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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Trim Galore Resource Report Resource Website 5000+ mentions Rating or validation data |
Trim Galore (RRID:SCR_011847) | Trim Galore! | software resource, software application, data processing software | Software tool to automate quality and adapter trimming as well as quality control, with some added functionality to remove biased methylation positions for RRBS sequence files for directional, non-directional or paired-end sequencing. Wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for Reduced Representation Bisulfite Sequencing data. | Automate, quality, adapter, trimming, remove, biased, methylation, position, RRBS, reduced, representation, bisulfite, data, sequence, wrapper, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Babraham Institute works with: cutadapt |
Free, Available for download, Freely available | biotools:trim_galore, OMICS_01096, SCR_016946 | https://github.com/FelixKrueger/TrimGalore https://bio.tools/trim_galore https://sources.debian.org/src/trim-galore/ |
SCR_011847 | TrimGalore | 2026-02-10 09:56:23 | 5797 | ||||||
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imctools Resource Report Resource Website 10+ mentions Rating or validation data |
imctools (RRID:SCR_017132) | IMCtools | software resource, software application, data processing software | Software Python package that implements preprocessing pipeline for imaging mass cytometry data. Can convert IMC raw files to tiff files that are used as inputs into CellProfiller, Ilastik, Fiji etc. | preprocessing, pipeline, imaging, mass, cytometry, data, convert, IMC, raw, file, TIFF |
has parent organization: University of Zurich; Zurich; Switzerland is a plug in for: Fiji |
Swiss National Science Foundation ; SNSF Assistant Professorship grant ; PhosphonetPPM and MetastasiX SystemsX grant ; NIDDK UC4 DK108132; European Research Council ; Roche Postdoctoral Fellowship |
PMID:29605184 | Free, Available for download, Freely available | https://bodenmillergroup.github.io/imctools/build/html/index.html | SCR_017132 | imaging mass spectrometry tools | 2026-02-10 09:57:24 | 21 | |||||
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UCSC Genome Browser Resource Report Resource Website 10000+ mentions Rating or validation data |
UCSC Genome Browser (RRID:SCR_005780) | portal, data or information resource, database, project portal, service resource | Portal to interactively visualize genomic data. Provides reference sequences and working draft assemblies for collection of genomes and access to ENCODE and Neanderthal projects. Includes collection of vertebrate and model organism assemblies and annotations, along with suite of tools for viewing, analyzing and downloading data. | Reference, sequence, assembly, collection, genome, visualize, genomic, data, ENCODE, Neanderthal, project, sequencing |
is used by: VizHub is used by: Blueprint Epigenome is used by: QmRLFS-finder is used by: International Human Epigenome Consortium Data Portal is used by: iPiG is listed by: re3data.org is listed by: OMICtools is listed by: Educational Resources in Neuroscience is listed by: SoftCite is related to: HEXEvent is related to: PicTar is related to: Phenotree is related to: Enhancer Trap Line Browser is related to: CistromeFinder is related to: ENCODE is related to: Human Epigenome Atlas is related to: ENCODE is related to: BigWig and BigBed is related to: PhenCode is related to: doRiNA is related to: ISCA Consortium is related to: WashU Epigenome Browser is related to: CRISPOR is related to: liftOver is related to: kent has parent organization: University of California at Santa Cruz; California; USA works with: TarBase |
UC BIOTEuropean UnionH ; Alfred P. Sloan Foundation ; David and Lucille Packard Foundation ; NIH ; HHMI ; CISI ; NHGRI ; DOE ; NSF DBI 9809007; NIGMS GM52848 |
PMID:12045153 PMID:22908213 PMID:23155063 |
OMICS_00926, SCR_017502, nif-0000-03603, SciEx_217, SCR_012479, r3d100010243 | http://genome.cse.ucsc.edu https://doi.org/10.17616/R3RK5C |
SCR_005780 | The Human Genome Browser at UCSC, UCSC Genome Browser Group, University of California at Santa Cruz Genome Browser, UCSC Genome Bioinformatics | 2026-02-11 10:57:09 | 10026 | ||||||
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TopHat Resource Report Resource Website 5000+ mentions Rating or validation data |
TopHat (RRID:SCR_013035) | software application, alignment software, image analysis software, software resource, data analysis software, sequence analysis software, data processing software | 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 | 2026-02-11 10:58:40 | 9575 | ||||
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End Sequence Analysis ToolKit (ESAT) Resource Report Resource Website 1+ mentions Rating or validation data |
End Sequence Analysis ToolKit (ESAT) (RRID:SCR_015812) | ESAT | software application, software resource, software toolkit, data analysis software, sequence analysis software, source code, data processing software | Software for the analysis of short reads obtained from end-sequence RNA-seq. ESAT is designed for expression analysis of Digital expression (DGE) libraries that target transcript "ends." | short read, rna-seq, expression analysis, dge, digital expression library, transcript end, sequence analysis, alignment, sam file, bam file | PMID:27470110 | Free, Available for download | SCR_015812 | End Sequence Analysis ToolKit | 2026-02-11 10:59:25 | 9 | ||||||||
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NIS-Elements Resource Report Resource Website 1000+ mentions Rating or validation data |
NIS-Elements (RRID:SCR_014329) | software application, software resource, software toolkit, data analysis software, data processing software | Microscope imaging software suite used with Nikon products. NIS-Elements includes software applications for advanced and standard research, documentation, confocal microscopy, and high-content analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | element, microscope imaging software, software suite, nikon |
is listed by: SoftCite works with: Nikon ECLIPSE Ti2 inverted microscope |
THIS RESOURCE IS NO LONGER IN SERVICE | SCR_014329 | Nikon Instruments Software Elements, NIS Elements, Nikon Instruments Software | 2026-02-11 10:58:54 | 3462 | |||||||||
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LSM Image Examiner Resource Report Resource Website 1000+ mentions Rating or validation data |
LSM Image Examiner (RRID:SCR_014344) | data management software, software application, software resource | Software used to compile images obtained from the Zeiss LSM 510 confocal microscope. The browser can be used for general image archiving and handling and interactive measurement in labs and workgroups. Features include orthogonal sectioning, 3D cut function, 3D view with calculation of single projections, and interactive measurement functions in the overlay dialog, such as scale bar, distance, and area. | data management software, image archive, image management, interactive measurement | is listed by: SoftCite | Available for download | http://www.zeiss.com/microscopy/en_us/website/downloads/lsm-image-browser.html http://lsm-image-examiner.software.informer.com | SCR_014344 | LSM Image Browser | 2026-02-11 10:58:54 | 1508 | ||||||||
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Olympus cellSens Software Resource Report Resource Website 1000+ mentions Rating or validation data |
Olympus cellSens Software (RRID:SCR_014551) | software application, image analysis software, software resource, software toolkit, image acquisition software, data processing software, data acquisition software | Software suite for image acquisition and analysis. The software can be paired with high-quality cameras to maximize output quality and export it for sharing and research applications. | image, analysis, record, video, research, optimize, processing, acquisition, camera, Olympus | Restricted | SCR_016238, SCR_018869 | SCR_014551 | Olympus CellSens Imaging software, Olympus cellSens Dimension | 2026-02-11 10:59:08 | 3027 | |||||||||
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SCOM Resource Report Resource Website 1+ mentions Rating or validation data |
SCOM (RRID:SCR_023738) | simulation software, software resource, software application | Software application to Pan-cancer characterization of ncRNA synergistic competition. Used to predict ncRNA synergistic competition network from gene expression data and predicted ncRNA-related ceRNA networks. | Pan-cancer characterization, ncRNA synergistic competition, predict ncRNA synergistic competition network, gene expression data, ncRNA-related ceRNA networks, | Free, Available for download, Freely available | SCR_023738 | Synergistic COMpetition | 2026-02-10 09:58:33 | 1 | ||||||||||
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Integrated Islet Distribution Program (IIDP) Resource Report Resource Website 100+ mentions Rating or validation data |
Integrated Islet Distribution Program (IIDP) (RRID:SCR_014387) | IIDP | organization portal, portal, resource, data or information resource | The goal of the Integrated Islet Distribution Program (IIDP) is to work with the leading islet isolation centers in the U.S. to distribute high quality human islets to the diabetes research community, in order to advance scientific discoveries and translational medicine. | program, islet, distribution, diabetes |
is listed by: NIDDK Information Network (dkNET) is listed by: NIDDK Research Resources |
Diabetes | NIDDK | http://www.niddk.nih.gov/research-funding/research-resources/Pages/default.aspx | SCR_014387 | Integrated Islet Distribution Program | 2026-02-11 10:58:54 | 294 | ||||||
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National Disease Research Interchange Resource Report Resource Website 100+ mentions Rating or validation data |
National Disease Research Interchange (RRID:SCR_000550) | NDRI | biomaterial supply resource, tissue bank, material resource | NDRI is a Not-For-Profit (501c3) Corporation dedicated to providing the highest quality human biomaterials for research. NDRI makes it easy for researchers to get the human tissues and organs they need, prepared, preserved and shipped precisely according to their specific scientific protocols, as quickly as possible, and in the largest available quantities. NDRI provides researchers with protocol specific human neurological tissues such as brain stem, spinal cord, and basal ganglia, among others. In addition to control specimens, NDRI recovers tissues from donors with a variety of diseases, including Down syndrome, Parkinsons disease, Alzheimers disease, schizophrenia, and dementia. Through the NDRI 24/7 referral and procurement system, research consented biospecimens can be provided from low post mortem interval donors preserved at 4ºC, frozen or snap frozen, fixed, paraffin embedded, or as unstained slides. | neurological, tissue, organ, cell, neurological tissue, brainstem, spinal cord, basal ganglia, cerebral cortex, hippocampus, frozen, snap frozen, fixed, paraffin embedded, unstained slide, disease, down syndrome, parkinson's disease, alzheimer's disease, schizophrenia, dementia, control, normal, catalog |
is listed by: One Mind Biospecimen Bank Listing is listed by: Multiple Sclerosis Discovery Forum is listed by: Biospecimens/Biorepositories: Rare Disease-HUB (RD-HUB) is parent organization of: Human Tissue and Organ for Research Resource (HTORR) is parent organization of: Human Biological Data Interchange is parent organization of: NDRI Dorsal Root Ganglia Program |
Down syndrome, Parkinson's disease, Alzheimer's disease, Schizophrenia, Dementia | NIH OD011158 | Public: NDRI is a nonprofit organization that procures and distributes normal and diseased human biomaterials to biomedical researchers in academia, government, and industry. | nlx_99804 | SCR_000550 | 2026-02-11 10:56:04 | 190 | ||||||
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Constant distance Mode Nanospray Desorption Electrospray Ionization Mass Spectrometry Resource Report Resource Website Rating or validation data |
Constant distance Mode Nanospray Desorption Electrospray Ionization Mass Spectrometry (RRID:SCR_017130) | nano-DESI MSI | instrument resource | System to extend constant distance mode mass spectrometry imaging using nanospray desorption electrospray ionization by integrating shear force probe with nano DESI probe to improve imaging capabilities. Used for imaging biological samples of complex topography in their native states. Enables ambient imaging of biological samples with high sensitivity and minimal sample pretreatment. | extend, constant, distance, mode, mass, spectrometry, imaging, nanospray, electrospray, ionization, probe, DESI, topography, native, state | has parent organization: Pacific Northwest National Laboratory | DOE Office of Biological and Environmental Research | PMID:27973782 | SCR_017130 | constant-mode nano-DESI MSI | 2026-02-07 02:09:35 | 0 | |||||||
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FP-3W Resource Report Resource Website Rating or validation data |
FP-3W (RRID:SCR_015808) | resource | Equipment that is a re-sealable 3 well fluidic platform optimized for effective perfusion. It supports the dynamic testing of pancreatic islets for glucose-stimulated insulin secretion (GSIS) and concomitant live-cell imaging. | fluidic platform, hardware, perfusion, pancreatic islet, insulin secretion, live-cell imaging, instrument, equipment | PMID:28157238 | Commercially available | SCR_015808 | FP-3W Fluidic Platform | 2026-02-07 02:09:40 | 0 | |||||||||
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CaTCh FISH Chip Resource Report Resource Website Rating or validation data |
CaTCh FISH Chip (RRID:SCR_015810) | resource | Equipment that is a magnetic micropore chip for rapid unbiased circulating tumor cell isolation and in situ RNA analysis. The chip detects tumor cells and can help doctors treat patients with these tumors. | hardware, instrument, equipment, magnetic micropore, micropore chip, tumor cell isolation, rna analysis, in situ, microtechnology, microchip, bioengineering | Pancreatic cancer, cancer | PMID:28809985 | Commercially available | SCR_015810 | 2026-02-07 02:09:21 | 0 | |||||||||
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Ingenuity Pathway Analysis Resource Report Resource Website 5000+ mentions Rating or validation data |
Ingenuity Pathway Analysis (RRID:SCR_008653) | IPA | pathway analysis tool | A web-based software application that enables users to analyze, integrate, and understand data derived from gene expression, microRNA, and SNP microarrays, metabolomics, proteomics, and RNA-Seq experiments, and small-scale experiments that generate gene and chemical lists. Users can search for targeted information on genes, proteins, chemicals, and drugs, and build interactive models of experimental systems. IPA allows exploration of molecular, chemical, gene, protein and miRNA interactions, creation of custom molecular pathways, and the ability to view and modify metabolic, signaling, and toxicological canonical pathways. In addition to the networks and pathways that can be created, IPA can provide multiple layering of additional information, such as drugs, disease genes, expression data, cellular functions and processes, or a researchers own genes or chemicals of interest. | software, drug, gene, analysis, chemical, metabolic, model, pathway, protein, signal, molecular signaling, genomic, pathway analysis tool |
uses: Ingenuity Pathways Knowledge Base is listed by: Biositemaps is listed by: OMICtools is listed by: SoftCite |
Commercial license | nif-0000-33144, OMICS_00399 | http://www.ingenuity.com/products/ipa http://www.ingenuity.com/products/ipa/microrna-research |
SCR_008653 | QIAGEN Ingenuity Pathway Analysis | 2026-02-07 02:07:52 | 6464 | ||||||
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GraphPad Prism Resource Report Resource Website 10000+ mentions Rating or validation data |
GraphPad Prism (RRID:SCR_002798) | software application, data visualization software, software resource, data analysis software, data processing software | Statistical analysis software that combines scientific graphing, comprehensive curve fitting (nonlinear regression), understandable statistics, and data organization. Designed for biological research applications in pharmacology, physiology, and other biological fields for data analysis, hypothesis testing, and modeling. | biostatistics, curve, fitting, nonlinear, regression, graphing, statistical, analysis, biology, pharmacology, physiology |
is listed by: SoftCite has parent organization: GraphPad |
Restricted | rid_000081, SCR_015807 | https://www.graphpad.com/updates/prism-920-release-notes http://graphpad-prism.software.informer.com/5.0/ https://www.graphpad.com/guides/prism/7/user-guide/index.htm |
SCR_002798 | Prism 9.2.0, Graph Pad Prism 7, Graph Pad Prism, GraphPad Prism, Graph pad Prism 5, GraphPad Prism version 9.2.0, Graphpad Prism software, Graph pad Prism 8, Graph pad Prism, Graphpad Prism | 2026-02-11 10:56:32 | 46700 | |||||||
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Vevo 2100 Resource Report Resource Website 10+ mentions Rating or validation data |
Vevo 2100 (RRID:SCR_015816) | software application, image analysis software, data management software, software resource, image acquisition software, data processing software, image processing software, data acquisition software | Imaging software for high-frequency processing and analysis. Some of its features include modes for blood flow quantification, single line acquisition, 3D-Mode imaging & volume analysis, nonlinear contrast imaging, and other image processing functions. | high-frequency imaging, imaging software, single line acquisition, blood flow quantification, 3d-imaging, nonlinear contrast | Commercially available, Available for purchase, Demo available | SCR_015816 | Vevo, Vevo® 2100 system, Vevo 2100 System | 2026-02-11 10:59:25 | 28 | ||||||||||
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FastQC Resource Report Resource Website 10000+ mentions Rating or validation data |
FastQC (RRID:SCR_014583) | software application, data management software, software resource, data analysis software, data processing software | Quality control software that perform checks on raw sequence data coming from high throughput sequencing pipelines. This software also provides a modular set of analyses which can give a quick impression of the quality of the data prior to further analysis. | quality control, sequence data, sequencing, analysis, data quality, pipeline, raw sequence data, modular set, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools is listed by: SoftCite |
Open source, Available for download | biotools:fastqc, SCR_005539, OMICS_01043 | https://omictools.com/fastqc-tool https://bio.tools/fastqc https://sources.debian.org/src/fastqc/ |
SCR_014583 | FastQC v0.11.5 | 2026-02-11 10:58:58 | 18745 | |||||||
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CellCycleTRACER Resource Report Resource Website Rating or validation data |
CellCycleTRACER (RRID:SCR_017128) | software application, software resource, web service, data analysis software, data access protocol, data processing software | Software tool as supervised machine learning algorithm that classifies and sorts single cell mass cytometry data according to their cell cycle, which allows to correct for cell cycle state and cell volume heterogeneity. Reveals signaling relationships and cell heterogeneity that were otherwise masked. Computational method to quantify cell cycle and cell volume variability. | classify, sort, single, cell, mass, cytometry, data, cycle, state, volume, heterogeneity, quantify, volume, variability | SNSF ; European Research Council ; NIDDK UC4 DK108132; SystemsX MetastasiX grant |
PMID:29434325 | Free, Restricted | SCR_017128 | 2026-02-11 10:59:38 | 0 | |||||||||
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Avadis Resource Report Resource Website 1+ mentions Rating or validation data |
Avadis (RRID:SCR_000644) | Avadis | software resource, software toolkit, software library | Software integrated platform that provides analysis, management and visualization tools for next-generation sequencing data. It supports workflows for RNA-Seq, DNA-Seq, ChIP-Seq and small RNA-Seq experiments. Avadis has a built-in Gene Ontology browser to view ontology hierarchies. There are common ontology paths for multiple genes. Platform has collection of data / text mining algorithms, data visualization libraries, workflow/application automation layers, and enterprise data organization functions. These functions are available as libraries that allow developers to rapidly build software prototypes, applications and off-the-shelf products. The collection of algorithms and visualizations in AVADIS grows as new applications using the platform are developed. Currently, the algorithms that AVADIS platform contains range from general purpose statistical mining and modelling algorithms, to text mining algorithms, to very application-specific algorithms for microarray / NGS data analysis, QSAR modelling and biological networks analysis. AVADIS has a collection of powerful mining algorithms like PCA, ANOVA, T-test, clustering, classification and regression methods. The range of visualizations includes most statistical and data modelling related graphing views, and very application-specific visualizations. Some of the statistical views include 2D/3D scatter plots, profile plots, heat maps, histograms and matrix plot; data modelling relevant views include dendrograms, cluster profiles, similarity images and SOM U-matrices. Application-specific views in AVADIS include pathway network views, genome browsers, chemical structure views and pipe-line views. Platform: Windows compatible, Mac OS X compatible, Linux compatible, | pathway network views, genome browsers, chemical structure views, pipe-line views, next-generation sequencing data, integrated platform, view ontology hierarchies, statistical mining and modelling, collection of data, text mining algorithms collection, data visualization libraries, |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01120, nlx_149208 | http://www.strandls.com/Avadis | SCR_000644 | Access Visualize Analyze Discover, Avadis NGS | 2026-02-11 10:56:05 | 2 |
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