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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Primer Express Resource Report Resource Website 1000+ mentions |
Primer Express (RRID:SCR_014326) | software resource, software application, standalone software | Software that allows users to manually or automatically design custom primers and probes for gene quantitation and allelic discrimination (SNP) real-time PCR applications. It supports assays based on TaqMan and SYBR Green I dye chemistries. | primer, probe, design, gene quantitation, allelic discrimination, real time pcr | is listed by: SoftCite | Pay for product, Specifically made for ThermoFisher Scientific RT-PCR systems | SCR_014326 | 2026-08-03 09:35:36 | 4773 | ||||||||||
|
HKL-2000 Resource Report Resource Website 100+ mentions |
HKL-2000 (RRID:SCR_015547) | 3-d visualization software, software resource, software application, data processing software | Software package for structural determination and other functions in the field of structural biology. Its programs can perform strategy and simulation, 3-D processing, mosaicity refinement during processing, variable spot size, easy change of the space group, report generation, and other functions. | structural biology, structure determination process, simulation, 3d processing, mosaicity, strategy, | is listed by: SoftCite | PMID:27754618 | Commercially available, License required, Runs on Linux, Runs on Mac OS | www.hkl-xray.com | SCR_015547 | 2026-08-03 09:36:00 | 205 | ||||||||
|
SigmaPlot Resource Report Resource Website 10000+ mentions |
SigmaPlot (RRID:SCR_003210) | SigmaPlot | software resource, commercial organization | Statistical analysis and scientific graphing software for Windows OS. | statistics, windows, graph, data analysis | is listed by: SoftCite | Commercial license | SciRes_000184 | SCR_003210 | sigma plot | 2026-08-03 09:32:01 | 17371 | |||||||
|
Strelka2 Resource Report Resource Website 100+ mentions |
Strelka2 (RRID:SCR_005109) | software resource, source code | Software for somatic single nucleotide variant (SNV) and small indel detection from sequencing data of matched tumor-normal samples. Strelka2 germline and somatic small variant caller. | single nucleotide variant, indel, somatic snv, next-generation sequencing, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: Illumina |
Cancer, Tumor, Normal | PMID:22581179 PMID:30013048 |
Free, Available for download, Freely available | biotools:strelka | https://bio.tools/strelka, https://sources.debian.org/src/strelka/ | http://bioinformatics.oxfordjournals.org/content/early/2012/05/10/bioinformatics.bts271.full.pdf | SCR_005109 | Strelka | 2026-08-03 09:32:47 | 261 | ||||
|
University of Texas at Austin; Texas; USA Resource Report Resource Website 1+ mentions |
University of Texas at Austin; Texas; USA (RRID:SCR_005900) | UT Austin | university, institution | A major university |
is related to: LungMap is related to: RobotReviewer has parent organization: University of Texas System; Texas; USA is parent organization of: Academic Seismic Portal at UTIG is parent organization of: FUGOID: a Database for Functional Genomics of Organelle Introns is parent organization of: Aptamer Database - The Ellington Lab is parent organization of: Poldracklab Portal is parent organization of: Synapse Web Reconstruct is parent organization of: Cognitive Atlas is parent organization of: Synapse Web is parent organization of: DigiMorph is parent organization of: Amino Acid-Nucleotide Interaction Database is parent organization of: VolumeRover is parent organization of: Phenologs is parent organization of: NeuroSynth is parent organization of: Open Proteomics Database is parent organization of: University of Texas at Austin College of Pharmacy is parent organization of: University of Texas at Austin Labs and Facilities is parent organization of: Texas Advanced Computing Center is parent organization of: Aging Status and Sense of Control (ASOC) is parent organization of: HumanNet is parent organization of: Culture Collection of Algae at the University of Texas is parent organization of: CiteAs is parent organization of: University of Texas at Austin Genomic Sequencing and Analysis Core Facility is parent organization of: University of Texas at Austin Biological Mass Spectrometry Proteomics Core Facility is parent organization of: University of Texas at Austin Microscopy and Flow Cytometry Core Facility is parent organization of: University of Texas at Austin Biomedical Imaging Center Core Facility is parent organization of: University of Texas at Austin Mouse Genetic Engineering Core Facility is parent organization of: University of Texas at Austin Biomedical Research Computing Core Facility is parent organization of: University of Texas at Austin Computational Biology and Bioinformatics Core Facility is parent organization of: University of Texas at Austin Cryo Electron Microscopy Core Facility is parent organization of: University of Texas at Austin Advanced Protein Therapeutics Core Facility is parent organization of: SoftCite is parent organization of: University of Texas at Austin Shared Instrumentation Facility |
grid.89336.37 | https://ror.org/00hj54h04 | SCR_005900 | University of Texas at Austin | 2026-08-03 09:32:57 | 5 | ||||||||
|
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 | 2026-08-03 09:38:18 | 2 | |||||||||
|
PicTar Resource Report Resource Website 1000+ mentions |
PicTar (RRID:SCR_003343) | PicTar | software resource | An algorithm for the identification of microRNA targets. Details are provided (3' UTR alignments with predicted sites, links to various public databases etc) regarding: # microRNA target predictions in vertebrates (Krek et al, Nature Genetics 37:495-500 (2005)) # microRNA target predictions in seven Drosophila species (Grn et al, PLoS Comp. Biol. 1:e13 (2005)) # microRNA targets in three nematode species (Lall et al, Current Biology 16, 1-12 (2006)) # human microRNA targets that are not conserved but co-expressed (i.e. the microRNA and mRNA are expressed in the same tissue) (Chen and Rajewsky, Nat Genet 38, 1452-1456 (2006)) co-expressed targets | microrna target, microrna, bio.tools, FASEB list |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: UCSC Genome Browser has parent organization: Max Delbruck Center for Molecular Medicine; Berlin; Germany |
PMID:15806104 | Free, Available for download, Freely available | OMICS_00411, biotools:pictar, nif-0000-31983 | http://pictar.mdc-berlin.de/, https://bio.tools/pictar | SCR_003343 | 2026-08-01 12:02:20 | 1636 | ||||||
|
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 | 2026-08-01 12:03:49 | 6581 | ||||||
|
CEAS Resource Report Resource Website 100+ mentions |
CEAS (RRID:SCR_010946) | CEAS | software resource | Integrates many useful tools to simplify ChIP-chip analysis for biologists., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. |
is listed by: OMICtools is listed by: SoftCite |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00802 | SCR_010946 | 2026-08-01 12:04:18 | 397 | |||||||||
|
Chimera Resource Report Resource Website 100+ mentions |
Chimera (RRID:SCR_002959) | software resource | A Bioconductor package that organizes, annotates, analyses and validates fusions reported by different fusion detection tools. The current implementation can deal with output from bellerophontes, chimeraScan, deFuse, fusionCatcher, FusionFinder, FusionHunter, FusionMap, mapSplice, Rsubread, tophat-fusion, tophat-fusion-post and STAR. The core of Chimera is a fusion data structure that can store fusion events detected with any of the aforementioned tools. | software package, unix/linux, mac os x, windows, r, infrastructure |
is listed by: OMICtools is listed by: SoftCite has parent organization: Bioconductor |
PMID:25286921 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_06335 | SCR_002959 | chimera - A package for secondary analysis of fusion products | 2026-08-01 12:01:59 | 377 | |||||||
|
arrayQualityMetrics Resource Report Resource Website 100+ mentions |
arrayQualityMetrics (RRID:SCR_001335) | arrayQualityMetrics | software resource | Software package that generates microarray quality metrics reports for data in Bioconductor microarray data containers (ExpressionSet, NChannelSet, AffyBatch). Reports contain both general and platform-specific sections. Both one and two color array platforms are supported. | microarray, quality control, report writing |
is listed by: OMICtools is listed by: SoftCite has parent organization: Bioconductor |
PMID:19106121 | Free, Available for download, Freely available | OMICS_02005 | SCR_001335 | Quality metrics on microarray data sets | 2026-08-01 12:01:48 | 180 | ||||||
|
MuTect Resource Report Resource Website 50+ mentions |
MuTect (RRID:SCR_000559) | MuTect | software resource | Software for the reliable and accurate identification of somatic point mutations in next generation sequencing data of cancer genomes. | next-generation sequencing, somatic mutation, tumor, normal, genome, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: Broad Institute |
Cancer | PMID:23396013 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:mutect, OMICS_00087 | https://bio.tools/mutect | SCR_000559 | Mutect | 2026-08-01 12:01:25 | 91 | ||||
|
PeptideProphet Resource Report Resource Website 1+ mentions |
PeptideProphet (RRID:SCR_000274) | software resource | Software that automatically validates peptide assignments to MS/MS spectra made by database search programs such as SEQUEST. | standalone software, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: SourceForge |
PMID:12403597 | Free, Available for download, Freely available | OMICS_02520, biotools:peptideprophet | https://bio.tools/peptideprophet | SCR_000274 | 2026-08-01 12:01:10 | 4 | |||||||
|
ART Resource Report Resource Website 1+ mentions |
ART (RRID:SCR_006538) | ART | software resource | A set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles. ART supports simulation of single-end, paired-end/mate-pair reads of three major commercial next-generation sequencing platforms: Illumina''''s Solexa, Roche''''s 454 and Applied Biosystems'''' SOLiD. ART can be used to test or benchmark a variety of method or tools for next-generation sequencing data analysis, including read alignment, de novo assembly, SNP and structure variation discovery. ART is implemented in C++ with optimized algorithms and is highly efficient in read simulation. ART outputs reads in the FASTQ format, and alignments in the ALN format. ART can also generate alignments in the SAM alignment or UCSC BED file format. | next-generation sequencing |
is listed by: OMICtools is listed by: Debian is listed by: SoftCite is related to: 1000 Genomes: A Deep Catalog of Human Genetic Variation has parent organization: National Institute of Environmental Health Sciences |
PMID:22199392 DOI:10.1093/bioinformatics/btr708 |
Free, Public | OMICS_00247 | https://sources.debian.org/src/augustus/ | SCR_006538 | ART - Set of Simulation Tools | 2026-08-01 12:03:14 | 9 | |||||
|
MOE Resource Report Resource Website 10+ mentions |
MOE (RRID:SCR_014882) | software resource | Drug discovery software package which can be used in structure-based design, fragment-based design, pharmacophore discovery, medicinal chemistry, protein and antibody modelling, and molecular modeling and simulations. Each aspect of the software package has its own unique features: for example, features for structure-based design include active site detection, scaffold replacement, multi fragment search, and solvent analysis. | drug discovery, software package, structure based design, fragment based design, pharmacophore, medicinal chemistry, protein modeling, antibody modeling, molecular modeling, molecular simulations | is listed by: SoftCite | SCR_014882 | 2026-08-01 12:05:09 | 23 | |||||||||||
|
CGView Resource Report Resource Website 100+ mentions |
CGView (RRID:SCR_011779) | CGView | software resource | A Java package for generating high quality, zoomable maps of circular genomes. Its primary purpose is to serve as a component of sequence annotation pipelines, as a means of generating visual output suitable for the web., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: University of Alberta; Alberta; Canada |
DOI:10.1093/bioinformatics/bti054 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00905, biotools:cgview | https://bio.tools/cgview, https://sources.debian.org/src/cgview/ | SCR_011779 | Circular Genome Viewer | 2026-08-01 12:04:17 | 304 | |||||
|
Infernal Resource Report Resource Website 500+ mentions |
Infernal (RRID:SCR_011809) | Infernal | software resource | Software for searching DNA sequence databases for RNA structure and sequence similarities. | FASEB list |
is listed by: OMICtools is listed by: Debian is listed by: SoftCite is related to: ANNOgesic has parent organization: Janelia Research |
PMID:24008419 DOI:10.1093/bioinformatics/btp157 |
GNU General Public License, v3 | OMICS_00977 | https://sources.debian.org/src/infernal/ | SCR_011809 | Infernal: inference of RNA alignments, INFERence of RNA Alignment | 2026-08-01 12:04:19 | 687 | |||||
|
AutoDock Vina Resource Report Resource Website 1000+ mentions |
AutoDock Vina (RRID:SCR_011958) | AutoDock Vina | software resource | An open-source program for doing molecular docking. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: Scripps Research Institute |
PMID:34278794 PMID:19499576 DOI:10.1002/jcc.21334 |
Open unspecified license | biotools:autodock_vina, OMICS_01595, OMICS_03790 | https://bio.tools/autodock_vina, https://sources.debian.org/src/avogadro/ | SCR_011958 | 2026-08-01 12:04:32 | 1885 | ||||||
|
MrBayes Resource Report Resource Website 10000+ mentions |
MrBayes (RRID:SCR_012067) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE.Documented on February 28,2023. Software program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. | applet, mac os x, unix/linux, windows |
is listed by: OMICtools is listed by: SoftCite has parent organization: SourceForge |
PMID:22357727 DOI:10.1093/sysbio/sys029 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_04237 | https://sources.debian.org/src/mrbayes/ | SCR_012067 | 2026-08-01 12:04:33 | 10711 | |||||||
|
lumi Resource Report Resource Website 100+ mentions |
lumi (RRID:SCR_012781) | lumi | software resource | Software that provides an integrated solution for the Illumina microarray data analysis. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: Bioconductor |
biotools:lumi, OMICS_00770 | https://bio.tools/lumi | SCR_012781 | 2026-08-01 12:04:51 | 318 |
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