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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Agile Protein Interactomes DataServer Resource Report Resource Website 10+ mentions |
Agile Protein Interactomes DataServer (RRID:SCR_008871) | APID | analysis service resource, data access protocol, data analysis service, data or information resource, database, production service resource, service resource, software resource, web service | APID Interactomes (Agile Protein Interactomes DataServer) provides information on the protein interactomes of numerous organisms, based on the integration of known experimentally validated protein-protein physical interactions (PPIs). The interactome data includes a report on quality levels and coverage over the proteomes for each organism included. APID integrates PPIs from primary databases of molecular interactions (BIND, BioGRID, DIP, HPRD, IntAct, MINT) and also from experimentally resolved 3D structures (PDB) where more than two distinct proteins have been identified. This collection references protein interactors, through a UniProt identifier. | protein, protein interaction, interactions, ppi, interactomes, analysis, gene, ontology, functional, environment, data, network, graphic, visualize |
is listed by: Gene Ontology Tools is related to: PSICQUIC Registry is related to: Gene Ontology is related to: BIND is related to: Biological General Repository for Interaction Datasets (BioGRID) is related to: Database of Interacting Proteins (DIP) is related to: HPRD - Human Protein Reference Database is related to: IntAct is related to: MINT has parent organization: University of Salamanca; Salamanca; Spain |
Junta de Castilla y Leon ; Spanish Ministerio de Sanidad y Consumo |
PMID:27131791 PMID:30715274 |
Free for academic use | r3d100012339, nlx_149321 | https://doi.org/10.17616/R3407P, https://doi.org/10.17616/R3407P | SCR_008871 | Agile Protein Interactomes DataServer, APID, APID Interactomes, Agile Protein Interactomes DataServer (APID), APID (Agile Protein Interactomes DataServer) | 2026-09-03 04:49:48 | 14 | ||||
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GMA Resource Report Resource Website |
GMA (RRID:SCR_009212) | GMA | data analysis software, data processing software, software application, software resource, time-series analysis software | Software package to perform Granger mediation analysis for time series. Includes single level GMA model and two-level GMA model, for time series with hierarchically nested structure. | Granger, meditation, analysis, time, series, level, GMA, model, BRAIN Initiative, bio.tools |
is recommended by: BRAIN Initiative is listed by: Genetic Analysis Software is listed by: Debian is listed by: bio.tools |
NIBIB EB022911 | PMID:31070732 | Free, Available for download, Freely available | nlx_154361, biotools:GMA | https://github.com/chaoning/GMA, https://bio.tools/GMA | http://www.montana.edu/kalinowski/GMA/GMA_Home.htm | SCR_009212 | Granger Mediation Analysis | 2026-09-03 04:49:53 | 0 | |||
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Neural Decoding Toolbox Resource Report Resource Website 10+ mentions |
Neural Decoding Toolbox (RRID:SCR_009012) | NDT | data analysis software, data processing software, software application, software resource, software toolkit | Matlab toolbox that makes it easy to apply decoding analyses to neural data. The design of the toolbox revolves around four abstract object classes which enables users to interchange particular modules in order to try different analyses while keeping the rest of the processing stream intact. The toolbox is capable of analyzing data from many different types of recording modalities, and examples are given on how it can be used to decode basic visual information from neural spiking activity and how it can be used to examine how invariant the activity of a neural population is to stimulus transformations. | population decoding, neuron, analysis, matlab, data analysis, machine learning, multivariate pattern analysis, neural decoding | has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; | DARPA ; IPTO ; DSO ; AFSOR-THRL ; Adobe Systems ; Honda Research Institute USA ; King Abdullah University of Science and Technology ; NEU ; Sony ; Eugene McDermott Foundation ; NSF 0640097; NSF 0827427; NSF FA8650-05-C-7262 |
PMID:23734125 | Acknowledgement requested, Account required | nlx_152729 | SCR_009012 | 2026-09-03 04:50:08 | 19 | ||||||
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affy Resource Report Resource Website 1000+ mentions |
affy (RRID:SCR_012835) | Affy | data analysis software, data processing software, software application, software resource | Software R package of functions and classes for the analysis of oligonucleotide arrays manufactured by Affymetrix. Used to process probe level data and for exploratory oligonucleotide array analysis. | analysis, oligonucleotide, array, Affymetrix, process, probe, data, function, bio.tools |
is listed by: OMICtools is listed by: Bioconductor is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: affydata is related to: R Project for Statistical Computing is related to: OMICtools |
Danish Biotechnology Instrument Center | PMID:14960456 | Free, Available for download, Freely available | BioTools:affy, OMICS_00740, biotools:affy | https://bio.tools/affy, https://sources.debian.org/src/r-bioc-affy/ | SCR_012835 | Affymetrix, analysis of Affymetrix GeneChip data at the probe level, analysis of Affymetrix GeneChip data | 2026-09-03 04:51:55 | 3073 | ||||
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TopHat Resource Report Resource Website 5000+ mentions Rating or validation data |
TopHat (RRID:SCR_013035) | alignment software, data analysis software, data processing software, image analysis software, sequence analysis software, software application, software resource | Software tool for fast and high throughput alignment of shotgun cDNA sequencing reads generated by transcriptomics technologies. Fast splice junction mapper for RNA-Seq reads. Aligns RNA-Seq reads to mammalian-sized genomes using ultra high-throughput short read aligner Bowtie, and then analyzes mapping results to identify splice junctions between exons.TopHat2 is accurate alignment of transcriptomes in presence of insertions, deletions and gene fusions. | align, RNA-Seq, read, cDNA, sequencing, transcriptomics, fast, splice, junction, mapper, exon, analysis, bio.tools |
uses: Bowtie is used by: CIRCexplorer is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: HISAT2 has parent organization: University of Maryland; Maryland; USA has parent organization: University of California at Berkeley; Berkeley; USA has parent organization: Johns Hopkins University; Maryland; USA has parent organization: University of Washington; Seattle; USA works with: GeneScissors |
NHGRI R01 HG006102; NHGRI R01 HG006677 |
PMID:23618408 PMID:19289445 DOI:10.1093/bioinformatics/btp120 |
Free, Available for download, Freely available | biotools:tophat, OMICS_01257 | https://github.com/infphilo/tophat, https://bio.tools/tophat, https://sources.debian.org/src/tophat/ | http://tophat.cbcb.umd.edu/ | SCR_013035 | tophat, TopHat1, Tophat2 | 2026-09-03 04:51:54 | 9789 | ||||
|
Neuroimaging in Python Resource Report Resource Website 10+ mentions |
Neuroimaging in Python (RRID:SCR_013141) | NIPY, | community building portal, data or information resource, portal, software application, software development environment, software development tool, software resource | Community site to make brain imaging research easier that aims to build software that is clearly written, clearly explained, a good fit for the underlying ideas, and a natural home for collaboration. | brain, imaging, neuroimaging, analysis, python, fmri, fmri analysis, magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Python Programming Language has parent organization: SourceForge has parent organization: University of California at Berkeley; Berkeley; USA has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; is parent organization of: Dipy is parent organization of: NiLearn is parent organization of: NIPY is parent organization of: NiBabel is parent organization of: Nipype is parent organization of: Nitime |
NIMH 5R01MH081909-02; NIBIB 1R03EB008673-01 |
PMID:21897815 | Revised BSD license | nlx_149365 | http://www.nitrc.org/projects/nipy-community http://www.nitrc.org/projects/nipype | SCR_013141 | NIPY Community | 2026-09-03 04:52:07 | 27 | ||||
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PlasmoDB Resource Report Resource Website 1000+ mentions |
PlasmoDB (RRID:SCR_013331) | analysis service resource, data access protocol, data analysis service, data or information resource, data repository, database, production service resource, service resource, software resource, storage service resource, web service | Functional genomic database for malaria parasites. Database for Plasmodium spp. Provides resource for data analysis and visualization in gene-by-gene or genome-wide scale. PlasmoDB 5.5 contains annotated genomes, evidence of transcription, proteomics evidence, protein function evidence, population biology and evolution data. Data can be queried by selecting from query grid or drop down menus. Results can be combined with each other on query history page. Search results can be downloaded with associated functional data and registered users can store their query history for future retrieval or analysis.Key community database for malaria researchers, intersecting many types of laboratory and computational data, aggregated by gene. | Functional, genomic, database, malaria, parasite, data, analysis, visualization, gene, genome, annotation, transcription, proteomics, protein, evolution, FASEB list |
uses: SynView is related to: GeneDB Pfalciparum has parent organization: Eukaryotic Pathogen Database Resources has parent organization: Pennsylvania State University has parent organization: University of Georgia; Georgia; USA |
malaria | NIAID | PMID:18957442 | nif-0000-03314, SCR_017665, r3d100011569 | SCR_013331 | PlasmoDB, Plasmodium Genomics Resource, PlasmoDB 5.5, Plasmodium genome-resource | 2026-09-03 04:51:57 | 1324 | ||||||
|
Leica Application Suite X Resource Report Resource Website 500+ mentions |
Leica Application Suite X (RRID:SCR_013673) | LAS X | resource | Software for image capture, processing and analysis with Leica fluorescence and confocal microscopes. | confocal, image, analysis, leica, microscope, microbiology | has parent organization: Leica Microsystems | Commercially available | http://www.leica-microsystems.com/products/microscope-software/software-for-life-science-research/las-easy-and-efficient/ | SCR_013673 | Leica LAS, Leica LAS AF Image Acquisition Software, Leica Application Suite X, Leica Application Suite X (LAS X), Leica LAS X Life Science Microscope Software, Leica LAS X LS, LASX, Leica LAS X Life Science software, LAS X | 2026-09-03 04:52:24 | 579 | |||||||
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WinMDI Software Resource Report Resource Website 10+ mentions |
WinMDI Software (RRID:SCR_013745) | Software to analyze flow cytometry listmode data files. | flow cytometry, analysis | http://facs.scripps.edu/software.html | SCR_013745 | Windows Multiple Document Interface software, Windows Multiple Document Interface for Flow Cytometry | 2026-09-03 04:52:14 | 28 | |||||||||||
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InterProScan Resource Report Resource Website 5000+ mentions |
InterProScan (RRID:SCR_005829) | analysis service resource, data access protocol, data analysis service, data analysis software, data processing software, production service resource, service resource, software application, software resource, web service | Software package for functional analysis of sequences by classifying them into families and predicting presence of domains and sites. Scans sequences against InterPro's signatures. Characterizes nucleotide or protein function by matching it with models from several different databases. Used in large scale analysis of whole proteomes, genomes and metagenomes. Available as Web based version and standalone Perl version and SOAP Web Service. | functional, analysis, sequence, protein, nucleotide, predict, presence, domain, site, proteome, genome, metagenome, bio.tools |
is listed by: Gene Ontology Tools is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: Gene Ontology is related to: RARTF is related to: InterPro is related to: LegumeIP is related to: UniProtKB has parent organization: European Bioinformatics Institute |
Biotechnology and Biological Sciences Research Council ; EMBL ; European Union |
PMID:15980438 PMID:17202162 PMID:24451626 |
Free, Available for download, Freely available | OMICS_01479, biotools:interproscan_4, nlx_149337 | https://www.ebi.ac.uk/interpro/download.html, https://bio.tools/interproscan_4 | SCR_005829 | InterProScan Sequence Search, InterProScan 2, InterProScan 3, InterProScan 4, InterProScan 5 | 2026-09-03 04:48:39 | 7512 | |||||
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GOEx - Gene Ontology Explorer Resource Report Resource Website 10+ mentions |
GOEx - Gene Ontology Explorer (RRID:SCR_005779) | GOEx | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented July 5, 2018. Gene Ontology Explorer (GOEx) combines data from protein fold changes with GO over-representation statistics to help draw conclusions in proteomic experiments. It is tightly integrated within the PatternLab for Proteomics project and, thus, lies within a complete computational environment that provides parsers and pattern recognition tools designed for spectral counting. GOEx offers three independent methods to query data: an interactive directed acyclic graph, a specialist mode where key words can be searched, and an automatic search. A recent hack included in GOEx is to load the sparse matrix index file directly into GOEx, instead of going through the report generation using the AC/T-fold methods. This makes it easy for GOEx to analyze any list of proteins as long as the list follows the index file format (described in manuscript) . Please note that if using this alternative strategy, there will be no protein fold information. Platform: Windows compatible | proteomics, visualization, statistical analysis, gene ontology, parse, pattern recognition, spectral counting, analysis, protein fold |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Scripps Research Institute |
CNPq ; CAPES ; FAPERJ BBP grant ; PAPES ; PDTIS ; Ary Frauzino Foundation ; NIAID ; NIH ; genesis molecular biology laboratory ; Fiocruz-INCA collaboration ; NIAID UCSD/MCB0237059; NCRR P41RR011823; NIMH 5R01 MH067880 |
PMID:19239707 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149249 | http://pcarvalho.com/patternlab/goex.shtml | SCR_005779 | Gene Ontology Explorer, GO Explorer | 2026-09-03 04:48:15 | 32 | ||||
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Onto-Translate Resource Report Resource Website 1+ mentions |
Onto-Translate (RRID:SCR_005725) | Onto-Translate | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | In the annotation world, the same piece of information can be stored and viewed differently across different databases. For instance, more than one Affymetrix probe ID can refer to the same GenBank sequence (accession number) and more than one nucleotide sequence from GenBank can be grouped in a single UniGene cluster. The result of Onto-Express depends on whether the input list contains Affymetrix probe IDs, GenBank accession numbers or UniGene cluster IDs. The user has to be aware of relations between the different forms of the data in order to interpret correctly the results. Even if the user is aware of the relationships and knows how to convert them, most existing tools allow conversions of individual genes. Onto-Translate is a tool that allows the user to perform easily such translations. Affymetrix probe IDs, etc., translate GO terms into other identifiers like GenBank accession number, Uniprot IDs. User account required. Platform: Online tool | annotation, gene, analysis, database or data warehouse, other analysis, affymetrix probe id, affymetrix, probe id, translate go terms into other identifiers like genbank accession number, genbank accession number, uniprot id, gene ontology, translate |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Wayne State University; Michigan; USA |
PMID:15215428 | Free for academic use | nlx_149182 | SCR_005725 | 2026-09-03 04:48:05 | 3 | |||||||
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Brede Toolbox Resource Report Resource Website 1+ mentions |
Brede Toolbox (RRID:SCR_006204) | Brede Toolbox | data processing software, image analysis software, image processing software, software application, software resource | A package for neuroinformatics and neuroimaging analysis mostly programmed in Matlab with a few additional programs in Python and Perl. It allows coordinate-based meta-analysis and visualization, neuroimaging analysis of voxel or regional data - not the original data but rather the summary images (e.g., statistical parametric images) and location data in stereotactic space. Among the algorithms implemented are kernel density estimation (for coordinate-based meta-analysis), independent component analysis, non-negative matrix factorization, k-means clustering, singular value decomposition, partial correlation analysis with permutation testing and partial canonical correlation analysis. Visualization of coordinate, surfaces and volumes are possible in 2D and 3D. Generation of HTML for results are possible and algorithms can be accessed from the command line or via a flexible graphical interface. With the Brede Toolbox comes the Brede Database with a small coordinate database from published neuroimaging studies, and ontologies for, e.g., brain function and brain regions. | ontology, database application, independent component analysis, principal component analysis, regression, neuroinformatics, neuroimaging, analysis, matlab, python, perl, coordinate, kernel density estimation, brain function, brain region, visualization, voxel, region |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps is related to: Brede Database is related to: Brede Database is related to: Brede Wiki has parent organization: THOR Center for Neuroinformatics |
Free for academic use, Acknowledgement requested | nif-0000-00275 | SCR_006204 | 2026-09-03 04:48:20 | 1 | ||||||||
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Knime Resource Report Resource Website 500+ mentions |
Knime (RRID:SCR_006164) | KNIME | data processing software, software application, software resource, software toolkit, text-mining software, workflow software | KNIME (Konstanz Information Miner) is a user-friendly and comprehensive Open-Source data integration, processing, analysis, and exploration platform. KNIME (naim) is a user-friendly graphical workbench for the entire analysis process: data access, data transformation, initial investigation, powerful predictive analytics, visualization and reporting. The open integration platform provides over 1000 modules (nodes), including those of the KNIME community and its extensive partner network. KNIME can be downloaded onto the desktop and used free of charge. KNIME products include additional functionalities such as shared repositories, authentication, remote execution, scheduling, SOA integration and a web user interface as well as world-class support. Robust big data extensions are available for distributed frameworks such as Hadoop. KNIME is used by over 3000 organizations in more than 60 countries. The modular data exploration platform, initially developed at the University of Konstanz, Germany, enables the user to visually create data flows, execute selected analysis steps, and later investigate the results through interactive views on data and models. KNIME is a proven integration platform for tools of numerous vendors due to its open and modular API. The KNIME.com product pipeline includes an Enterprise Server, Cluster Execution, Reporting solutions, and professional KNIME support subscriptions. KNIME.com also offer services such as data analysis, hands-on training and the development of customized components for KNIME. | platform, next-generation sequencing, data analysis, visualization, selection, analysis, high-throughput screening, data mining, drug discovery | has parent organization: University of Konstanz; Baden-Wurttemberg; Germany | PMID:23110532 PMID:22644661 PMID:22607449 PMID:21984761 PMID:21873641 |
nlx_151666 | SCR_006164 | Konstanz Information Miner | 2026-09-03 04:48:33 | 770 | |||||||
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Array Studio Resource Report Resource Website 1+ mentions |
Array Studio (RRID:SCR_010970) | analysis service resource, data analysis software, data processing software, production service resource, service resource, software application, software resource, software toolkit | Software package which provides statistics and visualization for analysis of high dimensional quantification data including microarray or RTPCR data or Taqman data, genotype data including SNP or Copy Number data and Next Generation Sequencing data. Provides integrated environment for analyzing and visualizing high dimensional data. | Statistic, visualization, data, analysis, quantification, integrated environment, microarray data, RTPCR data, Taqman data, genotype data, copy number data, next generation sequencing data | Free, Available for download, Freely available | OMICS_00850 | https://omicsoftdocs.github.io/ArraySuiteDoc/tutorials/ArrayStudio/ArrayStudio/ | http://www.omicsoft.com/array-studio.php | SCR_010970 | 2026-09-03 04:51:02 | 5 | ||||||||
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LIMMA Resource Report Resource Website 10000+ mentions |
LIMMA (RRID:SCR_010943) | LIMMA | data analysis software, data processing software, software application, software resource | Software package for the analysis of gene expression microarray data, especially the use of linear models for analyzing designed experiments and the assessment of differential expression. | analysis, gene, expression, microarray, data, linear, model, bio.tools |
is used by: Glimma is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: GEO2R is related to: Bioconductor |
Free, Available for download, Freely available | biotools:limma, OMICS_00769 | https://omictools.com/limma-tool, https://bio.tools/limma, https://sources.debian.org/src/r-bioc-limma/ | SCR_010943 | Linear Models for Microarray Data | 2026-09-03 04:50:33 | 27197 | ||||||
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HOMER Resource Report Resource Website 5000+ mentions |
HOMER (RRID:SCR_010881) | HOMER | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tools for Motif Discovery and next-gen sequencing analysis. Used for analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and numerous other types of functional genomics sequencing data sets. Collection of command line programs for unix style operating systems written in Perl and C++. | motif, discovery, next, generation, sequencing, analysis, genomic, data |
is listed by: OMICtools is related to: findMotif.pl has parent organization: University of California at San Diego; California; USA |
Foundation Leducq Transatlantic Network Grant ; NCI CA52599; NIDDK DK063491; NIGMS P50 GM081892; NIH HC088093; NURSA consortium grant |
PMID:20513432 | OMICS_00483 | http://biowhat.ucsd.edu/homer/index.html | SCR_010881 | HOMER, Hypergeometric Optimization of Motif EnRichment, Homer, Homer v4.5 | 2026-09-03 04:50:30 | 5929 | |||||
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JCB DataViewer Resource Report Resource Website 10+ mentions |
JCB DataViewer (RRID:SCR_002633) | JCB DataViewer | data or information resource, data repository, database, image repository, service resource, storage service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. A web-based, multi-dimensional image data-viewing application for original microscopy image datasets associated with articles published in The Journal of Cell Biology, a peer-reviewed journal published by The Rockefeller University Press. The JCB DataViewer can host multidimensional fluorescence microscopy images, 3D tomogram data, very large (gigapixel) images, and high content imaging screens. Images are presented in an interactive viewer, and the scores from high content screens are presented in interactive graphs with data points linked to the relevant images. The JCB DataViewer uses the Bio-Formats library to read over 120 different imaging file formats and convert them to the OME-TIFF image data standard. Image data are archived by the Journal and may be freely accessed by readers using the JCB DataViewer. Download of author-provided image data and associated metadata in OME-TIFF format is also possible with author permission, allowing for independent analysis of image data irrespective of acquisition or viewing software. Although the JCB DataViewer is designed to host and facilitate sharing and analysis of original microscopy image data, authors may also upload other types of original image data as supplements to their manuscripts, including histology and electron micrographs and digital scans of gels or blots. | microscopy, standardization, data sharing, archiving, data management, metadata standard, visualization, analysis, image collection, histology, electron micrograph, digital scan, gel, blot |
is listed by: FORCE11 is listed by: SoftCite is related to: OME-TIFF Format has parent organization: Rockefeller University; New York; USA |
Glencoe Software ; OME - Open Microscopy Environment |
PMID:22869591 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156057, r3d100010895 | https://doi.org/10.17616/R3PW4G | SCR_002633 | 2026-09-03 04:45:30 | 14 | |||||
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Rainbow Resource Report Resource Website 10+ mentions |
Rainbow (RRID:SCR_002724) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software developed to provide an ultra-fast and memory-efficient solution to clustering and assembling short reads produced by RAD-seq. | software, tool, clustering, assembling, short, read, restriction, site, DNA, sequence, analysis, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:22942077 DOI:10.1093/bioinformatics/bts482 |
Free, Freely available, Available for download | SCR_015992, OMICS_03722, biotools:rainbow | https://bio.tools/rainbow, https://sources.debian.org/src/bio-rainbow/ | SCR_002724 | RAD-seq: Restriction-site Associated DNA sequencing, Bio-rainbow, RAD-seq | 2026-09-03 04:45:41 | 41 | ||||||
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Time-series RNA-seq Analysis Package Resource Report Resource Website 1+ mentions |
Time-series RNA-seq Analysis Package (RRID:SCR_002935) | TRAP | software resource | A comprehensive software package integrating all necessary tasks such as mapping short reads, measuring gene expression levels, finding differentially expressed genes (DEGs), clustering and pathway analysis for time-series data in a single environment. | time-series, rna-seq, analysis |
is listed by: OMICtools has parent organization: Seoul National University; Seoul; South Korea |
PMID:24518221 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02590 | SCR_002935 | 2026-09-03 04:46:00 | 3 |
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