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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Flowlogic Resource Report Resource Website 50+ mentions |
Flowlogic (RRID:SCR_020942) | data analysis software, data processing software, software application, software resource | Software tool for flow cytometry data analysis by Miltenyi Biotec. | Flow cytometry data, data analysis, flow cytometry, Miltenyi Biotec | is listed by: SoftCite | Restricted | SCR_020942 | SciCrunch Registry | Flowlogic TM Software, Flowlogic Software | 2026-11-07 12:00:13 | 81 | |||||||||
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GRADEpro Resource Report Resource Website 500+ mentions |
GRADEpro (RRID:SCR_021308) | data management software, software application, software resource | Software tool used to create summary of findings tables for cochrane systematic reviews. Web application to create, manage and share summaries of research evidence called Evidence Profiles and Summary of Findings Tables. | Summary of findings tables, cochrane systematic reviews, research evidence creating, research evidence management, research evidence sharing summaries, evidence profiles, | is listed by: SoftCite | Restricted | https://cebgrade.mcmaster.ca/gradepro.html | SCR_021308 | SciCrunch Registry | Guideline Development Tool, GRADEpro GDT, GDT, GRADE Guideline Development Tool, G2DT | 2026-11-07 12:00:17 | 650 | ||||||||
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jcvi Resource Report Resource Website 10+ mentions |
jcvi (RRID:SCR_021641) | software library, software resource, software toolkit | Software tool as collection of Python libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparative genomics. | Python libraries, parse bioinformatics files, assembly, annotation, comparative genomics | is listed by: SoftCite | Free, Available for download, Freely available | https://github.com/tanghaibao/jcvi/tree/v0.5.7, https://zenodo.org/record/31631#.YRaieYhKhPa | SCR_021641 | SciCrunch Registry | jcvi_PyPI, jcvi 1.1.17 | 2026-11-07 12:00:21 | 20 | ||||||||
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CalcuSyn Resource Report Resource Website 50+ mentions |
CalcuSyn (RRID:SCR_020251) | data analysis software, data processing software, software application, software resource | Software tool for drug mixtures study and establishing efficacy. Dose effect analyzer of combined drugs. Able to quantify synergism and inhibition. CalcuSyn Version 2.0 has Undo and Redo tools. | Biosoft, drug mixtures study, drug efficacy, dose effect, quantify synergism, quantify inhibition | is listed by: SoftCite | Restricted | SCR_020251 | SciCrunch Registry | CalcuSyn Version 2.0 | 2026-11-07 12:00:03 | 68 | |||||||||
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MutationAssessor Resource Report Resource Website 500+ mentions |
MutationAssessor (RRID:SCR_005762) | mutationassessor.org | analysis service resource, data analysis service, production service resource, service resource | A web server that predicts the functional impact of amino-acid substitutions in proteins, such as mutations discovered in cancer or nonsynonymous polymorphisms. The functional impact is assessed based on evolutionary conservation of the affected amino acid in protein homologs. The method has been validated on a large set (51k) of disease associated (OMIM) and polymorphic variants., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | cancer, protein, mutation, function, amino-acid, substitution |
is listed by: OMICtools is listed by: SoftCite |
PMID:21727090 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00134, nlx_149228 | SCR_005762 | SciCrunch Registry | MutationAssessor - functional impact of protein mutations, MutationAssessor - functional impact of mutations, mutationassessor.org - functional impact of protein mutations | 2026-11-07 12:02:10 | 693 | ||||||
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mitopred Resource Report Resource Website 1+ mentions |
mitopred (RRID:SCR_006135) | MITOPRED | analysis service resource, data analysis service, production service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. It predicts nuclear-encoded mitochondrial proteins from all eukaryotic species including plants. Prediction is based on the occurrence patterns of Pfam domains (version 16.0) in different cellular locations, amino acid composition and pI value differences between mitochondrial and non-mitochondrial locations. Additionally, you may download MITOPRED predictions for complete proteomes. Re-calculated predictions are instantly accessible for proteomes of Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila, Homo sapiens, Mus musculus and Arabidopsis species as well as all the eukaryotic sequences in the Swiss-Prot and TrEMBL databases. Queries, at different confidence levels, can be made through four distinct options: (i) entering Swiss-Prot/TrEMBL accession numbers; (ii) uploading a local file with such accession numbers; (iii) entering protein sequences; (iv) uploading a local file containing protein sequences in FASTA format. The Mitopred algorithm works based on the differences in the Pfam domain occurrence patters and amino acid composition differences in different cellular compartments. Location specific Pfam domains have been determined from the entire eukaryotic set of Swissprot database. Similarly, differences in the amino acid composition between mitochondrial and non-mitochondrial sequences were pre-calculated. This information is used to calculate location-specific amino acid weights that are used to calculate amino acid score. Similarly, pI average values of the N-terminal 25 residues in different cellular location were also determined. This knowledge-base is accessed by the program during execution. | yeast, c. elegans, drosophila, mouse, human, arabidopsis, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: University at Albany; New York; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:mitopred, nif-0000-03956, BioTools:mitopred | https://bio.tools/mitopred, https://bio.tools/mitopred, https://bio.tools/mitopred | SCR_006135 | SciCrunch Registry | A genome-scale method for predicting mitochondrial proteins | 2026-11-07 12:02:39 | 7 | ||||||
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GBrowse Resource Report Resource Website 10+ mentions |
GBrowse (RRID:SCR_006829) | GBrowse | data or information resource, database | A database and interactive web site for manipulating and displaying annotations on genomes. Features include: detailed views of the genome; use of a variety of premade or personally made glyphs ; customizable order and appearance of tracks by administrators and end-users; search by annotation ID, name, or comment; support of third party annotation using GFF formats; DNA and GFF dumps; connectivity to different databases, including BioSQL and Chado; and a customizable plug-in architecture (e.g. run BLAST, find oligonucleotides, design primers, etc.). GBrowse is distributed as source code for Macintosh OS X, UNIX and Linux platforms, and as pre-packaged binaries for Windows machines. It can be installed using the standard Perl module build procedure, or automated using a network-based install script. In order to use the net installer, you will need to have Perl 5.8.6 or higher and the Apache web server installed. The wiki portion accepts data submissions. | genome, annotation, database, perl, virus, dna, protein, reference sequence, chromosome, visualization, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: WormBase is related to: FlyBase is related to: International HapMap Project has parent organization: Generic Model Organism Database Project has parent organization: Indiana University; Indiana; USA |
Howard Hughes Medical Institute ; NHGRI HG00739; NHGRI P41HG02223 |
PMID:19957275 PMID:18428797 PMID:12368253 PMID:21400697 PMID:20194461 PMID:19357095 DOI:10.1002/0471250953.bi0909s28 |
The community can contribute to this resource, Requires Perl 5.8.6 or higher and the Apache web server | OMICS_00910, biotools:gbrowse, nif-0000-30597 | http://gmod.org/wiki/GBrowse, https://bio.tools/gbrowse, https://sources.debian.org/src/gbrowse/ | SCR_006829 | SciCrunch Registry | Generic Genome Browser | 2026-11-07 12:02:51 | 43 | ||||
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Openlab Resource Report Resource Website 1000+ mentions |
Openlab (RRID:SCR_012158) | Openlab | commercial organization, software resource | A software package for performing 2D microscope image processing and integrating and controlling a diverse array of instrumentation in a laboratory environment. The software suite has four basic areas of operation acquisition, image presentation, and storage, analysis, and automation., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | fluorescence imaging, cell biology | is listed by: SoftCite | THIS RESOURCE IS NO LONGER IN SERVICE | rid_000096 | SCR_012158 | SciCrunch Registry | 2026-11-07 12:05:04 | 1134 | ||||||||
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piRNABank Resource Report Resource Website 100+ mentions |
piRNABank (RRID:SCR_007858) | data or information resource, database | A web analysis system and resource, which provides comprehensive information on piRNAs in the widely studied mammals. It compiles all the possible clusters of piRNAs and also depicts piRNAs along with the associated genomic elements like genes and repeats on a genome wide map. piRNABank mainly provides data onnamely Human, Mouse, Rat, Zebrafish, Platypus and a fruit fly, Drosophila.Search options have been designed to query and obtain useful data from this online resource. It also facilitates abstraction of sequences and structural features from piRNA data. piRNABank provides the following features: * Simple search * Search piRNA clusters * Search homologous piRNAs * piRNA visualization map * Analysis tools, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | FASEB list | is listed by: SoftCite | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03293 | SCR_007858 | SciCrunch Registry | piRNABank | 2026-11-07 12:02:25 | 172 | ||||||||
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Gemma Resource Report Resource Website 1000+ mentions |
Gemma (RRID:SCR_008007) | Gemma | data or information resource, database | Resource for reuse, sharing and meta-analysis of expression profiling data. Database and set of tools for meta analysis, reuse and sharing of genomics data. Targeted at analysis of gene expression profiles. Users can search, access and visualize coexpression and differential expression results. | chip, microarray, functional genomics, gene expression, coexpression, differential expression, FASEB list |
is used by: NIF Data Federation is used by: Integrated Data Annotation is listed by: Debian is listed by: SoftCite is related to: Gene Ontology is related to: Gene Expression Omnibus is related to: Phenocarta has parent organization: University of British Columbia; British Columbia; Canada is parent organization of: Neurocarta |
Canadian Foundation for Innovation ; Canadian Institutes for Health Research ; Michael Smith Foundation for Health Research ; NIGMS GM076990 |
PMID:22782548 | Free, Freely available | nif-0000-08127, r3d100012747 | https://sources.debian.org/src/gemma/, https://doi.org/10.17616/R36R54, https://doi.org/10.17616/R36R54 | SCR_008007 | SciCrunch Registry | 2026-11-07 12:02:59 | 1145 | |||||
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Ingenuity Pathways Knowledge Base Resource Report Resource Website 1000+ mentions |
Ingenuity Pathways Knowledge Base (RRID:SCR_008117) | data or information resource, database | A horizontally and vertically structured database that pulls scientific and medical information and describes it consistently using the Ingenuity Ontology. The Knowledge Base pulls information from journals, public molecular content databases, and textbooks. Data is curated and and integrated into the Knowledge Base . | gene, life science, molecule, protein, research, software, ontology, knowledge base, FASEB list |
is used by: Ingenuity Pathway Analysis is listed by: SoftCite has parent organization: QIAGEN |
Available to the research community, Commercial | nif-0000-20858 | SCR_008117 | SciCrunch Registry | Ingenuity Knowledge Base | 2026-11-07 12:02:45 | 4808 | ||||||||
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MutationTaster Resource Report Resource Website 1000+ mentions |
MutationTaster (RRID:SCR_010777) | MutationTaster | analysis service resource, data analysis service, production service resource, service resource | Evaluates disease-causing potential of sequence alterations. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
PMID:20676075 | Acknowledgement requested | biotools:mutation_taster, OMICS_00153 | https://bio.tools/mutation_taster | SCR_010777 | SciCrunch Registry | 2026-11-07 12:03:07 | 4781 | ||||||
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WU-BLAST Resource Report Resource Website 100+ mentions |
WU-BLAST (RRID:SCR_011824) | WU-BLAST | analysis service resource, data analysis service, production service resource, service resource | Tool to find regions of sequence similarity within selected protein databases quickly, with minimum loss of sensitivity. | protein, dna, rna |
is listed by: OMICtools is listed by: SoftCite has parent organization: European Bioinformatics Institute |
OMICS_01001 | SCR_011824 | SciCrunch Registry | 2026-11-07 12:02:39 | 135 | |||||||||
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miRanda Resource Report Resource Website 100+ mentions |
miRanda (RRID:SCR_017496) | data or information resource, database, service resource | Comprehensive resource of microRNA target predictions and expression profiles. Used for whole genome prediction of miRNA target genes. For each miRNA, target genes are selected on basis of sequence complementarity using position weighted local alignment algorithm, free energies of RNA-RNA duplexes, and conservation of target sites in related genomes. Provides information about set of genes potentially regulated by particular microRNA, co-occurrence of predicted target sites for multiple microRNAs in mRNA and microRNA expression profiles in tissues. Users are allowed to customize algorithm, numerical parameters, and position-specific rules., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | Whole, genome, prediction, miRNA, target, gene, expression, profile, data, FASEB list | is listed by: SoftCite | Alfred W. Bressler Scholars Endowment Fund ; Atlantic Philanthropies ; NIGMS |
PMID:18158296 | THIS RESOURCE IS NO LONGER IN SERVICE | http://www.microrna.org/microrna/home.do | SCR_017496 | SciCrunch Registry | MicroRNA.org. microrna.org | 2026-11-07 12:03:17 | 281 | ||||||
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PostgreSQL Resource Report Resource Website 100+ mentions |
PostgreSQL (RRID:SCR_021067) | data or information resource, database | Open source object relational database system that uses and extends SQL language combined with many features that safely store and scale the most complicated data workloads. PostgreSQL runs on all major operating systems. | Object relational database system, SQL language, data storage, data, database system |
uses: pgAdmin is listed by: SoftCite has parent organization: University of California at Berkeley; Berkeley; USA |
Free, Available for download, Freely available | SCR_021067 | SciCrunch Registry | Postgres | 2026-11-07 12:02:54 | 166 | |||||||||
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Scopus Resource Report Resource Website 500+ mentions |
Scopus (RRID:SCR_022559) | data or information resource, database | Abstract and indexing database with full text links that is produced by Elsevier Co. Combines expertly curated abstract and citation database with enriched data and linked scholarly literature across wide variety of disciplines. | Elsevier Co, abstract and citation database, data, scholarly literature, abstract and indexing database, full text links | is listed by: SoftCite | PMID:16522216 | SCR_022559 | SciCrunch Registry | 2026-11-07 12:03:20 | 788 | ||||||||||
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CLC Main Workbench Resource Report Resource Website 10+ mentions |
CLC Main Workbench (RRID:SCR_000354) | CLC Main Workbench | software resource, software toolkit | A suite of software for DNA, RNA and protein sequence data analysis. The software allows for the analysis and visualization of Sanger sequencing data as well as gene expression analysis, molecular cloning, primer design, phylogenetic analyses, and sequence data management. | sequencing, analysis, cloning, data, management, molecular, gene, genome, dna, rna |
is listed by: OMICtools is listed by: SoftCite |
Restricted | OMICS_01813 | SCR_000354 | SciCrunch Registry | 2026-11-07 12:02:58 | 31 | ||||||||
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BREAKDANCER Resource Report Resource Website 100+ mentions |
BREAKDANCER (RRID:SCR_001799) | BreakDancer | software application, software resource | A Perl/C++ software package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads. BreakDancerMax predicts five types of structural variants: insertions, deletions, inversions, inter- and intra-chromosomal translocations from next-generation short paired-end sequencing reads using read pairs that are mapped with unexpected separation distances or orientation. (entry from Genetic Analysis Software) | gene, genetic, genomic, perl, c++, next generation sequencing, structural variant, insertion, deletion, inversion, inter-chromosomal translocation, intra-chromosomal translocation, chromosomal translocation, indel, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA |
PMID:19668202 | Free, Available for download, Freely available | biotools:breakdancer, nlx_154253, OMICS_00307 | https://bio.tools/breakdancer | SCR_001799 | SciCrunch Registry | 2026-11-07 12:03:26 | 390 | ||||||
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MBF BioScience: Stereo Investigator Resource Report Resource Website 100+ mentions |
MBF BioScience: Stereo Investigator (RRID:SCR_002526) | instrument resource, software resource | Stereo Investigator system includes microscope, computer, and Stereo Investigator software. Software works with Brightfield, Multi-Channel Fluorescence, Confocal, and Structured Illumination Microscopes. System used to provide estimates of number, length, area, and volume of cells or biological structures in tissue specimen in areas of neuroscience including neurodegenerative diseases, neuropathy, memory, and behavior, pulmonary research, spinal cord research, and toxicology. | stereology, MBF Bioscience, number, length, area, volume cells, biological structures, tissue specimen |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: SoftCite |
Restricted | SciRes_000114, SCR_024705, SCR_018948 | http://www.nitrc.org/projects/si_stereology | SCR_002526 | SciCrunch Registry | Stereo Investigator system | 2026-11-07 12:03:04 | 162 | |||||||
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Alien hunter Resource Report Resource Website 1+ mentions |
Alien hunter (RRID:SCR_004575) | software application, software resource | Alien_hunter is an application for the prediction of putative Horizontal Gene Transfer (HGT) events with the implementation of Interpolated Variable Order Motifs (IVOMs). This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. An IVOM approach exploits compositional biases using variable order motif distributions and captures more reliably the local composition of a sequence compared to fixed-order methods. Optionally the predictions can be parsed into a 2-state 2nd order Hidden Markov Model (HMM), in a change-point detection framework, to optimize the localization of the boundaries of the predicted regions. The predictions (embl format) can be automatically loaded into the freely available Artemis genome viewer. |
is listed by: SoftCite has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:16837528 | nlx_56835 | SCR_004575 | SciCrunch Registry | Alien_hunter: Interpolated Variable Order Motifs for Identification of Horizontally Acquired DNA | 2026-11-07 12:03:33 | 3 |
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