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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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HALO Resource Report Resource Website 100+ mentions |
HALO (RRID:SCR_018350) | HALO | data processing software, image analysis software, software application, software resource | Software image analysis platform for quantitative tissue analysis in digital pathology by Indica Labs. Used for high-throughput, quantitative tissue analysis in oncology, neuroscience, metabolism, toxicology. | Image analysis platform, digital pathology, quantitative tissue analysis, image, analysis, tissue | is listed by: SoftCite | Restricted | SCR_018350 | SciCrunch Registry | Indica Labs HALO software | 2026-11-07 12:01:39 | 108 | ||||||||
|
Adobe Illustrator Resource Report Resource Website 10000+ mentions |
Adobe Illustrator (RRID:SCR_010279) | Illustrator CC | software application, software resource, software toolkit | 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 | SciCrunch Registry | Illustrator CC, Adobe Illustrator CS5, Adobe Illustrator CS6 | 2026-11-07 12:03:35 | 13886 | |||||||
|
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 | SciCrunch Registry | and Linkage, Trait Analysis by aSSociation, Evolution | 2026-11-07 12:03:50 | 2476 | |||||||
|
G*Power Resource Report Resource Website 10000+ mentions |
G*Power (RRID:SCR_013726) | data analytics software, software application, 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 | SciCrunch Registry | G Star Power, G Power, G*Power - Statistical Power Analyses for Windows and Mac | 2026-11-07 12:03:49 | 18041 | ||||||||
|
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 | SciCrunch Registry | 2026-11-07 12:03:50 | 13870 | ||||||||||
|
STATISTICA Resource Report Resource Website 5000+ mentions |
STATISTICA (RRID:SCR_014213) | data analytics software, software application, 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 | SciCrunch Registry | Statistica 10, STATISTICS Product Index, Statistica | 2026-11-07 12:03:58 | 8076 | ||||||||
|
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 | SciCrunch Registry | 2026-11-07 12:03:43 | 691 | ||||||||||
|
glmnet Resource Report Resource Website 500+ mentions |
glmnet (RRID:SCR_015505) | software resource, software toolkit | 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 | SciCrunch Registry | Lasso and Elastic-Net Regularized Generalized Linear Models | 2026-11-07 12:03:44 | 533 | ||||||||
|
PhyML Resource Report Resource Website 5000+ mentions |
PhyML (RRID:SCR_014629) | software resource, source code, web application | 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 | SciCrunch Registry | 2026-11-07 12:03:59 | 7951 | |||||||
|
QmRLFS-finder Resource Report Resource Website 10+ mentions |
QmRLFS-finder (RRID:SCR_014584) | data analytics software, software application, 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 | SciCrunch Registry | QmRLFS finder | 2026-11-07 12:03:51 | 16 | |||||
|
topGO Resource Report Resource Website 1000+ mentions |
topGO (RRID:SCR_014798) | software resource, software toolkit | 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 | SciCrunch Registry | 2026-11-07 12:03:54 | 3080 | ||||||||
|
Hologic Resource Report Resource Website 100+ mentions |
Hologic (RRID:SCR_015529) | material service resource, production service resource, 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 | SciCrunch Registry | Hologic Inc | 2026-11-07 12:03:55 | 148 | ||||||||||
|
Design-Expert Resource Report Resource Website 50+ mentions |
Design-Expert (RRID:SCR_022671) | data analytics software, software application, software resource | Statistical software package from Stat-Ease Inc. to perform design of experiments. Offers comparative tests, screening, characterization, optimization, robust parameter design, mixture designs and combined designs. | Stat-Ease Inc., experiments design, comparative tests, screening, characterization, optimization, parameter design, mixture designs, combined designs | is listed by: SoftCite | Restricted | SCR_022671 | SciCrunch Registry | 2026-11-07 12:04:00 | 52 | ||||||||||
|
SABmark Resource Report Resource Website 1+ mentions |
SABmark (RRID:SCR_011817) | SABmark | data or information resource, data set | Downloadable data set designed to assess the performance of both multiple and pairwise (protein) sequence alignment algorithms, and is extremely easy to use. Currently, the database contains 2 sets, each consisting of a number of subsets with related sequences. It''s main features are: * Covers the entire known fold space (SCOP classification), with subsets provided by the ASTRAL compendium * All structures have high quality, with 100% resolved residues * Structure alignments have been derived carefully, using both SOFI and CE, and Relaxed Transitive Alignment * At most 25 sequences in each subset to avoid overrepresentation of large folds* Automated running, archiving and scoring of programs through a few Perl scripts The Twilight Zone set is divided into sequence groups that each represent a SCOP fold. All sequences within a group share a pairwise Blast e-value of at least 1, for a theoretical database size of 100 million residues. Sequence similarity is thus very low, between 0-25% identity, and a (traceable) common evolutionary origin cannot be established between most pairs even though their structures are (distantly) similar. This set therefore represents the worst case scenario for sequence alignment, which unfortunately is also the most frequent one, as most related sequences share less than 25% identity. The Superfamilies set consists of groups that each represent a SCOP superfamily, and therefore contain sequences with a (putative) common evolutionary origin. However, they share at most 50% identity, which is still challenging for any sequence alignment algorithm. Frequently, alignments are performed to establish whether or not sequences are related. To benchmark this, a second version of both the Twilight Zone and the Superfamilies set is provided, in which to each alignment problem a number of false positives, i.e. sequences not related to the original set, are added. Database specifications: * Current version: 1.65 (concurrent with PDB, SCOP and ASTRAL) * Twilight Zone set (with false positives): 209 groups, 1740 (3280) sequences, 10667 (44056) related pairs * Superfamilies set (with false positives): 425 groups, 3280 (6526) sequences, 19092 (79095) related pairs |
is listed by: OMICtools is listed by: SoftCite has parent organization: Vrije Universiteit Brussel; Brussels; Belgium |
PMID:15333456 | OMICS_00988 | SCR_011817 | SciCrunch Registry | SABmark - Sequence and structure Alignment Benchmark, Sequence Alignment Benchmark, Sequence and structure Alignment Benchmark | 2026-11-07 12:04:45 | 8 | ||||||||
|
Stata Resource Report Resource Website 10000+ mentions |
Stata (RRID:SCR_012763) | software application, software resource | Software package for statistical analysis and presentation of graphics. Statistical software for data science. | statistical analysis, presentation of graphics, data science, | is listed by: SoftCite | Restricted | nlx_156918 | SCR_012763 | SciCrunch Registry | 2026-11-07 12:05:19 | 49366 | |||||||||
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pyPCcazip Resource Report Resource Website 1+ mentions |
pyPCcazip (RRID:SCR_024423) | software resource, source code | Software PCA-based toolkit for compression and analysis of molecular simulation data. Used for compression and analysis of molecular dynamics (MD) simulation data. | data compression and analysis, molecular simulation data, | is listed by: SoftCite | DOI:10.1016/j.softx.2016.04.002 | Free, Available for download, Freely available | SCR_024423 | SciCrunch Registry | 2026-11-07 12:05:38 | 4 |
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