dynamic Modes (PDMs). These enable input-output modeling of dynamic nonlinear systems with relatively short data-records (even in the presence of considerable noise). System Requirements * Operating System ** Windows XP/Vista/7 ** Sun/Unix: Solaris 2.x | modeling, data analysis, system modeling, analysis, nonlinear, principal dynamic modes, nonlinear modeling, windows, matlab | has parent organization: Biomedical Simulations Resource | NIBIB P41-EB001978; NCRR P41-RR01861 |
Free, Freely Available | nlx_152571 | SCR_001385 | 2026-09-05 06:29:53 | 56 | |||||||
|
NeuroExplorer Resource Report Resource Website 1000+ mentions |
NeuroExplorer (RRID:SCR_001818) | NeuroExplorer | commercial organization, data analysis software, data processing software, software application, software resource | Data analysis software for neurophysiology with a multitude of features, including: * Import of native data files created by many popular data acquisition systems * All standard histogram and raster analyses * Shift predictors in crosscorrelograms and color markers in perievent rasters * Joint PSTH, burst analysis and many more analyses of timestamped data * Spectral analysis of spike and continuous data * 3D data view and animation * Fully customizable WYSIWYG graphics * Custom analysis and batch mode processing with internal scripting language * Direct data link to Matlab and Excel * Statistical tests via direct link to R-project | neurophysiology, spike train, spike, statistical test, analysis, windows, mac, 3d data, animation, burst analysis, channel, cross correlogram, electrophysiology, matlab, raster analysis, scripting | is listed by: 3DVC | Free, Available for download, Freely available | nlx_158483, nif-0000-10382 | http://www.plexon.com/products/neuroexplorer | SCR_001818 | NeuroExplorer: Neurophysiological Data Analysis Package | 2026-09-05 06:29:53 | 1297 | ||||||
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Neuronland: NLMorphologyConverter Resource Report Resource Website 1+ mentions |
Neuronland: NLMorphologyConverter (RRID:SCR_001817) | data analysis software, data processing software, data visualization software, rendering software, simulation software, software application, software resource | NLMorphologyConverter is a simple command-line program for converting between the various neuron morphology data formats which are used to describe the three-dimensional physical branching structure of biological neurons. The aim is to provide coverage of all formats, old and new, in which data is available online, and/or which are supported by free and commercial software packages (e.g. software for neuron reconstruction, generation, simulation, visualization, and analysis of neuron morphology). Permission is granted for this software to be freely copied. Main Features Currently 21 different morphology file formats fully or partially supported. Automatic detection of input file format. Faithful reproduction of output file formatting. Many command line options for manipulating the imported data Intensively tested using over 10000 publicly available morphology data files. Sponsors. This software is supported by NeuronLand. | format, generation, analysis, biological, morphology, neuron, reconstruction, simulation, three-dimensional, visualization | Free, Available for download, Freely available | nif-0000-10381 | SCR_001817 | NLMorphologyConverter | 2026-09-05 06:29:53 | 8 | |||||||||
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ImageJ Resource Report Resource Website 10000+ mentions |
ImageJ (RRID:SCR_003070) | data processing software, image analysis software, image processing software, software application, software resource, software toolkit | Open source Java based image processing software program designed for scientific multidimensional images. ImageJ has been transformed to ImageJ2 application to improve data engine to be sufficient to analyze modern datasets. | image, data, processing, analysis, datasets, visualization, |
uses: NeuriteTracer is used by: Mouse Behavioral Analysis Toolbox is used by: Focinator is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is listed by: SoftCite is related to: uManager is related to: Fiji is related to: NIH Image is related to: TrakEM2 is related to: BioVoxxel Toolbox is related to: Golddigger is related to: Analyze Complex Roots Tool is related to: Analyze Spheroid Cell Invasion In 3D Matrix is related to: PyImageJ has parent organization: Research Services Branch National Institutes of Mental Health has plug in: Diffusing Tensor Imaging in Java has plug in: OrientationJ has plug in: GRatio for ImageJ has plug in: BioVoxxel Toolbox has plug in: WormSizer has plug in: MultiStackReg has plug in: Iterative Deconvolve 3D has plug in: Thunder STORM has plug in: Whisker tracking macro has plug in: 3D Roi Manager has plug in: 3D Objects Counter has plug in: BoneJ has plug in: QuickFigures has plug in: ObjectJ has plug in: ADAPT has plug in: DHM Utilities has plug in: Sholl Analysis has plug in: nTracer has plug in: IHC Profiler has plug in: MicrobeJ has plug in: AccPbFRET has plug in: RiFRET has plug in: JaCoP has plug in: Cell Counter Plugin for ImageJ has plug in: Puncta Analyzer has plug in: SpinalJ has plug in: ColonyArea works with: Intensity Ratio Nuclei Cytoplasm Tool works with: 3D ImageJ Suite works with: Wound Healing Tool works with: MorphoLibJ |
NIGMS RC2 GM092519; NIH ; NIMH ; NINDS ; the Laboratory for Optical and Computational Instrumentation ; the Morgridge Institute for Research ; Wellcome Trust Strategic Award 095931 |
PMID:22930834 PMID:29187165 DOI:10.1038/nmeth.2089 |
Free, Available for download, Freely available | ascl:1206.013, rid_000070, Q1659584, 2012ascl.soft06013R, SCR_018407, nif-0000-30467 | https://imagej.net/ij/, http://rsbweb.nih.gov/ij, https://imagej.nih.gov/ij/download.html, https://imagej.nih.gov/ij/, https://sources.debian.org/src/imagej/, | https://imagej.nih.gov/ij/, http://www.nitrc.org/projects/incf_imagej, | SCR_003070 | Image J, ImageJ - Image Processing and Analysis in Java, ImageJ2, ImageJ | 2026-09-05 06:29:56 | 29025 | ||||
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Accelerating Medicines Partnership Type 2 Diabetes Knowledge Portal (AMP-T2D) Resource Report Resource Website 50+ mentions |
Accelerating Medicines Partnership Type 2 Diabetes Knowledge Portal (AMP-T2D) (RRID:SCR_003743) | AMP T2D, T2DKP | data or information resource, data repository, database, disease-related portal, portal, service resource, storage service resource, topical portal | Portal and database of DNA sequence, functional and epigenomic information, and clinical data from studies on type 2 diabetes and analytic tools to analyze these data. .Provides data and tools to promote understanding and treatment of type 2 diabetes and its complications. Used for identifying genetic biomarkers correlated to Type 2 diabetes and development of novel drugs for this disease. | type 2 diabetes, diabetes, knowledge, portal, database, repository, type II, diabetic, genetic, data, analysis, FASEB list |
is recommended by: NIDDK Information Network (dkNET) is recommended by: National Library of Medicine is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: Consortia-pedia is listed by: NIDDK Information Network (dkNET) is related to: Accelerating Medicines Partnership - Alzheimers is related to: Accelerating Medicines Partnership - Alzheimers is related to: Accelerating Medicines Partnership Autoimmune Diseases of Rheumatoid Arthritis and Lupus is related to: Type 1 Diabetes Knowledge Portal is related to: Common Metabolic Diseases Knowledge Portal has parent organization: Foundation for the National Institutes of Health has parent organization: Accelerating Medicines Partnership |
Type 2 diabetes, Diabetes | Broad Institute ; Fundacion Carlos Slim ; NIDDK ; NIH ; University of Michigan |
Free, Freely available | SCR_014533, nlx_157976 | http://www.nih.gov/science/amp/type2diabetes.htm | SCR_003743 | , AMP Diabetes, AMP, T2D, AMP-T2D, Type 2 Diabetes Knowledge Portal, Accelerating Medicines Partnership Type 2 Diabetes, Accelerating Medicines Partnership Type 2 Diabetes Knowledge Portal, The AMP-T2D Knowledge Portal, AMP T2D, AMP Type 2 Diabetes | 2026-09-05 06:29:56 | 83 | ||||
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University of Bergen Computational Biology Unit Resource Report Resource Website 1+ mentions |
University of Bergen Computational Biology Unit (RRID:SCR_002970) | UiB CBU | data or information resource, department portal, organization portal, portal | An inter-department center that conducts bioinformatics research and expands the interface between bioinformatics and experimental biological and biomedical research. The unit is closely associated with the the Bioinformatics group at the Department of Informatics (II) and has tight links with the Sars Centre for Marine Molecular biology (SARS) and the Department of Molecular Biology (MBI). Six research groups are currently associated with CBU with projects that include sequence and structure analysis, molecular evolution, genome annotation and genomics data analysis. CBU also provides services and contributes to bioinformatics education primarily through training courses. | computational, biology, bioinformatics, analysis, structure, molecular, evolution, genome, annotation, functional genomic, programming, rna, dna, molecular biology, protein modelling, integrated genomics, evolutionary genomics | has parent organization: University of Bergen; Bergen; Norway | Research Council of Norway ; FUGE programme |
nif-0000-30147 | http://www.cbu.uib.no | SCR_002970 | UiB Computational Biology Unit | 2026-09-05 06:29:56 | 1 | ||||||
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MetaMorph Microscopy Automation and Image Analysis Software Resource Report Resource Website 5000+ mentions |
MetaMorph Microscopy Automation and Image Analysis Software (RRID:SCR_002368) | MetaMorph | data acquisition software, data processing software, image acquisition software, image analysis software, software application, software resource | Software tool for automated microscope acquisition, device control, and image analysis. Used for integrating dissimilar fluorescent microscope hardware and peripherals into a single custom workstation, while providing all the tools needed to perform analysis of acquired images. Offers user friendly application modules for analysis such as cell signaling, cell counting, and protein expression. | automated, microscope, acquisition, device, control, image, analysis, fluorescent, cell, signaling, counting, protein, expression, Molecular Devices | PMID:18367250 | Commercially available | SciRes_000136 | SCR_002368 | MetaMorph version 7.8.0.0, Molecular Devices Metamorph Premier Software, MetaMorph image analysis software, MetaMorph Microscopy Automation and Image Analysis Software | 2026-09-05 06:29:54 | 8382 | |||||||
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GeneMerge Resource Report Resource Website 10+ mentions |
GeneMerge (RRID:SCR_005744) | GeneMerge | analysis service resource, data analysis service, production service resource, service resource, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. Web-based and standalone application that returns a wide range of functional genomic data for a given set of study genes and provides rank scores for over-representation of particular functions or categories in the data. It uses the hypergeometric test statistic which returns statistically correct results for samples of all sizes and is the #2 fastest GO tool available (Khatri and Draghici, 2005). GeneMerge can be used with any discrete, locus-based annotation data, including, literature references, genetic interactions, mutant phenotypes as well as traditional Gene Ontology queries. GeneMerge is particularly useful for the analysis of microarray data and other large biological datasets. The big advantage of GeneMerge over other similar programs is that you are not limited to analyzing your data from the perspective of a pre-packaged set of gene-association data. You can download or create gene-association files to analyze your data from an unlimited number of perspectives. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | gene, genomics, functional genomic data, analysis, post-genomic analysis, data mining, hypothesis testing, statistical analysis, slimmer-type tool, term enrichment, text mining, false discovery rate, bonferroni correction, false discovery rate and bonferroni correction, perl, microarray |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Harvard University; Cambridge; United States |
PMID:12724301 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149203 | http://genemerge.cbcb.umd.edu/ | SCR_005744 | 2026-09-05 06:29:59 | 26 | ||||||
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Synapse Resource Report Resource Website 1000+ mentions |
Synapse (RRID:SCR_006307) | Synapse | data or information resource, data repository, database, service resource, storage service resource | A cloud-based collaborative platform which co-locates data, code, and computing resources for analyzing genome-scale data and seamlessly integrates these services allowing scientists to share and analyze data together. Synapse consists of a web portal integrated with the R/Bioconductor statistical package and will be integrated with additional tools. The web portal is organized around the concept of a Project which is an environment where you can interact, share data, and analysis methods with a specific group of users or broadly across open collaborations. Projects provide an organizational structure to interact with data, code and analyses, and to track data provenance. A project can be created by anyone with a Synapse account and can be shared among all Synapse users or restricted to a specific team. Public data projects include the Synapse Commons Repository (SCR) (syn150935) and the metaGenomics project (syn275039). The SCR provides access to raw data and phenotypic information for publicly available genomic data sets, such as GEO and TCGA. The metaGenomics project provides standardized preprocessed data and precomputed analysis of the public SCR data. | data sharing, collaboration, data management, analysis, genome, phenotype, crowd sourcing, open data, provenance, resource management, annotation, authoring, markup, r, python, java, command-line, cloud, FASEB list |
is used by: NF Data Portal is listed by: FORCE11 is listed by: DataCite is listed by: re3data.org is related to: clearScience is related to: Exemplar Microscopy Images of Tissues has parent organization: Sage Bionetworks |
Cancer, Normal, Cardiovascular disease, Floppy hat syndrome | Life Sciences Discovery Fund ; NCI ; NHLBI ; Alfred P. Sloan Foundation |
The community can contribute to this resource | nlx_151983, DOI:10.17616/R3B934, r3d100011894, DOI:10.7303 | https://doi.org/10.17616/R3B934, https://doi.org/10.48550/arxiv.1506.00272, https://doi.org/10.7303/, https://dx.doi.org/10.7303, https://doi.org/10.17616/R3B934 | SCR_006307 | 2026-09-05 06:30:00 | 1104 | |||||
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Clair library Resource Report Resource Website |
Clair library (RRID:SCR_007019) | Clairlib | data analysis software, data processing software, software application, software resource, software toolkit, text extraction software, text-mining software | A suite of open-source Perl modules intended to simplify a number of generic tasks in natural language processing (NLP), information retrieval (IR), and network analysis (NA). Its architecture also allows for external software to be plugged in with very little effort. The latest version of clairlib is 1.06 which was released on March 2009 and includes about 130 modules implementing a wide range of functionalities. Clairlib is distributed in two forms: * Clairlib-core, which has essential functionality and minimal dependence on external software, and * Clairlib-ext, which has extended functionality that may be of interest to a smaller audience. Much can be done using Clairlib on its own. Some of the things that Clairlib can do are: Tokenization, Summarization, Document Clustering, Document Indexing, Web Graph Analysis, Network Generation, Power Law Distribution Analysis, Network Analysis, RandomWalks on Graphs, Tf-IDF, Perceptron Learning and Classification, and Phrase Based Retrieval and Fuzzy OR Queries. | analysis, information, linguistic, module, network, process, retrieval, perl, natural language processing, information retrieval, network analysis |
is listed by: Biositemaps has parent organization: University of Michigan; Ann Arbor; USA |
NSF IIS 0534323; NSF IIS 0329043; NSF BCS 0527513; NLM R01 LM008106; NIDA U54 DA021519 |
Open unspecified license: Content is available under GNU Free Documentation License 1.3 or later. | nif-0000-33210 | SCR_007019 | Computational Linguistics And Information Retrieval Library | 2026-09-05 06:30:00 | 0 | ||||||
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Atlases of amygdala and hippocampus for pediatric populations Resource Report Resource Website |
Atlases of amygdala and hippocampus for pediatric populations (RRID:SCR_014085) | atlas, data or information resource | Anatomical atlases constructed by Computational Anatomy of Johns Hopkins University for analysis of shape vectors. The atlases were generated from segmented hippocampal and amygdala structures in acquired populations of children, adolescents and young adults in neuroimaging studies of major depression disorder (MDD) at Washington University at St Louis. | atlas, amygdala, hippocampus, children, adolescent, young adult, human brain, depression, shape vector, analysis |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Johns Hopkins University; Maryland; USA |
SCR_014085 | 2026-09-05 06:32:09 | 0 | |||||||||||
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HumanBase Resource Report Resource Website 50+ mentions |
HumanBase (RRID:SCR_016145) | data or information resource, database | Formerly known as GIANT (Genome-scale Integrated Analysis of gene Networks in Tissues), HumanBase applies machine learning algorithms to learn biological associations from massive genomic data collections. These integrative analyses reach beyond existing "biological knowledge" represented in the literature to identify novel, data-driven associations. | genome, analysis, tissue, network, gene, machine, learning, biology | NCI T32 CA009528; NHGRI R01 HG005998; NHGRI T32 HG003284; NHLBI U54 HL117798; NIGMS P20 GM103534; NIGMS P50 GM071508; NIGMS R01 GM071966; US Department Of Health And Human Services HHSN272201000054C |
PMID:25915600 | Free, Public | SCR_016145 | GIANT (Genome-scale Integrated Analysis of gene Networks in Tissues), GIANT | 2026-09-05 06:32:13 | 95 | ||||||||
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Examl Resource Report Resource Website 50+ mentions |
Examl (RRID:SCR_016087) | Examl | software application, software resource, source code | Source code for large-scale phylogenetic analyses on whole-transcriptome and whole-genome alignments using supercomputers. | phylogenetic, analysis, database, large scale, whole genome, whole transcriptome, alignment, efficiency, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools |
Heidelberg Institute for Theoretical Studies | PMID:25819675 | Free, Available for download | OMICS_08024, biotools:ExaML | https://bio.tools/ExaML, https://sources.debian.org/src/examl/ | SCR_016087 | Examl:Exascale Maximum Likelihood | 2026-09-05 06:32:12 | 62 | ||||
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Intra- and inter-scanner reliability of RS-fMRI BOLD and ASL with eyes closed vs. eyes open Resource Report Resource Website |
Intra- and inter-scanner reliability of RS-fMRI BOLD and ASL with eyes closed vs. eyes open (RRID:SCR_016935) | data or information resource, database | Data collected from subjects scanned 3 times (V1, V2, V3), with V1 and V2 on a scanner, V3 on another scanner in another site. Resting state blood oxygenation level dependent functional MRI (BOLD fMRI), pseudo continuous arterial spin labeling (pCASL), and high resolution 3D T1 imaging were performed under eyes open (EO) and eyes closed (EC) conditions. | neuroimaging, dataset, resting, state, functional, magnetic, resonance, imaging, investigate, intra, inter, scanner, reliability, scaled, subprofile, model, principal, component, analysis, blood, oxygenation, level, dependent, image, arterial, spin, labeling |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Hangzhou Normal University; Hangzhou; China |
Natural Science Foundation of China ; Qian Jiang Distinguished Professor program |
PMID:29887795 | SCR_016935 | 2026-09-05 06:32:14 | 0 | |||||||||
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MitoCarta Resource Report Resource Website 100+ mentions |
MitoCarta (RRID:SCR_018165) | data or information resource, database | Collection of genes encoding proteins with strong support of mitochondrial localization. Inventory of genes encoding mitochondrial-localized proteins and their expression across 14 mouse tissues. Database is based on human and mouse RefSeq proteins that are mapped to NCBI Gene loci. MitoCarta 2.0 inventory provides molecular framework for system-level analysis of mammalian mitochondria. | Gene, protein, mitochondrial protein, protein expression, data, human, mouse, RefSeq protein, analysis, mammalian mitochondra, FASEB list | Australian NHMRC ; Burroughs Wellcome Fund Career Award in the Biomedical Sciences ; Charles E. Culpeper Scholarship in Medical Science ; Howard Hughes Medical Institute ; NIDDK DK43351; NIDDK DK57521; NIGMS GM0077465 |
PMID:26450961 PMID:18614015 |
Free, Freely available | SCR_018165 | MitoCarta2.0 | 2026-09-05 06:32:15 | 208 | ||||||||
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Molecular Signatures Database Resource Report Resource Website 1000+ mentions |
Molecular Signatures Database (RRID:SCR_016863) | MSigDB | data or information resource, database | Collection of annotated gene sets for use with Gene Set Enrichment Analysis (GSEA) software. | collection, annotated, gene, set, GSEA, enrichment, analysis, genome, RNA, expression, data, FASEB list, DRKB |
uses: GSEA uses: Gene Set Enrichment Analysis has parent organization: Broad Institute |
NCI CA295532; NIGMS ; NIH |
Free, Freely available, Registration required to download GSEA software | https://www.gsea-msigdb.org/gsea/msigdb/ | SCR_016863 | Molecular Signatures Database, The Molecular Signatures Database, MSigDB, MSigDB database v6.2 | 2026-09-05 06:32:14 | 1702 | ||||||
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Good Calculators Resource Report Resource Website |
Good Calculators (RRID:SCR_017123) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web service as calculator for statistics and analysis. Used on variety of browsers as well as mobile and tablet devices.They include Z-score, sample size, t value, One Way ANOVA Calculator, Percentile Calculator, Chi Square, p Value, and more. | statistics, analysis, calculator | Free, Freely available | SCR_017123 | 2026-09-05 06:28:19 | 0 | |||||||||||
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Bulked segregation analysis tools for outbreeding species Resource Report Resource Website 1+ mentions |
Bulked segregation analysis tools for outbreeding species (RRID:SCR_017009) | BSATOS | 1d time-series analysis software, data analysis software, data processing software, software application, software resource, time-series analysis software | Software tools for next generation sequencing based bulked segregation analysis for outbreeding species including fruit trees such as apple or cirtus. Used to improve gene mapping efficiency of next generation sequencing based segregant analysis in outbreeding species and realize rapid candidate gene mining based on multi-omics data. | next, generation, sequencing, bulked, segregation, analysis, outbreeting, specie, gene, mapping, data | Free, Available for download, Freely available | SCR_017009 | Bulked segregation analysis tools for outbreeding species, Bulked Segregation Analysis Tools for Outbreeding Species, BSATOS | 2026-09-05 06:28:17 | 2 |
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