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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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 | SciCrunch Registry | functional ANNOtation of genetic VARiants, ANNOVAR: Functional annotation of genetic variants | 2026-11-07 12:03:54 | 6463 | |||||
|
Cluster Resource Report Resource Website 5000+ mentions |
Cluster (RRID:SCR_013505) | Cluster | software resource, software toolkit | 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 | SciCrunch Registry | Cluster 3.0 | 2026-11-07 12:03:39 | 5814 | |||||
|
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 | SciCrunch Registry | 2026-11-07 12:04:00 | 413 | |||||||||
|
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 | SciCrunch Registry | 2026-11-07 12:03:54 | 566 | ||||||||||
|
Primer Express Resource Report Resource Website 1000+ mentions |
Primer Express (RRID:SCR_014326) | software application, software resource, 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 | SciCrunch Registry | 2026-11-07 12:03:53 | 4805 | ||||||||||
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HKL-2000 Resource Report Resource Website 100+ mentions |
HKL-2000 (RRID:SCR_015547) | 3-d visualization software, data processing software, software application, software resource | 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 | SciCrunch Registry | 2026-11-07 12:03:52 | 215 | ||||||||
|
SQLite Resource Report Resource Website 50+ mentions |
SQLite (RRID:SCR_017672) | software application, software resource | Relational database management system contained in C library. SQLite is not client server database engine but it is embedded into the end program. | Database, management, system, C library, engine, embedded, the end program | is listed by: SoftCite | Free, Freely available | SCR_017672 | SciCrunch Registry | 2026-11-07 12:04:05 | 83 | ||||||||||
|
survival Resource Report Resource Website 500+ mentions |
survival (RRID:SCR_021137) | software resource, software toolkit | Software R package contains core survival analysis routines, including definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox models, and parametric accelerated failure time models. | Survival analysis routines, Surv objects, Kaplan-Meier curve, Aalen-Johansen curve, Cox models, parametric accelerated failure time models |
is listed by: CRAN is listed by: SoftCite |
Free, Available to download, Freely available | https://github.com/therneau/survival | SCR_021137 | SciCrunch Registry | 2026-11-07 12:03:56 | 566 | |||||||||
|
caret Resource Report Resource Website 50+ mentions |
caret (RRID:SCR_021138) | software resource, software toolkit | Software R package provides misc functions for training and plotting classification and regression models.Contains tools for data splitting, pre-processing, feature selection, model tuning using resampling, and variable importance estimation, as well as other functionality. | Plotting classification, regression models, data splitting, pre processing, feature selection, model tuning using resampling, estimation |
is listed by: CRAN is listed by: SoftCite |
Free, Available for download, Freely available | https://github.com/topepo/caret/ | SCR_021138 | SciCrunch Registry | Classification And REgression Training | 2026-11-07 12:03:54 | 96 | ||||||||
|
ScanProsite Resource Report Resource Website 100+ mentions |
ScanProsite (RRID:SCR_024425) | PMID:16845026 | data access protocol, software resource, web service | 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 | SciCrunch Registry | 2026-11-07 12:00:58 | 106 | |||||||
|
PyWavelets Resource Report Resource Website 10+ mentions |
PyWavelets (RRID:SCR_024421) | data analysis software, data processing software, software application, software resource | Software Python package for wavelet analysis. | Python, wavelet analysis, | is listed by: SoftCite | Free, Available for download, Freely available | SCR_024421 | SciCrunch Registry | 2026-11-07 12:01:17 | 17 | ||||||||||
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ProteinPilot Resource Report Resource Website 100+ mentions |
ProteinPilot (RRID:SCR_024414) | data analysis software, data processing software, software application, software resource | 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 | SciCrunch Registry | 2026-11-07 12:00:58 | 265 | |||||||||
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pRRophetic Resource Report Resource Website 10+ mentions |
pRRophetic (RRID:SCR_024417) | simulation software, software application, software resource | Software R package for prediction of clinical chemotherapeutic response from tumor gene expression levels. Used to predict phenotypes from gene expression microarray data, gene expression microarray data, | clinical chemotherapeutic response prediction, tumor gene expression levels, predict phenotypes, | is listed by: SoftCite | U01GM61393 ; GM089941 ; CA139278 ; University of Chicago ; UL1RR024999 |
PMID:25229481 | Free, Available for download, Freely available | SCR_024417 | SciCrunch Registry | 2026-11-07 12:01:13 | 33 | ||||||||
|
VSEARCH Resource Report Resource Website 1000+ mentions |
VSEARCH (RRID:SCR_024494) | data analysis software, data processing software, software application, software resource | 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 | SciCrunch Registry | 2026-11-07 12:01:15 | 1553 | |||||||||
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TomoStudio Resource Report Resource Website 1+ mentions |
TomoStudio (RRID:SCR_024498) | data analysis software, data processing software, software application, software resource | 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 | SciCrunch Registry | 2026-11-07 12:01:18 | 4 | ||||||||||
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Ocular Resource Report Resource Website 1+ mentions |
Ocular (RRID:SCR_024490) | data acquisition software, data processing software, software application, software resource | 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 | SciCrunch Registry | Teledyne Photometrics Ocular | 2026-11-07 12:01:15 | 4 | |||||||||
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Umediation Resource Report Resource Website 1+ mentions |
Umediation (RRID:SCR_024492) | data analysis software, data processing software, software application, software resource | 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 | SciCrunch Registry | 2026-11-07 12:01:18 | 1 | |||||||||
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IntFOLD Resource Report Resource Website 1+ mentions |
IntFOLD (RRID:SCR_024523) | data access protocol, software resource, web service | 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 | SciCrunch Registry | 2026-11-07 12:01:16 | 8 | |||||||||
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OMNISEC Resource Report Resource Website 10+ mentions |
OMNISEC (RRID:SCR_024485) | data analysis software, data processing software, software application, software resource | 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 | SciCrunch Registry | 2026-11-07 12:01:14 | 39 | ||||||||||
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PHYLDOG Resource Report Resource Website 1+ mentions |
PHYLDOG (RRID:SCR_024487) | data analysis software, data processing software, software application, software resource | 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 | SciCrunch Registry | 2026-11-07 12:01:16 | 1 |
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