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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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MitoScience Resource Report Resource Website 1+ mentions |
MitoScience (RRID:SCR_001130) | commercial organization | Commercial supplier and developer of mitochondrial antibodies and mitochondrial assays. The company focuses on supporting critical research areas in cancer, neurodegeneration and metabolic disorders. | mitochondrial antibody, mitochondria, assay, abcam, antibody, cancer, neurodegeneration, metabolic disorders | is affiliated with: Abcam | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152413 | SCR_001130 | MitoScience LLC | 2026-08-15 11:21:52 | 1 | ||||||||
|
Aves Labs Resource Report Resource Website 10+ mentions |
Aves Labs (RRID:SCR_001136) | commercial organization | An antibody supplier that specializes in high-affinity custom chicken antibody production, providing clients with chicken IgY and other immunoreagents for biomedical research and antibody manufacturing. | antibody, high affinity, chicken antibody, chicken igy, immunoreagents, biomedical, research, immunoglobulin | nlx_152287 | SCR_001136 | 2026-08-15 11:21:52 | 23 | |||||||||||
|
CUDA-EC Resource Report Resource Website 1+ mentions |
CUDA-EC (RRID:SCR_001090) | CUDA-EC | software resource | A fast parallel error correction tool for short reads. | c, gpu/cuda, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:20426693 | Free, Available for download, Freely available | OMICS_01100, biotools:cuda-ec | https://bio.tools/cuda-ec | SCR_001090 | Compute Unified Device Architecture | 2026-08-15 11:21:52 | 1 | |||||
|
DSRC Resource Report Resource Website 1+ mentions |
DSRC (RRID:SCR_001005) | DSRC | software application, software resource, data management software | An application designed for compression of data files containing reads from DNA sequencing in FASTQ format. Its main features include multithreaded compression of FASTQ output, python and C++ libraries, and support for lossy IDs compression. | fastq, dna sequence, compression, multithread, data management software, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:21252073 | Free, Available as binary, Available as source code | biotools:dsrc, OMICS_00955 | https://bio.tools/dsrc | SCR_001005 | DNA Sequence Reads Compression, DNA Sequence Reads Compression (DSRC) | 2026-08-15 11:22:01 | 1 | |||||
|
Australian National University; Acton; Australia Resource Report Resource Website 1+ mentions |
Australian National University; Acton; Australia (RRID:SCR_001086) | ANU | university | A national research university in Canberra, Australia. It offers undergraduate and graduate degrees in fields such as law, medicine, business, arts and the social sciences. | national university, research, australia, law, medicine, business, arts, social sciences |
uses: Writefull is parent organization of: ANU Centre for Advanced Microscopy Core Facility is parent organization of: ARC Centre of Excellence in Vision Science is parent organization of: Informant Questionnaire on Cognitive Decline in the Elderly is parent organization of: Australian Phenomics Network is parent organization of: Centre for Visual Sciences is parent organization of: CBiS is parent organization of: Eutherian comparative genomic analysis protocol |
nlx_23045, ISNI:0000 0001 2180 7477, Wikidata:Q127990, Crossref funder ID:501100000995, grid.1001.0 | https://ror.org/019wvm592 | SCR_001086 | Australian National University | 2026-08-15 11:21:51 | 1 | |||||||
|
JBrowse Resource Report Resource Website 10+ mentions |
JBrowse (RRID:SCR_001004) | JBrowse | software resource | A high-performance visualization tool for interactive exploration of large, integrated genomic datasets written primarily in JavaScript. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations. | genome |
is used by: Genome Resources for Yeast Chromosomes is listed by: OMICtools is listed by: Debian has parent organization: Broad Institute |
NHGRI 5R01HG004483-09 | PMID:22517427 PMID:21221095 |
GNU Lesser General Public License, Account required | OMICS_00918 | https://sources.debian.org/src/jbrowse/ | SCR_001004 | 2026-08-15 11:21:51 | 32 | |||||
|
Washington University School of Medicine Genome Technology Access Center Core Facility Resource Report Resource Website 1+ mentions |
Washington University School of Medicine Genome Technology Access Center Core Facility (RRID:SCR_001030) | WUSTL GTAC, GTAC | service resource, access service resource, core facility | Genome Access Technology Center at the McDonnell Genome Institute offers comprehensive next generation sequencing, microarray, PCR and Bioinformatic services. In addition to generating high quality genomic, transcriptomic, and proteomic data, performs data analysis and provides technological support to users. Full service facility, from hypothesis to publication. Offers advanced analysis of microarray data. Provides free initial consultation to discuss project and offers several tiers of analysis packages to best suit your needs. NGS equipment includes NovaSeqs, Seqwell II, Oxford. Microarray expression and genotyping - all platforms. | Next generation sequencing, microarray, PCR, bioinformatic service, data analysis, ABRF, USEDit |
is listed by: ScienceExchange is listed by: ABRF CoreMarketplace is related to: Washington University in St. Louis School of Medicine Division of Biology and Biomedical Sciences has parent organization: Washington University in St. Louis; Missouri; USA |
Open | SCR_018204, SCR_018300, SciEx_32, ABRF_279 | https://coremarketplace.org/?FacilityID=279 | http://www.scienceexchange.com/facilities/genome-technology-access-center-gtac-wustl | SCR_001030 | Washington University McDonnell Genome Institute Genome Technology Access Center, , Genome Technology Access Center, Washington University School of Medicine GTAC Core Facility, Washington University in St. Louis Genome Technology Access Center, McDonnell Genome Institute Genome Technology Access Center, Washington University in St. Louis School of Medicine Genome Technology Access Center Core Facility, Washington University in St. Louis McDonnell Genome Institute Genome Technology Access Center, Washington University School of Medicine GTAC | 2026-08-15 11:21:51 | 6 | |||||
|
PNA Bio Resource Report Resource Website 1+ mentions |
PNA Bio (RRID:SCR_001037) | service resource, production service resource | A company which provides peptide nucleic acid products for use in research. It also provides engineered nuclease services to laboratories. | peptide nucleic acid, commercial, lab services, production service resource | is listed by: ScienceExchange | Available to the research community, Products are for research use only | SciEx_13409 | http://www.scienceexchange.com/facilities/pna-bio | SCR_001037 | PNA Bio Inc | 2026-08-15 11:21:51 | 2 | |||||||
|
flowWorkspace Resource Report Resource Website 1+ mentions |
flowWorkspace (RRID:SCR_001155) | software resource | Software package that facilitates comparison of automated gating methods against manual gating done in flowJo. This package allows you to import basic flowJo workspaces into BioConductor and replicate the gating from flowJo using the flowCore functionality. Gating hierarchies, groups of samples, compensation, and transformation are performed so that the output matches the flowJo analysis. | software package, mac os x, unix/linux, windows, r, data import, data representation, flow cytometry, preprocessing |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:23020243 | Free, Available for download, Freely available | OMICS_05616 | SCR_001155 | flowWorkspace - Import flowJo Workspaces into BioConductor and replicate flowJo gating with flowCore | 2026-08-15 11:21:52 | 3 | |||||||
|
Renovo Neural Resource Report Resource Website 1+ mentions |
Renovo Neural (RRID:SCR_001035) | service resource, production service resource | A specialized preclinical research organization that provides services for biological research and development on neural therapies. Renovo offers preclinical assays and 3D-electron microscopy services that provide routine and customized solutions for basic science, preclinical and clinical research, and drug development. | commercial, solution, production service resource, preclinical, research, biological service | is listed by: ScienceExchange | THIS RESOURCE IS NO LONGER IN SERVICE | SciEx_12107 | SCR_001035 | Renovo Neural Inc, Renovo | 2026-08-15 11:21:50 | 1 | ||||||||
|
Insight Segmentation and Registration Toolkit Resource Report Resource Website 50+ mentions |
Insight Segmentation and Registration Toolkit (RRID:SCR_001149) | ITK | data or information resource, portal, topical portal, software resource | Open source, cross platform library that provides developers with extensive suite of software tools for image analysis. Developed through extreme programming methodologies, ITK builds on proven, spatially oriented architecture for processing, segmentation, and registration of scientific images in two, three, or more dimensions. | registration, segmentation, multidimension, image processing, reusable library, analyze, bshort/bfloat, c++, console (text based), dicom, java, minc2, nifti, nrrd, os independent, philips par/rec, python, tcl/tk |
uses: Laplace Beltrami Filter on QuadEdge Meshes uses: VTK is used by: Joint Anisotropic LMMSE Filter for Stationary Rician noise removal in DWI is used by: Displacement Field Viewer is used by: Joint Anisotropic LMMSE Filter for Stationary Rician noise removal in DWI is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Vaa3D is related to: elastix is related to: VMTK in 3D Slicer is related to: NA-MIC Kit is related to: SimpleITK |
NIBIB EB006733; NIBIB EB008374; NIBIB EB009634; NCRR P41RR013218 |
Free, Available for download, Freely available | nif-0000-00319 | http://www.nitrc.org/projects/insighttoolkit | SCR_001149 | Insight Toolkit, National Library of Medicine Insight Segmentation and Registration Toolkit (ITK), Insight Segmentation and Registration Toolkit | 2026-08-15 11:21:52 | 84 | |||||
|
GimmeMotifs Resource Report Resource Website 1+ mentions |
GimmeMotifs (RRID:SCR_001146) | GimmeMotifs | software resource | Software that provides a de novo motif prediction pipeline, especially suited for ChIP-seq datasets. It incorporates several existing motif prediction algorithms in an ensemble method to predict motifs and clusters these motifs using the WIC similarity scoring metric., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | linux, chip-seq, motif, cluster, python, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Radboud University; Nijmegen; The Netherlands |
PMID:21081511 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:gimmemotifs, OMICS_02150 | https://bio.tools/gimmemotifs | SCR_001146 | GimmeMotifs: a systematic de novo motif prediction pipeline | 2026-08-15 11:22:02 | 4 | |||||
|
Visualization and Analysis of Networks containing Experimental Data (VANTED) Resource Report Resource Website 10+ mentions |
Visualization and Analysis of Networks containing Experimental Data (VANTED) (RRID:SCR_001138) | VANTED | data processing software, software application, data analysis software, software resource, data visualization software | Software tool for extendable network visualization and analysis for the life sciences. It is Java-based and allows users to create, edit and map data onto existing or new networks. Experimental datasets can be visualized on network elements as graphical charts to show time series data or data of different treatments, as well as environmental conditions in the context of the underlying biological processes. Users can utilize built-in statistical algorithms to evaluate mapped data. | binary executable, simulation software, signal processing software, java, network visualization, statistical analysis, bio.tools |
is listed by: bio.tools is listed by: Debian |
PMID:23140568 | Open source | biotools:vanted, nif-0000-00373 | https://bitbucket.org/vanted-dev/vanted/src, https://bio.tools/vanted | http://vanted.ipk-gatersleben.de/ | SCR_001138 | Visualization and Analysis of Networks containing Experimental Data, VANTED v2 | 2026-08-15 11:21:52 | 14 | ||||
|
rbsurv Resource Report Resource Website 1+ mentions |
rbsurv (RRID:SCR_001175) | rbsurv | software resource | Software package that selects genes associated with survival. | microarray, gene, survival, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
Free, Available for download, Freely available | biotools:rbsurv, BioTools:rbsurv, OMICS_02088 | https://bio.tools/rbsurv, https://bio.tools/rbsurv, https://bio.tools/rbsurv | SCR_001175 | rbsurv - Robust likelihood-based survival modeling with microarray data | 2026-08-15 11:22:03 | 1 | ||||||
|
CrossMap Resource Report Resource Website 10+ mentions |
CrossMap (RRID:SCR_001173) | CrossMap | software resource | A software program for convenient conversion of genome coordinates (or annotation files) between different assemblies. It supports most commonly used file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF. It is designed to liftover genome coordinates between assemblies. It?s not a program for aligning sequences to reference genome. CrossMap is not recommend for converting genome coordinates between species. | genome, assembly |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24351709 | GNU General Public License | OMICS_02184 | SCR_001173 | 2026-08-15 11:21:52 | 19 | |||||||
|
Sherman Resource Report Resource Website 100+ mentions |
Sherman (RRID:SCR_001294) | Sherman | software resource | Software tool to simulate FastQ files for high-throughput sequencing experiments. It allows the user to introduce various "contaminants" into the sequences, such as basecall errors, SNPs, adapter fragments etc., in order to evaluate the influence of common problems observed in many Next-Gen Sequencing experiments. | perl, bisulfite sequencing, high-throughput sequencing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Babraham Institute |
Free, Available for download, Freely available | biotools:sherman, OMICS_02041 | http://www.bioinformatics.babraham.ac.uk/projects/sherman/ | SCR_001294 | Sherman - bisulfite-treated Read FastQ Simulator | 2026-08-15 11:21:55 | 124 | ||||||
|
STRViper Resource Report Resource Website 1+ mentions |
STRViper (RRID:SCR_001179) | STRViper | software resource | Software tool for detection of short tandem repeat (STR) variations from paired-end next generation sequencing data. It makes variant calls based on deviations in sequence fragment sizes, allowing the analysis of repeats of size up to fragment length. This stratergy also helps avoiding false calls resulting from errors arised from sequencing of repeat DNA. | next-generation sequencing, short tandem repeat variation, short tandem repeat, java, unix, linux, macos, paired-end read |
is listed by: OMICtools has parent organization: University of Queensland; Brisbane; Australia |
PMID:24353318 | Free, Available for download, Freely available | OMICS_02177 | SCR_001179 | Short Tandem Repeat Variation Indentification from Paired-End Reads, STRViper: Short Tandem Repeat Variation Indentification from Paired-End Reads | 2026-08-15 11:22:03 | 1 | ||||||
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Golden Helix GenomeBrowse Resource Report Resource Website 1+ mentions |
Golden Helix GenomeBrowse (RRID:SCR_001213) | GenomeBrowse | commercial organization, data processing software, software application, software resource, data visualization software | Software tool that delivers visualizations of your genomic data that give you the power to see what is occurring at each base pair in your samples. A high performance backend is paired with an user interface to make sure that your discovery process is fluid and streamlined. | Golden Helix, variant, visualization, genome |
is listed by: OMICtools has parent organization: Golden Helix Incorporated |
Free, Available for download, Freely available | OMICS_02129 | SCR_001213 | 2026-08-15 11:21:53 | 2 | ||||||||
|
PARalyzer Resource Report Resource Website 1+ mentions |
PARalyzer (RRID:SCR_001208) | PARalyzer | software resource | Software tool to generate a high resolution map of interaction sites between RNA-binding proteins and their targets. The algorithm utilizes the deep sequencing reads generated by the newly developed PAR-CLIP (Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation) protocol. The use of photoactivatable nucleotides in the PAR-CLIP protocol results in a more efficient crosslinking between the RNA-binding protein and its target relative to other CLIP methods; in addition a nucleotide substitution occurs at the site of crosslinking during Illumina library preparation. PARalyzer utilizes this nucleotide substition in a kernel density estimate classifier to generate the high resolution set of Protein-RNA interaction sites. | interaction, rna-binding protein, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Duke University; North Carolina; USA |
PMID:21851591 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:paralyzer, OMICS_02137 | https://bio.tools/paralyzer | SCR_001208 | PAR-CLIP data analyzer, PARalyzer (PAR-CLIP data analyzer) | 2026-08-15 11:21:53 | 7 | |||||
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CGH-Explorer Resource Report Resource Website 10+ mentions |
CGH-Explorer (RRID:SCR_001283) | CGH-Explorer | software resource | Software program for visualization and statistical analysis of microarray-based comparative genomic hybridization (array-CGH) data. The program has preprocessing facilities, tools for graphical exploration of individual arrays or groups of arrays, and tools for statistical identification of regions of amplification and deletion. | microarray, comparative genomic hybridization, visualization, statistics, java, windows |
is listed by: OMICtools has parent organization: University of Oslo; Oslo; Norway |
PMID:15531610 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02054 | SCR_001283 | 2026-08-15 11:21:55 | 15 |
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