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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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BaCelLo Resource Report Resource Website 10+ mentions |
BaCelLo (RRID:SCR_011965) | BaCelLo | analysis service resource, data analysis service, production service resource, service resource | A predictor for the subcellular localization of proteins in eukaryotes that is based on a decision tree of several support vector machines (SVMs). It classifies up to four localizations for Fungi and Metazoan proteins and five localizations for Plant ones. BaCelLo's predictions are balanced among different classes and all the localizations are considered as equiprobable. | protein, data set, proteome |
is listed by: OMICtools is listed by: SoftCite has parent organization: University of Bologna; Bologna; Italy |
PMID:16873501 | OMICS_01616 | SCR_011965 | 2026-09-12 01:02:07 | 46 | ||||||||
|
CASAVA Resource Report Resource Website 1000+ mentions |
CASAVA (RRID:SCR_001802) | CASAVA | software application, software resource | Software package that creates genomic builds, calls SNPs, detects indels, and counts reads from data generated from one or more sequencing runs. In addition, CASAVA automatically generates a range of statistics, such as mean depth and percentage chromosome coverage, to enable comparison with previous builds or other samples. CASAVA analyzes sequencing reads in three stages: * FASTQ file generation and demultiplexing * Alignment to a reference genome * Variant detection and counting | gene, genetic, genomic, linux |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: SoftCite |
Free, Available for download, Freely available | nlx_154257, OMICS_01123 | http://www.illumina.com/software/genome_analyzer_software.ilmn | SCR_001802 | Consensus Assessment of Sequence And VAriation | 2026-09-12 01:02:26 | 1960 | ||||||
|
SciPy Resource Report Resource Website 10000+ mentions |
SciPy (RRID:SCR_008058) | software application, software resource | A Python-based environment of open-source software for mathematics, science, and engineering. The core packages of SciPy include: NumPy, a base N-dimensional array package; SciPy Library, a fundamental library for scientific computing; and IPython, an enhanced interactive console. | python, software, open source |
uses: Python Programming Language is used by: PyDSTool is used by: Elephant is used by: Stimfit is used by: Sklearn is listed by: SoftCite is related to: IPython is related to: NumPy is related to: IPython Notebook is related to: MNE software is related to: DE-Sim is required by: TomoMiner is required by: Short Read Sequence Typing for Bacterial Pathogens |
Public, Free | nif-0000-10422 | SCR_008058 | SciPy, Scientific Tools for Python | 2026-09-12 01:02:37 | 16188 | ||||||||
|
Ensembl Genome Browser Resource Report Resource Website 1000+ mentions |
Ensembl Genome Browser (RRID:SCR_013367) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 17,2022. Genome databases for vertebrates and other eukaryotic species. Analysis and annotation maintained on current data.Distribution of analysis to other bioinformatics laboratories. Ensembl concentrates on vertebrate genomes, but other groups have adapted system for use with plant and fungal genomes (see Powered by Ensembl list on website). |
is listed by: SoftCite has parent organization: Ensembl |
European Bioinformatics Institute ; Wellcome Trust Sanger Institute |
THIS RESOURCE IS NO LONGER IN SERVICE. | nif-0000-30518 | http://uswest.ensembl.org/index.html | SCR_013367 | 2026-09-12 01:02:11 | 1199 | ||||||||
|
Web of Science Resource Report Resource Website 10+ mentions |
Web of Science (RRID:SCR_022706) | data or information resource, database | Database of bibliographic citations of multidisciplinary areas that covers various journals of medical, scientific, and social sciences including humanities.Publisher independent global citation database. | Clarivate, publisher independent, global citation database, bibliographic citations of multidisciplinary areas, various journals | is listed by: SoftCite | Free | SCR_022706 | Web of Knowledge | 2026-09-12 01:02:20 | 24 | |||||||||
|
ImageQuant Resource Report Resource Website 5000+ mentions |
ImageQuant (RRID:SCR_014246) | IQTL | data processing software, image analysis software, software application, software resource | Software for automatic general image analysis. It provides fully automatic analysis of 1-D gels including lane creation, background subtraction, band detection, molecular weight calibration, quantity calibration, and normalization. Editing tools are provided for cropping, rotating, and filtering images., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | automatic image analysis, general image analysis, image analysis software |
is listed by: SoftCite has parent organization: GE Healthcare |
THIS RESOURCE IS NO LONGER IN SERVICE | SCR_014246 | ImageQuant TL | 2026-09-12 01:01:02 | 9231 | ||||||||
|
ImageScope Resource Report Resource Website 1000+ mentions |
ImageScope (RRID:SCR_014311) | data processing software, image analysis software, software application, software resource | Slide image modification software that allows the user to adjust the magnification, compare slides, pan and zoom, annotate specific areas, and perform image analysis of digital slides. Users can create macros and algorithms to automate analysis and create plots, respectively., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | slide image modification, viewing program |
is listed by: SoftCite has parent organization: University of Chicago; Illinois; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | http://www.leicabiosystems.com/digital-pathology/digital-pathology-management/imagescope/ | SCR_014311 | 2026-09-12 01:01:02 | 3691 | |||||||||
|
ATSAS Resource Report Resource Website 1000+ mentions |
ATSAS (RRID:SCR_015648) | data processing software, software application, software resource, software toolkit | Software toolkit for small-angle scattering data analysis from biological macromolecules. | macromolecule, small-angle scattering, ab initio method, rigid body modeling, pbd oriented tool, mixture, flexible system |
is listed by: SoftCite is related to: DAMMIF |
PMID:28808438 | SCR_015648 | Data Analysis Software ATSAS | 2026-09-12 01:01:03 | 1377 | |||||||||
|
ProteinLynx Global Server Resource Report Resource Website 100+ mentions |
ProteinLynx Global Server (RRID:SCR_016664) | PLGS | data or information resource, organization portal, portal, service resource | Platform for quantitative and qualitative proteomics research for Waters Corporation proteomics systems. | Waters Corporation, quantitative, qualitative, proteomics, research, system | is listed by: SoftCite | SCR_016664 | ProteinLynx Global SERVER™ (PLGS), ProteinLynx Global Server, PLGS, ProteinLynx Global Server (PLGS), Protein Lynx Global Server 2.4, Protein Lynx Global Server | 2026-09-12 01:01:04 | 215 | |||||||||
|
Maestro Resource Report Resource Website 50+ mentions |
Maestro (RRID:SCR_016748) | data or information resource, portal | Software tool for all purpose molecular modeling environment. Maestro is the portal to all of Schrödinger's computational technology. Helps researchers organize and analyze data. | molecular, modeling, environment, computation, data, analyze, organize |
is listed by: SoftCite has parent organization: Schrodinger |
Commercially available, Trial available | SCR_016748 | 2026-09-12 01:01:04 | 88 | ||||||||||
|
BlobFinder Resource Report Resource Website 100+ mentions |
BlobFinder (RRID:SCR_015788) | data processing software, image analysis software, software application, software resource | Software that can perform calculations on cells from fluorescence microscopy images. BlobFinder can perform two types of analysis: an average count analysis to count the number of fluorescent signals and nuclei in an image, and a single cell analysis to simulate a cytoplasm and assign each signal to a particular cell. | fluorescence, microscopy, average count analysis, single cell analysis, cell calculation |
is listed by: SoftCite has parent organization: Uppsala University; Uppsala; Sweden |
Free, Available for download, Runs on Windows, Tutorial available | SCR_015788 | 2026-09-12 01:01:03 | 129 | ||||||||||
|
Phenix.refine Resource Report Resource Website 10+ mentions |
Phenix.refine (RRID:SCR_016736) | Phenix.refine | data processing software, software application, software resource | Software tool for a general purpose crystallographic structure refinement within the PHENIX package. Serves as a critical component in automated model building, final structure refinement, structure validation and deposition to the wwPDB. | crystallographic, structure, refinement, Phenix, model, building, validation |
is listed by: SoftCite is provided by: Phenix |
NIGMS GM063210; US Department of Energy |
PMID:22505256 | Free, Available for download for non profit, For profit access PHENIX through a Consortium agreement, Tutorial available, Acknowledgement requested | SCR_016736 | Python-based Hierarchical ENvironment for Integrated Xtallography.refine, Phenix.refine, Phenix | 2026-09-12 01:01:04 | 39 | ||||||
|
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 | Indica Labs HALO software | 2026-09-12 01:01:07 | 108 | ||||||||
|
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 | G Star Power, G Power, G*Power - Statistical Power Analyses for Windows and Mac | 2026-09-12 01:02:49 | 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 | 2026-09-12 01:02:50 | 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 | Statistica 10, STATISTICS Product Index, Statistica | 2026-09-12 01:02:50 | 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 | 2026-09-12 01:02:51 | 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 | Lasso and Elastic-Net Regularized Generalized Linear Models | 2026-09-12 01:02:52 | 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 | 2026-09-12 01:02:51 | 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 | QmRLFS finder | 2026-09-12 01:02:51 | 16 |
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