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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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BREAKDANCER Resource Report Resource Website 100+ mentions |
BREAKDANCER (RRID:SCR_001799) | BreakDancer | software application, software resource | A Perl/C++ software package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads. BreakDancerMax predicts five types of structural variants: insertions, deletions, inversions, inter- and intra-chromosomal translocations from next-generation short paired-end sequencing reads using read pairs that are mapped with unexpected separation distances or orientation. (entry from Genetic Analysis Software) | gene, genetic, genomic, perl, c++, next generation sequencing, structural variant, insertion, deletion, inversion, inter-chromosomal translocation, intra-chromosomal translocation, chromosomal translocation, indel, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA |
PMID:19668202 | Free, Available for download, Freely available | biotools:breakdancer, nlx_154253, OMICS_00307 | https://bio.tools/breakdancer | SCR_001799 | 2026-02-15 09:18:10 | 370 | ||||||
|
WHONET Resource Report Resource Website 10+ mentions |
WHONET (RRID:SCR_024495) | software application, software resource | Software free desktop Windows application for the management and analysis of microbiology laboratory data with a particular focus on antimicrobial resistance surveillance developed and supported by the WHO Collaborating Centre for Surveillance of Antimicrobial Resistance at the Brigham and Women's Hospital in Boston, Massachusetts. WHONET, available in 44 languages, supports local, national, regional, and global surveillance efforts in over 2,300 hospital, public health, animal health, and food laboratories in over 130 countries worldwide. | management and analysis of microbiology laboratory data | is listed by: SoftCite | Free, Available for download, Freely available | SCR_024495 | 2026-02-15 09:23:33 | 17 | ||||||||||
|
WinNonlin Resource Report Resource Website 1000+ mentions |
WinNonlin (RRID:SCR_024504) | software application, software resource | Software to automate repetitive analysis steps and is widely considered the industry standard for NCA, TK, and PK/PD modeling. Used as non-compartmental analysis (NCA), pharmacokinetic/pharmacodynamic (PK/PD), and toxicokinetic (TK) modeling tool. | automate repetitive analysis steps, NCA, TK, PK/PD modeling, non-compartmental analysis, pharmacokinetic/pharmacodynamic, toxicokinetic, modeling tool, | is listed by: SoftCite | SCR_024504 | Phoenix WinNonlin | 2026-02-15 09:23:31 | 1804 | ||||||||||
|
NGmerge Resource Report Resource Website 10+ mentions |
NGmerge (RRID:SCR_024483) | software application, software resource | Software tool for merging paired-end reads via novel empirically derived models of sequencing errors. Used for merging paired-end reads and removing adapters. Corrects errors and ambiguous bases and assigns quality scores for merged bases that accurately reflect the error rates. | merging paired-end reads, sequencing errors, removing adapters, correct errors, correct ambiguous bases, assign quality scores for merged bases, error rates, | is listed by: SoftCite | PMID:30572828 | Free, Available for download, Freely available | SCR_024483 | 2026-02-15 09:23:33 | 23 | |||||||||
|
SigmaPlot Resource Report Resource Website 10000+ mentions |
SigmaPlot (RRID:SCR_003210) | SigmaPlot | commercial organization, software resource | 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 | 2026-02-15 09:18:28 | 17371 | |||||||
|
Strelka Resource Report Resource Website 100+ mentions |
Strelka (RRID:SCR_005109) | Strelka | commercial organization, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 7,2024. Software for somatic single nucleotide variant (SNV) and small indel detection from sequencing data of matched tumor-normal samples. The method employs a novel Bayesian approach which represents continuous allele frequencies for both tumor and normal samples, whilst leveraging the expected genotype structure of the normal. This is achieved by representing the normal sample as a mixture of germline variation with noise, and representing the tumor sample as a mixture of the normal sample with somatic variation. A natural consequence of the model structure is that sensitivity can be maintained at high tumor impurity without requiring purity estimates. The method has superior accuracy and sensitivity on impure samples compared to approaches based on either diploid genotype likelihoods or general allele-frequency tests. | 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 |
biotools:strelka | https://bio.tools/strelka https://github.com/Illumina/strelka/ https://sources.debian.org/src/strelka/ |
SCR_005109 | 2026-02-15 09:18:54 | 261 | ||||||
|
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 | 2026-02-15 09:20:18 | 1101 | |||||||||
|
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 | 2026-02-15 09:20:25 | 1816 | |||||||||
|
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 | 2026-02-15 09:20:27 | 1133 | ||||||||
|
ANALYZE Resource Report Resource Website 1000+ mentions |
ANALYZE (RRID:SCR_009120) | ANALYZE | software application, software resource | A set of useful accessory programs to the LINKAGE package. It simplifies the performance of a large array of parametric and nonparametric tests for linkage and association on data entered in LINKAGE format pedigree and parameter files. (entry from Genetic Analysis Software) | gene, genetic, genomic, pascal, unix, sunos, solaris, osf1 |
is listed by: Genetic Analysis Software is listed by: SoftCite |
nlx_154223 | SCR_009120 | 2026-02-15 09:19:38 | 1102 | |||||||||
|
QUANTO Resource Report Resource Website 500+ mentions |
QUANTO (RRID:SCR_009084) | QUANTO | software application, software resource | Software program that computes sample size or power for association studies of genes, environmental factors, gene-environment interaction, or gene-gene interaction. Available study designs for a disease (binary) outcome include the unmatched case-control, matched case-control, case-sibling, case-parent, and case-only designs. Study designs for a quantitative tra it include independent individuals and case parent designs. Quanto is a 32-bit Windows application requiring Windows 95, 98, NT, 2000, ME or XP to run. The graphical user interface allows th e user to easily change the model and view the results without having to edit an input file and rerun the program for every model. The results of a session are stored to a log file. This log can be printed or saved to a file for reviewing at a later date. An option is included to create a text file of the log that can be imported into other documents. (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, ms-windows, (98/nt/2000/..) |
is listed by: Genetic Analysis Software is listed by: SoftCite |
nlx_154095 | SCR_009084 | 2026-02-15 09:19:37 | 915 | |||||||||
|
IMPUTE Resource Report Resource Website 500+ mentions |
IMPUTE (RRID:SCR_009245) | IMPUTE | software application, software resource | Software application for estimating (imputing) unobserved genotypes in SNP association studies. The program is designed to work seamlessly with the output of the genotype calling program CHIAMO and the population genetic simulator HAPGEN, and it produces output that can be analyzed using the program SNPTEST. (entry from Genetic Analysis Software) | gene, genetic, genomic |
is listed by: Genetic Analysis Software is listed by: SoftCite |
nlx_154411 | SCR_009245 | 2026-02-15 09:20:06 | 628 | |||||||||
|
SAGE Resource Report Resource Website 1000+ mentions |
SAGE (RRID:SCR_009302) | SAGE | software application, software resource | Software application that provides researchers with the tools necessary for various types of statistical genetic analysis of human family data. (entry from Genetic Analysis Software) | gene, genetic, genomic, c, version 4.0 will be in c++, unix, (dec unix/solaris), ms-windows, (95/nt), linux |
is listed by: Genetic Analysis Software is listed by: SoftCite |
nlx_154606 | SCR_009302 | Statistical Analysis for Genetic Epidemiology | 2026-02-15 09:19:41 | 1029 | ||||||||
|
E-Prime Resource Report Resource Website 100+ mentions |
E-Prime (RRID:SCR_009567) | E-Prime | software application, software resource | A suite of applications to fulfill all of your computerized experiment needs. Used by more than 15,000 professionals in the research community, E-Prime provides a truly easy-to-use environment for computerized experiment design, data collection, and analysis. E-Prime provides millisecond precision timing to ensure the accuracy of your data. E-Prime's flexibility to create simple to complex experiments is ideal for both novice and advanced users. The E-Prime suite of applications includes: * E-Studio ? Drag and drop graphical interface for experiment design * E-Basic ? Underlying scripting language of E-Prime * E-Run ? Once the experiment is generated with a single click, E-Run affords you the millisecond precision of stimulus presentation, synchronizations, and data collection. * E-Merge ? Merges your single session data files for group analysis * E-DataAid ? Data management utility * E-Recovery ? Recovers data files | experimental control, microsoft, magnetic resonance, visual basic, win32 (ms windows), windows, windows vista, windows xp |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: SoftCite |
nlx_155747 | http://www.nitrc.org/projects/eprime | SCR_009567 | E-Prime 2.0 | 2026-02-15 09:20:04 | 162 | |||||||
|
TAGGER Resource Report Resource Website 50+ mentions |
TAGGER (RRID:SCR_009419) | software application, software resource | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic, web-based |
is listed by: Genetic Analysis Software is listed by: SoftCite |
nlx_154669 | SCR_009419 | 2026-02-15 09:20:11 | 91 | ||||||||||
|
ANNOVAR Resource Report Resource Website 5000+ mentions |
ANNOVAR (RRID:SCR_012821) | ANNOVAR | software application, software resource | An efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, as well as mouse, worm, fly, yeast and many others). Given a list of variants with chromosome, start position, end position, reference nucleotide and observed nucleotides, ANNOVAR can perform: 1. gene-based annotation. 2. region-based annotation. 3. filter-based annotation. 4. other functionalities. (entry from Genetic Analysis Software) | genomic analysis, imaging genomics, next generation sequencing, snp, gene, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: wANNOVAR has parent organization: OpenBioinformatics.org |
PMID:20601685 | Free | nlx_154225, biotools:annovar, OMICS_00165 | https://bio.tools/annovar https://bio.tools/annovar |
SCR_012821 | functional ANNOtation of genetic VARiants, ANNOVAR: Functional annotation of genetic variants | 2026-02-15 09:20:40 | 5946 | |||||
|
Cluster Resource Report Resource Website 5000+ mentions |
Cluster (RRID:SCR_013505) | Cluster | software toolkit, software resource | Software R package. Methods for Cluster analysis. Performs variety of types of cluster analysis and other types of processing on large microarray datasets. | Cluster analysis, processing on large microarray datasets |
is listed by: OMICtools is listed by: Debian is listed by: SoftCite has parent organization: University of California at Berkeley; Berkeley; USA |
PMID:14871861 | Free, Available for download, Freely available | OMICS_01571 | http://www.eisenlab.org/eisen/?page_id=42 https://sources.debian.org/src/cluster3/ |
SCR_013505 | Cluster 3.0 | 2026-02-15 09:20:29 | 5669 | |||||
|
LigandScout Resource Report Resource Website 100+ mentions |
LigandScout (RRID:SCR_014889) | software application, software resource | Software that takes a macromolecular structure containing a bound ligand and identifies the key features on the ligand which are interacting with points on a protein. Its features include: automatic interpretation of PDB ligands using geometry, dictionaries and rule; advanced handling of co-factors, ions, water molecules and covalently bound ligands; pharmacophore export to Catalyst(tm), MOE(tm) and PHASE(tm) for virtual screening; and the ability to treat co-factors and water molecules as part of the ligand or part of the macromolecule. | pharmacophore, macromolecular structure, bound ligand, pdb ligand, virtual screening, ligad based pharmacore design | is listed by: SoftCite | Available for purchase | https://www.chemistryworld.com/ligandscout/1012019.article | SCR_014889 | 2026-02-15 09:21:02 | 395 | |||||||||
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SPARTAN Resource Report Resource Website 500+ mentions |
SPARTAN (RRID:SCR_014901) | software application, software resource | Software program for determining molecular structure and calculating chemical properties. It has a graphical interface and accurate computational models that are compatible with the iPad, iPhone and iPod Touch. When combined with the Spartan'16 Parallel Suite, this enables the first fully-functional open-ended molecular modeling environment on popular mobile technology. | molecular structure, chemical properties, modeling, mobile technology, integration | is listed by: SoftCite | Commercial | SCR_014901 | 2026-02-15 09:21:02 | 534 | ||||||||||
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Primer Express Resource Report Resource Website 1000+ mentions |
Primer Express (RRID:SCR_014326) | software application, standalone software, software resource | 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 | 2026-02-15 09:20:55 | 4773 |
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