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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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CRISPResso2 Resource Report Resource Website 10+ mentions |
CRISPResso2 (RRID:SCR_024503) | software application, data processing software, data analysis software, software resource | Software pipeline designed to enable rapid and intuitive interpretation of genome editing experiments. Used for analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments. | sequencing data analysis, genome editing experiments interpretation, | is listed by: SoftCite | Free, Available for download, Freely available | SCR_024503 | 2026-02-15 09:23:33 | 44 | ||||||||||
|
OpenBUGS Resource Report Resource Website 100+ mentions |
OpenBUGS (RRID:SCR_024488) | software application, data processing software, data analysis software, software resource | Software for analysing complex statistical models using Markov chain Monte Carlo methods. | analysing complex statistical models, Markov chain Monte Carlo method, | is listed by: SoftCite | Free, Available for download, Freely available | SCR_024488 | Open Bayesian inference Using Gibbs Sampling | 2026-02-15 09:23:30 | 154 | |||||||||
|
AutoRT Resource Report Resource Website 1+ mentions |
AutoRT (RRID:SCR_024513) | software application, simulation software, software resource | Software tool for peptide retention time prediction using deep learning. Supports peptide retention prediction for tryptic peptides, MHC bound peptides and PTM peptides. | proteogenomics analysis | is listed by: SoftCite | PMID:32273506 | Free, Available for download, Freely available | SCR_024513 | 2026-02-15 09:23:45 | 2 | |||||||||
|
ModFOLD Resource Report Resource Website 1+ mentions |
ModFOLD (RRID:SCR_024518) | web service, data access protocol, software resource | Web server for the global and local quality estimation of 3D protein models | quality estimation, 3D protein models, | is listed by: SoftCite | PMID:28460136 | Restricted | SCR_024518 | ModFOLD6, ModFOLD8 | 2026-02-15 09:22:44 | 2 | ||||||||
|
MINC Resource Report Resource Website 100+ mentions |
MINC (RRID:SCR_002391) | MINC | software application, image analysis software, data processing software, software resource | A medical imaging data format and an associated set of tools and libraries including a 3 level API for medical image analysis with a particular focus on the needs of research. There are also a number of tools including Registration and Non-Uniformity correction. | reusable library, c, file format, fortran, information specification, minc, minc2, magnetic resonance, os independent, perl, sh/bash, unix shell |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: SoftCite is related to: MINC Example files is related to: Extensible MATLAB Medical image Analysis has parent organization: McConnell Brain Imaging Center |
Free, Available for download, Freely available | nlx_155794 | http://www.nitrc.org/projects/minc | SCR_002391 | MINC - Medical Image NetCDF, Medical Imaging NetCDF | 2026-02-15 09:18:17 | 122 | ||||||
|
Metscape Resource Report Resource Website 100+ mentions |
Metscape (RRID:SCR_014687) | source code, software resource, resource | A software program that allows users to visualize and interpret human metabolim and expression profiling data by providing users with a bioinformatics framework. Its features include bulding and analyzing networks of genes and compounds, identifying enriched pathways from expression profiling data, and visualizing changes in metabolite data. | metabolomics, metabolomics tool, visualization, expression profiling, gene, compound, metabolism, human |
is listed by: Metabolomics Workbench is listed by: SoftCite |
NIDDK U24 DK097153; NIDDK P30DK089503 |
PMID:22135418 | Freely available | SCR_014687 | 2026-02-15 09:21:08 | 145 | ||||||||
|
GENIE Resource Report Resource Website 100+ mentions |
GENIE (RRID:SCR_009197) | GENIE | software application, software resource | Software application that performs tests of association and transmission disequilibrium (TDT) between genetic markers and traits in studies of arbitrarily-sized families and/or independent individuals using Monte Carlo testing. For dichotomous traits, basic genotype-based or allele-based Chi-square statistics, OR, and a Chi-square trend statistic with user-defined weights, TDT, sib-TDT, combined-TDT are included. For quantitative outcomes, a difference in means test, ANOVA and QTDT are offered. Flexible haplotype testing and meta analysis across multiple centers are available. An automated haplotype building module, hapConstructor, is also offered that data mines multi-locus data for association signals. The Monte Carlo empirical significance assessment accounts for all relatedness between individuals for all tests. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, genetic, genomic, java 1.6, web-based |
is listed by: Genetic Analysis Software is listed by: SoftCite |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154344 | http://bioinformatics.med.utah.edu/Genie/index.html | SCR_009197 | PEDGENIE, HAPMC | 2026-02-15 09:19:58 | 361 | ||||||
|
PROFILER Resource Report Resource Website 1000+ mentions |
PROFILER (RRID:SCR_009339) | PROFILER | software application, software resource | A flexible software tool to generate the probability distribution of joint multilocus genotypes defined by sets of individuals within the pedigree and sets of markers within the framework map. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, genetic, genomic, linux, unix, solaris |
is listed by: Genetic Analysis Software is listed by: SoftCite |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154552 | SCR_009339 | 2026-02-15 09:19:42 | 1294 | ||||||||
|
Adobe Illustrator Resource Report Resource Website 10000+ mentions |
Adobe Illustrator (RRID:SCR_010279) | Illustrator CC | software application, software toolkit, software resource | Vector graphics software to create digital graphics, illustrations, and typography for several types of media: print, web, interactive, video, and mobile. | vector graphics, graphics, illustration, typography, adobe, software |
uses: National Gene Vector Laboratories is listed by: SoftCite is related to: Adobe Illustrator |
SCR_014198, nlx_157287 | http://www.adobe.com/products/cs6.html | SCR_010279 | Illustrator CC, Adobe Illustrator CS5, Adobe Illustrator CS6 | 2026-02-15 09:19:58 | 12706 | |||||||
|
TASSEL Resource Report Resource Website 1000+ mentions |
TASSEL (RRID:SCR_012837) | TASSEL | software application, software resource | Software package which performs a variety of genetic analyses including association mapping, diversity estimation and calculating linkage disequilibrium. The association analysis between genotypes and phenotypes can be performed by either a general linear model or a mixed linear model. The general linear model now allows users to analyze complex field designs, environmental interactions, and epistatic interactions. The mixed model is specially designed to handle polygenic effects at multiple levels of relatedness including pedigree information. These new analyses should permit association analysis in a wide range plant and animal species. (entry from Genetic Analysis Software) | gene, genetic, genomic, java, web-based, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian is listed by: SoftCite |
nlx_154674, biotools:tassel | http://sourceforge.net/projects/tassel/ https://bio.tools/tassel |
SCR_012837 | and Linkage, Trait Analysis by aSSociation, Evolution | 2026-02-15 09:20:36 | 2335 | |||||||
|
G*Power Resource Report Resource Website 10000+ mentions |
G*Power (RRID:SCR_013726) | software application, data analytics software, software resource | Data analytics software to compute statistical power analyses for many commonly used statistical tests in social and behavioral research. It can also be used to compute effect sizes and to graphically display the results of power analyses. | statistics, t-test, effect of size, power analysis |
is listed by: SoftCite has parent organization: Heinrich Heine University Dusseldorf; North Rhine-Westphalia; Germany |
PMID:17695343 | Free, Public | SCR_013726 | G Star Power, G Power, G*Power - Statistical Power Analyses for Windows and Mac | 2026-02-15 09:20:33 | 14558 | ||||||||
|
EndNote Resource Report Resource Website 10000+ mentions |
EndNote (RRID:SCR_014001) | software application, software resource | A software application which helps users build a bibliography as they write formatted papers, manuscripts and other research-rich documents. Users can search multiple databases and collect PDFs as references for papers, then organize them within EndNote. Bibliographies and citations can be compiled within Microsoft Word using built-in tools. Papers are stored within an EndNote library and can be shared with colleagues. | software application, bibliography, authoring |
is listed by: Connected Researchers is listed by: SoftCite is related to: Connected Researchers |
Available to the research community, Fee (for different packages) | SCR_014001 | 2026-02-15 09:20:49 | 12094 | ||||||||||
|
Prime Resource Report Resource Website 500+ mentions |
Prime (RRID:SCR_014887) | software application, software resource | Software package that uses homology modeling and fold recognition to make protein structure predictions. | software package, protein structure, protein strcuture prediction, homology modeling, fold recognition, drug design | is listed by: SoftCite | Commercial | SCR_014887 | 2026-02-15 09:20:47 | 676 | ||||||||||
|
glmnet Resource Report Resource Website 100+ mentions |
glmnet (RRID:SCR_015505) | software toolkit, software resource | Procedures for fitting the entire lasso or elastic-net regularization path for linear regression, logistic and multinomial regression models, Poisson regression and the Cox model. The algorithm uses cyclical coordinate descent in a path-wise fashion. | data regression, cyclical coordinate descent, linear model | is listed by: SoftCite | Free, Available for download | https://www.jstatsoft.org/article/view/v033i01 | SCR_015505 | Lasso and Elastic-Net Regularized Generalized Linear Models | 2026-02-15 09:20:55 | 464 | ||||||||
|
PhyML Resource Report Resource Website 5000+ mentions |
PhyML (RRID:SCR_014629) | web application, source code, software resource | Web phylogeny server based on the maximum-likelihood principle. | phylogenic software, phylogeny, maximum likelihood, web server, bio.tools |
is used by: ProtTest is listed by: bio.tools is listed by: Debian is listed by: OMICtools is listed by: SoftCite works with: PAML |
DOI:10.1093/molbev/msq060 | Public server, Source code is available on request | biotools:phyml, OMICS_04241 | https://bio.tools/phyml https://sources.debian.org/src/phyml/ |
SCR_014629 | 2026-02-15 09:21:00 | 7740 | |||||||
|
STATISTICA Resource Report Resource Website 5000+ mentions |
STATISTICA (RRID:SCR_014213) | software application, data analytics software, software resource | Analytics platform with various sub platforms, each with specific performance capabilities for tasks such as data analysis, data management, data visualization, and data mining procedures. | TIBCO, statistical, test, data, mining, |
is listed by: Metabolomics Workbench is listed by: SoftCite |
Commercially available, Free download available | http://statistica.software.informer.com/10.0/ http://statistica.io/products/ |
SCR_014213 | Statistica 10, STATISTICS Product Index, Statistica | 2026-02-15 09:20:52 | 7864 | ||||||||
|
QmRLFS-finder Resource Report Resource Website 10+ mentions |
QmRLFS-finder (RRID:SCR_014584) | software application, data analytics software, software resource | A software which predicts R-loop Forming Sequences (RLFSs) in nucleic acid sequences based on the experimentally supported structural models of RLFSs. The tool identifies and visualizes RLFS coordinates from natural or artificial DNA or RNA input sequences and creates standard-compliant output files for later annotation and analysis. | r-loop, r loop, rlf, rlfs, dna, rna, input sequences, output files, annotation, analysis, bio.tools |
uses: UCSC Genome Browser is listed by: bio.tools is listed by: Debian is listed by: SoftCite |
Singapore Agency for Science Technology and Research | PMID:26400173 PMID:25883153 |
Open Source | biotools:qmrlfs-finder | https://omictools.com/qmrlfs-finder-tool https://bio.tools/qmrlfs-finder |
SCR_014584 | QmRLFS finder | 2026-02-15 09:20:59 | 13 | |||||
|
topGO Resource Report Resource Website 1000+ mentions |
topGO (RRID:SCR_014798) | software toolkit, software resource | Software package which provides tools for testing GO terms while accounting for the topology of the GO graph. Different test statistics and different methods for eliminating local similarities and dependencies between GO terms can be implemented and applied. | r, go, go graph, local similarities, software tool, software package, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: SoftCite works with: Gene Ontology is hosted by: Bioconductor |
Available for download | biotools:topgo | https://bio.tools/topgo | SCR_014798 | 2026-02-15 09:21:03 | 2839 | ||||||||
|
Hologic Resource Report Resource Website 100+ mentions |
Hologic (RRID:SCR_015529) | service resource, material service resource, production service resource | Commercial organization that provides services and products in global healthcare and diagnostics. | healthcare service, healthcare products, diagnostic services, diagnostic products |
is listed by: SoftCite is related to: Gen-Probe |
SCR_015529 | Hologic Inc | 2026-02-15 09:21:20 | 140 | ||||||||||
|
qBasePLUS Resource Report Resource Website 100+ mentions |
qBasePLUS (RRID:SCR_003370) | qbase+ | commercial organization, software resource | Software program for quantitative PCR (qPCR) data analysis based on geNorm and qBase technology. | real-time quantitative pcr |
is listed by: OMICtools is listed by: SoftCite is related to: geNORM has parent organization: Biogazelle |
PMID:17291332 | Free, Available for download, Freely available | OMICS_02320 | https://biogazelle-qbaseplus.software.informer.com/2.0/ | http://medgen.ugent.be/qbase/ | SCR_003370 | 2026-02-15 09:18:30 | 343 |
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