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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Ocular Resource Report Resource Website 1+ mentions |
Ocular (RRID:SCR_024490) | data acquisition software, data processing software, software application, software resource | Scientific image acquisition software. Software allows color and monochrome cameras to capture high quality images and videos from their microscope or lens system. | Teledyne Photometrics, image acquisition, capture high quality images and video, | is listed by: SoftCite | Restricted | SCR_024490 | Teledyne Photometrics Ocular | 2026-09-19 12:55:44 | 4 | |||||||||
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Umediation Resource Report Resource Website 1+ mentions |
Umediation (RRID:SCR_024492) | data analysis software, data processing software, software application, software resource | Software R package that examines the role of unmeasured confounding in mediation analysis allowing for normally distributed or Bernoulli distributed exposures, outcomes, mediators, measured confounders, and unmeasured confounders. Umediation also accommodates multiple measured confounders, multiple unmeasured confounders, and allows for mediator exposure interaction on the outcome. Enables to simulate unmeasured confounding in mediation analysis in order to see how the results of the mediation analysis would change in the presence of unmeasured confounding. | simulate unmeasured confounding in mediation analysis, mediation analysis, unmeasured confounding, | is listed by: SoftCite | PMID:28724417 | Free, Available for download, Freely available | SCR_024492 | 2026-09-19 12:55:44 | 1 | |||||||||
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IntFOLD Resource Report Resource Website 1+ mentions |
IntFOLD (RRID:SCR_024523) | data access protocol, software resource, web service | Web integrated protein structure and function prediction server. Integrated server for modelling protein structures and functions from amino acid sequences. | protein structure prediction, protein function prediction, modelling protein structures and functions from amino acid sequences, | is listed by: SoftCite | PMID:25820431 | Free, Freely available | SCR_024523 | 2026-09-19 12:55:45 | 8 | |||||||||
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OMNISEC Resource Report Resource Website 10+ mentions |
OMNISEC (RRID:SCR_024485) | data analysis software, data processing software, software application, software resource | Software for OMNISEC instrument control, data acquisition, analysis and reporting. Used for advanced analysis of proteins and polymers by GPC/SEC, and is specifically designed for control of OMNISEC RESOLVE and OMNISEC REVEAL. | OMNISEC instrument control, data acquisition, analysis and reporting, proteins and polymers analysis, | is listed by: SoftCite | Restricted | SCR_024485 | 2026-09-19 12:55:44 | 39 | ||||||||||
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PHYLDOG Resource Report Resource Website 1+ mentions |
PHYLDOG (RRID:SCR_024487) | data analysis software, data processing software, software application, software resource | Software tool to simultaneously build gene and species trees when gene families have undergone duplications and losses. Can analyze thousands of gene families in dozens of genomes simultaneously. | probabilistic model, reconstruct species tree and all corresponding gene trees, build gene and species trees, gene families analysis, genomes analysis simultaneously, gene families duplications and losses, | is listed by: SoftCite | PMID:23132911 | Free, Freely available | SCR_024487 | 2026-09-19 12:55:44 | 1 | |||||||||
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ASTRAL-Pro Resource Report Resource Website 1+ mentions |
ASTRAL-Pro (RRID:SCR_024520) | simulation software, software application, software resource | Software tool for species tree reconstruction from multi-copy gene family trees.Used for estimating unrooted species tree given set of unrooted gene trees and is statistically consistent under the multi-species coalescent model. ASTRAL-pro extends ASTRAL to allow multi-copy genes. ASTRAL-Pro 2, ultrafast and memory efficient version of ASTRAL-Pro that adopts placement based optimization algorithm for significantly better scalability without sacrificing accuracy. | species tree reconstruction, reconstruction from multi-copy gene family trees | is listed by: SoftCite | PMID:32886770 | Free, Available for download, Freely available | SCR_024520 | ASTRAL for PaRalogs and Orthologs, ASTRAL-Pro 2 | 2026-09-19 12:55:45 | 3 | ||||||||
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Kaplan Meier Plotter Resource Report Resource Website 1+ mentions |
Kaplan Meier Plotter (RRID:SCR_024521) | data access protocol, software resource, web service | Web based survival analysis tool tailored for medical research. Used to assess correlation between expression of all genes (mRNA, miRNA, protein) and survival in samples from tumor types including breast, ovarian, lung, gastric, colon cancer, AML, and myeloma. | survival analysis, assess correlation between expression of genes and survival, tumor samples, | is listed by: SoftCite | PMID:34309564 | Free, Freely available | http://kmplot.com/analysis/index.php?p=service&cancer=custom_plot | SCR_024521 | Kaplan-Meier Plotter, KM Plotter | 2026-09-19 12:55:45 | 6 | |||||||
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ProgRes Capture Pro Resource Report Resource Website 10+ mentions |
ProgRes Capture Pro (RRID:SCR_024489) | data acquisition software, data processing software, software application, software resource | Software tool for image acquisition.Supports ProgRes microscope cameras and delivers optimal image quality and reproducible results.Included with all of Jenoptik ProgRes microscope cameras. | image acquisition, Jenoptik ProgRes microscope cameras, Jenoptik, | is listed by: SoftCite | PMID:34520656 | Free, Available for download, Freely available | SCR_024489 | Jenoptic ProgRes Capture Pro | 2026-09-19 12:55:44 | 12 | ||||||||
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MADOKA Resource Report Resource Website 1+ mentions |
MADOKA (RRID:SCR_024522) | data access protocol, software resource, web service | Web server as ultra fast approach for large scale protein structure similarity searching.The upload protein structure file should be in PDB format. Used for searching similar protein structures by aligning input structure with the whole PDB library. | large scale protein structure similarity searching, searching similar protein structures, aligning input structure with whole PDB library, | is listed by: SoftCite | PMID:31870277 | Free, Freely available | SCR_024522 | 2026-09-19 12:55:45 | 1 | |||||||||
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SPAdes Resource Report Resource Website 100+ mentions |
SPAdes (RRID:SCR_000131) | SPAdes | software resource, software toolkit | Software package for assembling single cell genomes and mini metagenomes. Uses short read sets as input. Used for genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. Works with Illumina or IonTorrent reads and can provide hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Intended for small genomes like bacterial or fungal., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | assembler, single, cell, small, genome, short, read, data |
is used by: shovill is listed by: OMICtools is listed by: Debian is listed by: SoftCite is related to: rnaSPAdes is related to: rnaQUAST has parent organization: Saint Petersburg Academic University; Saint Petersburg; Russia works with: Illumina: iSeq 100 Sequencing System |
Government of the Russian Federation ; NCRR P41 RR024851 |
PMID:24093227 PMID:22506599 DOI:10.1089/cmb.2012.0021 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01502 | https://sources.debian.org/src/spades/ | http://bioinf.spbau.ru/spades/ | SCR_000131 | SPAdes Genome Assembler | 2026-09-19 12:55:48 | 108 | |||
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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 | piRNABank | 2026-09-19 12:57:11 | 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 | 2026-09-19 12:57:14 | 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 | Ingenuity Knowledge Base | 2026-09-19 12:57:14 | 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 | 2026-09-19 12:57:25 | 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 | 2026-09-19 12:57:25 | 135 | |||||||||
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SyStat Resource Report Resource Website 1000+ mentions |
SyStat (RRID:SCR_010455) | SyStat | commercial organization, software resource | A commercial software tool for statistical analysis. | statistics | is listed by: SoftCite | nlx_157643 | SCR_010455 | 2026-09-19 12:58:55 | 1102 | |||||||||
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GeneSpring GX Resource Report Resource Website 1000+ mentions |
GeneSpring GX (RRID:SCR_010972) | GeneSpring GX | commercial organization, software resource | Powerful, accessible statistical tools for fast visualization and analysis of microarrays - expression arrays, miRNA, exon arrays and genomics copy number data. |
is listed by: OMICtools is listed by: SoftCite |
Commercial license | OMICS_00853 | SCR_010972 | 2026-09-19 12:58:56 | 1817 | |||||||||
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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 | 2026-09-19 12:59:03 | 1134 | ||||||||
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MetaPSICOV Resource Report Resource Website 1+ mentions |
MetaPSICOV (RRID:SCR_024517) | software resource, source code | Software tool for accurate prediction of contacts and long range hydrogen bonding in proteins. | accurate prediction, contacts and long range hydrogen bonding in proteins prediction, | is listed by: SoftCite | PMID:25431331 | Free, Available for download, Freely available | SCR_024517 | 2026-09-19 01:00:02 | 2 | |||||||||
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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 | Stereo Investigator system | 2026-09-19 12:57:45 | 162 |
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