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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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GeneMapper Resource Report Resource Website 5000+ mentions |
GeneMapper (RRID:SCR_014290) | sequence analysis software, software application, data processing software, data analysis software, software resource | Genotyping software package that provides DNA sizing and quality allele calls for all Applied Biosystems electrophoresis-based genotyping systems. GeneMapper specializes in multiapplication functionality, including amplified fragment length polymorphism, loss of heterozygosity, microsatellite, and SNP genotyping analysis. The software provides remote auto-analysis and command line operation, and allows for multiuser, client-server deployment. | genotyping software, sequence analysis software, multiplication functionality, dna sizing, allele call, electrophoresis genotyping system | is listed by: SoftCite | Restricted | https://www.thermofisher.com/order/catalog/product/de/en/4370784, https://www.thermofisher.com/document-connect/document-connect.html?url=https://assets.thermofisher.com/TFS-Assets%2FLSG%2Fmanuals%2F4476603A.pdf, | https://products.appliedbiosystems.com/ab/en/US/adirect/ab?cmd=catNavigate2&catID=600798&tab=DetailInfo | SCR_014290 | , GeneMapper Software 5, GeneMapper Software 6, GeneMapper Software | 2026-08-03 09:35:35 | 5231 | |||||||
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NONMEM Resource Report Resource Website 10+ mentions |
NONMEM (RRID:SCR_016986) | Nonmem | software application, data processing software, data analysis software, simulation software, software resource | Software tool for nonlinear mixed effects modelling. Used for population pharmacokinetic and pharmacodynamic analysis and to simulate data and to fit data. Used in the development of new drugs. NONMEM versions up through 6 are the property of the Regents of the University of California, San Francisco, but ICON Development Solutions has exclusive rights to license their use. NONMEM 7 up to the current version is the property of ICON Development Solutions. | nonlinear, mixed, effect, modeling, pharmacokinetic, pharmacodynamic, analysis, data | is listed by: SoftCite | Commercially available | SCR_016986 | NONMEM 7.4, NONMEM 7, Nonlinear mixed effects modelling software, NONMEM 7.2, NONlinear Mixed Effects Modeling software, population analysis | 2026-08-03 09:36:29 | 42 | ||||||||
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Rhinoceros Resource Report Resource Website 100+ mentions |
Rhinoceros (RRID:SCR_014339) | simulation software, software resource, software application, standalone software | 3D modeling software used to create, edit, analyze, document, render, animate, and translate surfaces, solids, point clouds, and polygon meshes. It can also be used to analyze and manufacture a variety of products. | 3d, modeling software, standalone software | is listed by: SoftCite | Pay for product | SCR_014339 | Rhino | 2026-08-03 09:35:41 | 288 | |||||||||
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SignalP Resource Report Resource Website 5000+ mentions |
SignalP (RRID:SCR_015644) | software resource, web application | Web application for prediction of the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms. The method incorporates a prediction of cleavage sites and a signal peptide/non-signal peptide prediction based on a combination of several artificial neural networks. | prediction, signal peptide, cleavage site, amino acid, sequence, artificial neural network |
is listed by: SoftCite has parent organization: DTU Center for Biological Sequence Analysis |
PMID:28451972 | Freely available, Acknowledgment requested, Free, Available for download, Runs on Windows, Runs on Mac OS | SCR_015644 | 2026-08-03 09:36:12 | 9406 | |||||||||
|
MRIcron Resource Report Resource Website 1000+ mentions |
MRIcron (RRID:SCR_002403) | MRIcron | software resource, data visualization software, software application, data processing software | Software tool as a cross-platform NIfTI format image viewer. Used for viewing and exporting of brain images. MRIcroGL is a variant of MRIcron. | NIfTI, format, image, viewer, exporting, brain, image, processing, data, bio.tools |
is used by: XFSL: An FSL toolbox is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps is listed by: neurodebian is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: Colour maps for brain imaging has parent organization: University of South Carolina; South Carolina; USA |
PMID:17583985 PMID:11568431 |
BSD License | biotools:MRIcron, nif-0000-00122 | https://sources.debian.org/src/mricron/, http://www.mccauslandcenter.sc.edu/mricro/, http://www.nitrc.org/projects/mricron, http://neuro.debian.net/pkgs/mricron.html, https://bio.tools/MRIcron | SCR_002403 | mricron - magnetic resonance image conversion viewing and analysis | 2026-08-03 09:31:56 | 2194 | |||||
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QuantPrime Resource Report Resource Website 100+ mentions |
QuantPrime (RRID:SCR_015498) | software resource, web application | Fully automated tool for primer pair design in small- to large-scale real-time reverse transcription qPCR analyses. It offers design and specificity checking with highly customizable parameters and is available for use with publicly available eukaryotic transcriptomes. | primer design, primer pair design, rt-qpcr, reverse transcription qpcr | is listed by: SoftCite | DOI:10.1186/1471-2105-9-465 | Acknowledgement requested, Available as a web application, Available as a desktop application | SCR_015498 | 2026-08-03 09:35:59 | 155 | |||||||||
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ModFit LT Resource Report Resource Website 100+ mentions |
ModFit LT (RRID:SCR_016106) | software resource, data visualization software, software application, data processing software | Modeling software for flow cytometry histograms. Models for cell-tracking dye studies and synchronized cell lines are built right into the software. | flow, cytometry, histogram, model, graph, cell, tracking, dye, cell line | is listed by: SoftCite | Commercially available, Available for purchase, Trial available | SCR_016106 | Verity Software House ModFit LT | 2026-08-03 09:36:17 | 143 | |||||||||
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ScanProsite Resource Report Resource Website 10+ mentions |
ScanProsite (RRID:SCR_024425) | PMID:16845026 | web service, data access protocol, software resource | Web tool for detecting PROSITE signature matches in protein sequences. | detecting PROSITE signature matches, protein sequences, | is listed by: SoftCite | Swiss National Science Foundation ; Swiss Federal Government |
Free, Freely available | https://www.expasy.org/resources/scanprosite | SCR_024425 | 2026-08-03 09:38:17 | 44 | |||||||
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VSEARCH Resource Report Resource Website 1000+ mentions |
VSEARCH (RRID:SCR_024494) | software resource, data processing software, software application, data analysis software | Software versatile open source tool for metagenomics. Used for processing and preparing metagenomics, genomics and population genomics nucleotide sequence data. | processing and preparing metagenomics, genomics and population genomics, nucleotide sequence data, | is listed by: SoftCite | PMID:27781170 | Free, Available for download, Freely available | SCR_024494 | 2026-08-03 09:38:18 | 1348 | |||||||||
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TomoStudio Resource Report Resource Website 1+ mentions |
TomoStudio (RRID:SCR_024498) | software resource, data processing software, software application, data analysis software | Software tool for acquisition and analysis, visualization and analysis of RI tomograms. Used to color code the image according to the refractive index and identify various types of quantitative data. | Tomocube, Inc., Daejeon, . Republic of Korea, visualization and analysis of RI tomograms, color code the image, | is listed by: SoftCite | Restricted | SCR_024498 | 2026-08-03 09:38:18 | 3 | ||||||||||
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Ocular Resource Report Resource Website 1+ mentions |
Ocular (RRID:SCR_024490) | data acquisition software, software resource, software application, data processing software | 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 | 2026-08-03 09:38:18 | 3 | |||||||||
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Umediation Resource Report Resource Website 1+ mentions |
Umediation (RRID:SCR_024492) | software resource, data processing software, software application, data analysis software | 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 | 2026-08-03 09:38:43 | 1 | |||||||||
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IntFOLD Resource Report Resource Website 1+ mentions |
IntFOLD (RRID:SCR_024523) | web service, data access protocol, software resource | 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 | 2026-08-03 09:38:18 | 3 | |||||||||
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PyWavelets Resource Report Resource Website 10+ mentions |
PyWavelets (RRID:SCR_024421) | software resource, data processing software, software application, data analysis software | Software Python package for wavelet analysis. | Python, wavelet analysis, | is listed by: SoftCite | Free, Available for download, Freely available | SCR_024421 | 2026-08-03 09:38:40 | 13 | ||||||||||
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ProteinPilot Resource Report Resource Website 100+ mentions |
ProteinPilot (RRID:SCR_024414) | software resource, data processing software, software application, data analysis software | Software tool for protein identification and protein expression analysis. Used to identify proteins and search large numbers of post translational modifications, without increasing search time or false positives. Compatible with all proteomics MS/MS systems. | protein identification, protein expression analysis, post translational modification search, | is listed by: SoftCite | Restricted | https://sciex.com/content/dam/SCIEX/pdf/posters/ProteinPilot-Software-Overview.pdf | SCR_024414 | 2026-08-03 09:38:16 | 228 | |||||||||
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OMNISEC Resource Report Resource Website 10+ mentions |
OMNISEC (RRID:SCR_024485) | software resource, data processing software, software application, data analysis software | 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 | 2026-08-03 09:38:42 | 38 | ||||||||||
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PHYLDOG Resource Report Resource Website 1+ mentions |
PHYLDOG (RRID:SCR_024487) | software resource, data processing software, software application, data analysis software | 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 | 2026-08-03 09:38:18 | 1 | |||||||||
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Kaplan Meier Plotter Resource Report Resource Website 1+ mentions |
Kaplan Meier Plotter (RRID:SCR_024521) | web service, data access protocol, software resource | 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 | 2026-08-03 09:38:43 | 4 | |||||||
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ProgRes Capture Pro Resource Report Resource Website 10+ mentions |
ProgRes Capture Pro (RRID:SCR_024489) | data acquisition software, software resource, software application, data processing software | 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 | 2026-08-03 09:38:42 | 12 | ||||||||
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MADOKA Resource Report Resource Website 1+ mentions |
MADOKA (RRID:SCR_024522) | web service, data access protocol, software resource | 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 | 2026-08-03 09:38:18 | 1 |
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