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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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SARTools Resource Report Resource Website 100+ mentions |
SARTools (RRID:SCR_016533) | data analysis software, data processing software, software application, software resource, software toolkit | Software package as a DESeq2- and EdgeR-Based R Pipeline for Comprehensive Differential Analysis of RNA-Seq Data. | R package, DESeq2, EdgeR, comprehensive, analysis, RNAseq, data, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: DESeq2 is related to: edgeR has parent organization: Pasteur Institute |
the France Génomique National Infrastructure | PMID:27280887 | Free, Available for download, Freely available | biotools:sartools | https://bio.tools/sartools | SCR_016533 | 2026-09-12 12:58:41 | 151 | ||||||
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TRANSIT Resource Report Resource Website 1+ mentions |
TRANSIT (RRID:SCR_016492) | data analysis software, data processing software, software application, software resource | Software tool Python based and open source for statistical analysis of TnSeq data. Provides a graphical interface to three different statistical methods for analyzing TnSeq data capable of identifying essential genes in individual datasets as well as comparative analysis between conditions. | statistical, analysis, TnSeq, data, identify, gene, dataset, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Texas A and M University; Texas; USA |
PMID:26447887 | Free, Available for download, Freely available | biotools:transit | https://github.com/mad-lab/transit, https://bio.tools/transit | SCR_016492 | 2026-09-12 12:58:40 | 4 | |||||||
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PiGx Resource Report Resource Website 1+ mentions |
PiGx (RRID:SCR_016476) | PiGx | data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit | Software application as a collection of genomic pipelines used for raw fastq read data of bisulfite experiments, RNAseq samples, single cell dropseq analysis, reads from ChIPseq experiments, analysis of sequence mutations in CRISPR-CAS9 targeted amplicon sequencing data. | collection, genomic, pipeline, bisulfite, sequencing, rnaseq, chipseq, single, cell, reproducibility, sample, analysis, mutation, data | European Union Horizon 2020 No 654248; German Federal Ministry of Education and Research (BMBF) 031 A538C RBC (de.NBI) |
Free, Available for download, Freely available | https://github.com/BIMSBbioinfo/pigx | SCR_016476 | Pipelines in Genomics | 2026-09-12 12:58:40 | 6 | |||||||
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Transcriptome Analysis Console Resource Report Resource Website 10+ mentions |
Transcriptome Analysis Console (RRID:SCR_016519) | TAC | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool for microarray analysis designed for biologists . Used for identification of differential expression by providing interactive visualizations. | transcriptome, analysis, console, data, array, gene, visualization, identify | Commercially available | SCR_016519 | TAC:Transcriptome Analysis Console | 2026-09-12 12:58:40 | 21 | |||||||||
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Viewbox4, Cephalometric software Resource Report Resource Website 1+ mentions |
Viewbox4, Cephalometric software (RRID:SCR_016481) | data analysis software, data processing software, image analysis software, software application, software resource | Software for cephalometric analysis. Customizable. Allows rendering, viewing and measuring of 3D data from CT scanners. Used in orthodontic departments for analysis of the dental and skeletal relationships of a human skull. | dHAL Software - The Company, cephalometric, analysis, rendering, viewing, measuring, data, CT scan, orthodontic, dental, skeletal, relationship, human, skull | Commercially available, Tutorial available | SCR_016481 | 2026-09-12 12:58:40 | 6 | |||||||||||
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SwarmSight Resource Report Resource Website |
SwarmSight (RRID:SCR_016451) | data analysis software, data processing software, image analysis software, software application, software resource | Software for video analysis with modules to track insect antenna and proboscis movements. Its purpose is to assess the aggregate movement or activity levels of groups or swarms of animals. | c language, bug, insect, antennae, proboscis, activity, research, subject, swarm, behavior, tracking, video, analysis | Free, Available for download, Acknowledgement requested | SCR_016451 | SwarmSight Software, Swarm Sight | 2026-09-12 12:58:40 | 0 | ||||||||||
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Exonic Splicing Enhancer Finder Resource Report Resource Website 50+ mentions |
Exonic Splicing Enhancer Finder (RRID:SCR_002835) | analysis service resource, data analysis service, production service resource, service resource | A web-based analysis service for identifying exonic splicing enhancers in eukaryotic genes. ESEfinder accept sequences in the FASTA format. A typical mammalian gene is composed of several relatively short exons that are interrupted by much longer introns. To generate correct mature mRNAs, the exons must be identified and joined together precisely and efficiently, in a process that requires the coordinated action of five small nuclear (sn)RNAs (U1, U2, U4, U5 and U6) and more than 60 polypeptides. The inaccurate recognition of exon/intron boundaries or the failure to remove an intron generates aberrant mRNAs that are either unstable or code for defective or deleterious protein isoforms. Exonic enhancers are thought to serve as binding sites for specific serine/arginine-rich (SR) proteins, a family of structurally related and highly conserved splicing factors characterized by one or two RNA-recognition motifs (RRM) and by a distinctive C-terminal domain highly enriched in RS dipeptides (the RS domain). The RRMs mediate sequence-specific binding to the RNA, and so determine substrate specificity, whereas the RS domain appears to be involved mainly in protein-protein interactions. SR proteins bound to ESEs can promote exon definition by directly recruiting the splicing machinery through their RS domain and/or by antagonizing the action of nearby silencer elements. Sponsors: ESEfinder is supported by the Cold Spring Harbor Laboratory. | element, enhancer, eukaryotic, exon, exonic, gene, analysis, arginine, boundary, c-terminal, dipeptide, intron, isoform, mammalian, mrna, nuclear, polypeptide, protein, recognition, rna, serine, service, snrna, splice | has parent organization: Cold Spring Harbor Laboratory | Free, Freely available | nif-0000-25204 | SCR_002835 | ESEfinder | 2026-09-12 01:01:26 | 66 | ||||||||
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Evolutionary Lineage Inferred from Structural Analysis Resource Report Resource Website 1+ mentions |
Evolutionary Lineage Inferred from Structural Analysis (RRID:SCR_002343) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. ELISA is an online database that combines functional annotation with structure and sequence homology modeling to place proteins into sequence-structure-function neighborhoods. The atomic unit of the database is a set of sequences and structural templates that those sequences encode. A graph that is built from the structural comparison of these templates is called PDUG (protein domain universe graph). It introduces a method of functional inference through a probabilistic calculation done on an arbitrary set of PDUG nodes. Further, all PDUG structures are mapped onto all fully sequenced proteomes allowing an easy interface for evolutionary analysis and research into comparative proteomics. ELISA is the first database with applicability to evolutionary structural genomics explicitly in mind. | evolutionary, function, functional, analysis, annotation, atomic unit, calculation, comparative, domain, genomic, homology, modeling, place, probabilistic, protein, protein domain and protein classification databases, proteome, proteomic, sequence, structural, structure, template | has parent organization: Boston University; Massachusetts; USA | PMID:12952559 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21141 | SCR_002343 | ELISA | 2026-09-12 01:01:25 | 1 | |||||||
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Human Experimental/FunctionAL MaPper: Providing Functional Maps of the Human Genome Resource Report Resource Website |
Human Experimental/FunctionAL MaPper: Providing Functional Maps of the Human Genome (RRID:SCR_003506) | HEFalMp | data or information resource, database, service resource | HEFalMp (Human Experimental/FunctionAL MaPper) is a tool developed by Curtis Huttenhower in Olga Troyanskaya's lab at Princeton University. It was created to allow interactive exploration of functional maps. Functional mapping analyzes portions of these networks related to user-specified groups of genes and biological processes and displays the results as probabilities (for individual genes), functional association p-values (for groups of genes), or graphically (as an interaction network). HEFalMp contains information from roughly 15,000 microarray conditions, over 15,000 publications on genetic and physical protein interactions, and several types of DNA and protein sequence analyses and allows the exploration of over 200 H. sapiens process-specific functional relationship networks, including a global, process-independent network capturing the most general functional relationships. Looking to download functional maps? Keep an eye on the bottom of each page of results: every functional map of any kind is generated with a Download link at the bottom right. Most functional maps are provided as tab-delimited text to simplify downstream processing; graphical interaction networks are provided as Support Vector Graphics files, which can be viewed using the Adobe Viewer, any recent version of Firefox, or the excellent open source Inkscape tool. | human, map, gene, functional, pathway, disease, genomic, analysis, microarray, dna, protein, sequence | has parent organization: Princeton University; New Jersey; USA | New Jersey Commission on Cancer Research ; PhRMA Foundation 2007RSGl9572; NIGMS R01 GM071966; NSF DBI-0546275; NSF IIS-0513552; NHGRI T32 HG003284; NIGMS P50 GM071508 |
PMID:19246570 | nif-0000-37186 | SCR_003506 | Human Experimental / FunctionAL MaPper, Human Experimental/FunctionAL MaPper | 2026-09-12 01:01:29 | 0 | ||||||
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BiSearch: Primer Design and Search Tool Resource Report Resource Website 50+ mentions |
BiSearch: Primer Design and Search Tool (RRID:SCR_002980) | BiSearch | analysis service resource, data analysis service, production service resource, service resource | BiSearch is a primer-design algorithm for DNA sequences. It may be used for both bisulfite converted as well as for original not modified sequences. You can search various genomes with the designed primers to avoid non-specific PCR products by our fast ePCR method. This is especially recommended when primers are designed to amplify the highly redundant bisulfite treated sequences. It has the unique property of analyzing the primer pairs for mispriming sites on the bisulfite-treated genome and determines potential non-specific amplification products with a new search algorithm. The options of primer-design and analysis for mispriming sites can be used sequentially or separately, both on bisulfite-treated and untreated sequences. In silico and in vitro tests of the software suggest that new PCR strategies may increase the efficiency of the amplification. | dna, sequence, primer, design, algorithm, analysis, priming, bisulfite, genome, amplification, in vitro, in silico, amplification, epcr, cytosines | has parent organization: Hungarian Academy of Sciences; Budapest; Hungary | PXE International Inc. GVOP-3.1.1-2004-05-0143/3.0; Boolyai Janos Scholarship ; OTKA T34131; OTKA D42207 |
PMID:17022803 PMID:15653630 |
nif-0000-30170 | SCR_002980 | 2026-09-12 01:01:27 | 54 | |||||||
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Babelomics Resource Report Resource Website 100+ mentions |
Babelomics (RRID:SCR_002969) | Babelomics | analysis service resource, data analysis service, production service resource, service resource | An integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling. Version 4 of Babelomics integrates primary (normalization, calls, etc.) and secondary (signatures, predictors, associations, TDTs, clustering, etc.) analysis tools within an environment that allows relating genomic data and/or interpreting them by means of different functional enrichment or gene set methods. Such interpretation is made not only using functional definitions (GO, KEGG, Biocarta, etc.) but also regulatory information (from Transfac, Jaspar, etc.) and other levels of regulation such as miRNA-mediated interference, protein-protein interactions, text-mining module definitions and the possibility of producing de novo annotations through the Blast2GO system . Babelomics has been extensively re-engineered and now it includes the use of web services and Web 2.0 technology features, a new user interface with persistent sessions and a new extended database of gene identifiers. In this release GEPAS and Babelomics have integrated into a unique web application with many new features and improvements: * Data input: import and quality control for the most common microarray formats * Normalization and base calling: for the most common expression, tiling and SNP microarrays (Affymetrix and Agilent). * Transcriptomics: diverse analysis options that include well established as well as novel algorithms for normalization, gene selection, class prediction, clustering and time-series analysis. * Genotyping: stratification analysis, association, TDT. * Functional profiling: functional enrichment and gene set enrichment analysis with functional terms (GO, KEGG, Biocarta, etc.), regulatory (Transfac, Jaspar, miRNAs, etc.), text-mining, derived bioentities, protein-protein interaction analysis. * Integrative analysis: Different variables can be related to each other (e.g. gene expression to gnomic copy number) and the results subjected to functional analysis. Platform: Online tool | platform, analysis, transcriptomics, proteomics, genomics, normalization, clustering, gene, mirna, protein, interaction, text mining, genotyping, bioentity, functional profiling, statistical analysis, functional annotation, regulatory motif, microarray, fatigo, biclustering, networkminer, gepas, gene expression, FASEB list |
is listed by: OMICtools is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: BioCarta Pathways is related to: KEGG is related to: TRANSFAC is related to: JASPAR has parent organization: CIPF Bioinformatics and Genomics Department |
Spanish Ministry of Science and Innovation BIO2008-04212; Spanish Ministry of Science and Innovation CEN-2008-1002; Red Temtica de Investigacion Cooperativa en Cancer RD06/0020/1019; Instituto de Salud Carlos III |
PMID:20478823 PMID:18515841 PMID:16845052 PMID:14990455 PMID:15980512 PMID:17478504 |
Free for academic use, Account required | OMICS_00748, nif-0000-30144 | http://www.fatigo.org/, http://www.gepas.org/, http://babelomics3.bioinfo.cipf.es | http://www.babelomics.org | SCR_002969 | Babelomics 4: Gene Expression and Functional Profiling Analysis Suite, Babelomics 4 | 2026-09-12 01:01:27 | 138 | |||
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TMA Navigator Resource Report Resource Website 1+ mentions |
TMA Navigator (RRID:SCR_005599) | TMA Navigator | analysis service resource, data analysis service, production service resource, service resource | A free web-based service open to all users for analysis of tissue microarray (TMA) data and related information, accommodating categorical, semi-continuous and continuous expression scores. There is no login requirement. | tissue microarray, network, analysis, visualization, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:23761446 | Acknowledgement requested, Free | biotools:tma_navigator, OMICS_00821 | https://bio.tools/tma_navigator | SCR_005599 | 2026-09-12 01:01:38 | 5 | ||||||
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ArcGIS for Desktop Basic Resource Report Resource Website 5000+ mentions |
ArcGIS for Desktop Basic (RRID:SCR_011081) | ArcGIS for Desktop | commercial organization, software resource | Geographical information system software produced by Esri. | spatial analysis, analysis, geoprocessing, data management, mapping, visualization, geocoding, imagery, data sharing | SciRes_000116 | http://www.esri.com/software/arcgis/arcview | SCR_011081 | ArcView | 2026-09-12 01:03:32 | 6342 | ||||||||
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University at Albany Center for Functional Genomics DNA Microarray Core Facility Resource Report Resource Website |
University at Albany Center for Functional Genomics DNA Microarray Core Facility (RRID:SCR_012502) | UAlbany CFG DNA Microarray Core Facility | access service resource, core facility, service resource | Core provides microarray services for Affymetrix GeneChip arrays, Agilent microarrays, NimbleGen microarrays and custom-produced spotted cDNA microarrays. Projects developed through DNA Microarray Center have made use of arrays from variety of genomes, eukaryotic, prokaryotic, and plant. Core services includes RNA/DNA isolation, gene expression, miRNA, Chip-chip, Rip-chip and DNA methylation services. Provides bioinformatics tools for further analysis of results of expression experiments. | DNA, microarray, functional, genomics, RNA, isolation, gene, expression, Chip-chip, Rip-chip, methylation, experiment, analysis |
is listed by: ScienceExchange has parent organization: University at Albany Center for Functional Genomics |
Restricted | SciEx_30 | SCR_012502 | CFG, University at Albany DNA Microarray Core Facility, University at Albany, UAlbany, Functional Genomics, Center for Functional Genomics, DNA Microarray | 2026-09-12 01:03:43 | 0 | |||||||
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McGill Cell Imaging and Analysis Network Core Facility Resource Report Resource Website 1+ mentions |
McGill Cell Imaging and Analysis Network Core Facility (RRID:SCR_012623) | McGill CIAN | access service resource, core facility, service resource | Core facility at Biology Department in McGill Faculty of Science. Expertise in Light Microscopy and Image Analysis. Provides light microscopes, ranging from Point Scanning and Spinning Disc Confocals to Multi-Photon, TIRF, Light Sheet and Super-Resolution microscopes. Provides services in Automation/High throughput screening (liquid handler, pinning robot), Protein expression and antibody production. Users get training. | Light, microscopy, image, analysis, service, automation, high, throughput, screening, protein, expression, antibody, production, training |
is listed by: ScienceExchange is related to: McGill University Labs and Facilities has parent organization: McGill University; Montreal; Canada |
Restricted | SciEx_569 | http://www.scienceexchange.com/facilities/cell-imaging-and-analysis-network-cian | SCR_012623 | McGill University Cell Imaging and Analysis Network, McGill Cell Imaging and Analysis Network (CIAN), McGill University Cell Imaging and Analysis Network (CIAN) | 2026-09-12 01:03:44 | 1 | ||||||
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DEAPdataset Resource Report Resource Website 10+ mentions |
DEAPdataset (RRID:SCR_001586) | DEAPdataset | data or information resource, data set | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on December 12,2025. Multimodal dataset for emotion analysis using EEG, Physiological and Video Signals of human affective states. The electroencephalogram (EEG) and peripheral physiological signals of 32 participants were recorded as each watched 40 one-minute long excerpts of music videos. Participants rated each video in terms of the levels of arousal, valence, like/dislike, dominance and familiarity. For 22 of the 32 participants, frontal face video was also recorded. A novel method for stimuli selection was used, utilizing retrieval by affective tags from the last.fm website, video highlight detection and an online assessment tool. The dataset is made publicly available and other researchers are encouraged to use it for testing their own affective state estimation methods. | emotion, analysis, eeg, physiological, video, signal, affective state, physiological recording, video recording | has parent organization: Queen Mary University of London; London; United Kingdom | European Community's Seventh Framework Program (FP7/2007-2011) grant agreement 216444; BrainGain Smart Mix Programme ; Swiss National Foundation for Scientific Research ; NCCR Interactive Multimodal Information Management |
THIS RESOURCE IS NO LONGER IN SERVICE. | nlx_153824 | SCR_001586 | DEAP: A Dataset for Emotion Analysis using EEG Physiological and Video Signals, DEAPDataset: A Dataset for Emotion Analysis using EEG Physiological and Video Signals | 2026-09-12 01:03:12 | 25 | ||||||
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TwoPhoton Resource Report Resource Website |
TwoPhoton (RRID:SCR_003596) | TwoPhoton | software resource, source code | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6,2023. Code used for analysis of TwoPhoton data. | photon, analysis | has parent organization: BCM Department of Neuroscience Andreas Tolias Lab | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_157742 | SCR_003596 | 2026-09-12 01:03:14 | 0 | ||||||||
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Classification of Human Lung Carcinomas by mRNA Expression Profiling Reveals Distinct Adenocarcinoma Sub-classes Resource Report Resource Website 1+ mentions |
Classification of Human Lung Carcinomas by mRNA Expression Profiling Reveals Distinct Adenocarcinoma Sub-classes (RRID:SCR_003010) | data or information resource, data set | Data set of a molecular taxonomy of lung carcinoma, the leading cause of cancer death in the United States and worldwide. Using oligonucleotide microarrays, researchers analyzed mRNA expression levels corresponding to 12,600 transcript sequences in 186 lung tumor samples, including 139 adenocarcinomas resected from the lung. Hierarchical and probabilistic clustering of expression data defined distinct sub-classes of lung adenocarcinoma. Among these were tumors with high relative expression of neuroendocrine genes and of type II pneumocyte genes, respectively. Retrospective analysis revealed a less favorable outcome for the adenocarcinomas with neuroendocrine gene expression. The diagnostic potential of expression profiling is emphasized by its ability to discriminate primary lung adenocarcinomas from metastases of extra-pulmonary origin. These results suggest that integration of expression profile data with clinical parameters could aid in diagnosis of lung cancer patients. | molecular, taxonomy, lung, carcinoma, cancer, death, mrna, expression, sequence, data, adenocarcinoma, neuroendocrine, gene, type ii pneumocyte, analysis, metastasis, integration, mrna expression profiling | has parent organization: Broad Institute | Lung cancer | NCI U01 CA84995 | PMID:11707567 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30292 | SCR_003010 | Cancer Genomics Publication | 2026-09-12 01:03:13 | 2 | |||||
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ONTO-PERL Resource Report Resource Website |
ONTO-PERL (RRID:SCR_005731) | ONTO-PERL | software resource, source code | ONTO-PERL is a collection of Perl modules to handle OBO-formatted ontologies (like the Gene Ontology). This code distribution gathers object-oriented modules (for dealing with ontology elements such as Term, Relationship and so forth), scripts (for typical tasks such as format conversions: obo2owl, owl2obo; besides, there are also many examples that can be easily adapted for specific applications), and a set of test files to ensure the suite''''s implementation quality. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | application programming interface, software library, ontology, analysis, development, biomedical |
is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: OBO has parent organization: Comprehensive Perl Archive Network has parent organization: Norwegian University of Science and Technology; Trondheim; Norway |
European Union FP6 LSHG-CT-2004-512143; European Union FP6 MEST-CT-2004-414632 |
PMID:18245124 | Free for academic use | nlx_149191 | SCR_005731 | 2026-09-12 01:03:15 | 0 | ||||||
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Bisque Resource Report Resource Website 10+ mentions |
Bisque (RRID:SCR_005564) | Bisque | software resource, source code | A scalable web-based system for biological image analysis, management and exploration. The Bisque system incorporates many features useful to imaging researchers from image capture to extensible image analysis and querying. At the core, bisque maintains a flexible database of images and experimental metadata. Image analyses can be incorporated into the system and deployed on clusters and desktops. Search and comparison of datasets by image data and content is supported. Novel semantic analyses are integrated into the system allowing high level semantic queries and comparison of image content. New features and testing of Bisque version: 0.5.1, among many others are: # Parallel execution of datasets # Rich interfaces for autogenerated module UI # Abstracted storage system for local, irods, etc.. They are using Mercurial for their source control system. This should be installed before proceeding. Browse source on-line, http://biodev.ece.ucsb.edu/projects/bisquik/browser Bisque Installation, http://biodev.ece.ucsb.edu/projects/bisquik/wiki/InstallationInstructions05 Bisque DOWNLOAD, http://biodev.ece.ucsb.edu/projects/bisquik/wiki/download, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | image, biology, annotate, metadata, analysis, magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Center for Bio-Image Informatics |
NSF ITR-0331697; NSF IIS-0808772 |
PMID:20031971 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_144653 | http://www.nitrc.org/projects/bisque | SCR_005564 | Bio-Image Semantic Query User Environment, Bisque - Bio-Image Semantic Query User Environment | 2026-09-12 01:03:15 | 20 |
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