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http://brainhealthregistry.org/

A website aimed at recruiting and assessing subjects for all types of neuroscience studies with the internet. The hope is to accelerate various types of observational studies and clinical trials, and also reduce costs. They are interested in having people, including healthy subjects of all ages, join the registry. Joining only takes a few minutes. The web-based project is designed to speed up cures for Alzheimer's, Parkinson's and other brain disorders. It uses online questionnaires and online neuropsychological tests (which are very much like online brain games).

Proper citation: Brain Health Registry (RRID:SCR_010230) Copy   

•   Source: SciCrunch Registry

http://www.pgbovine.net/cde.html

A software application which automatically packages up the code, data, and environment required to deploy and run Linux programs on other machines without any installation or configuration. Users can prepend any set of Linux commands with the "cde" binary, and CDE will run them and automatically package up all files accessed during execution. A package is a directory that can be compressed and delivered to any x86-Linux machine and contains all the files and environment variables required to run the original commands. After receiving the package, the user can run those same commands from within the package on any modern x86-Linux distro., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: CDE Tool (RRID:SCR_013981) Copy   

•   Source: SciCrunch Registry

https://www.cellosaurus.org/

Database of all cell lines used in biomedical research which include immortalized cell lines, naturally immortal cell lines (stem cells), widely used and distributed finite life cell lines, vertebrate cell lines (majority being human, mouse, and rat), and invertebrate (insects and ticks) cell lines, as well as cell line synonyms. Each cell line is provided with the following information: the recommended name (the name which appears in the original publication), a list of synonyms, a unique accession number, comments on a number of topics including misspellings and gene transfection, information on the tissue/organ origin with the UBERON code, the NCI Thesaurus or Orphanet ORDO code for the disease(s) the individual suffered from (for cancer and human genetic disease lines only), the species of origin, the parent cell line, cross-references of sister cell lines, the sex of the individual, the category in which the cell line belongs (Adult stem cell; Cancer cell line; Embryonic stem cell; Factor-dependent cell line; Finite cell line; Hybrid cell line; Hybridoma; Induced pluripotent stem cell; Spontaneously immortalized cell line; Stromal cell line; Telomerase immortalized cell line; Transformed cell line; Undefined cell line type), web links, publication references, and/or cross-references to cell line catalogs/collections, ontologies, cell lines databases/resources, and to databases that list cell lines as samples.

Proper citation: Cellosaurus (RRID:SCR_013869) Copy   

•   Source: SciCrunch Registry

http://huttenhower.sph.harvard.edu/galaxy

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Algorithm for high-dimensional biomarker discovery and explanation that identifies genes, pathways, or taxa characterizing the differences between two or more biological conditions. The algorithm identifies features that are statistically different among biological classes, then performs additional tests to assess whether these differences are consistent with respect to expected biological behavior. Statistical significance and biological relevance are emphasized., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: LEfSe (RRID:SCR_014609) Copy   

•   Source: SciCrunch Registry

https://imdevsoftware.wordpress.com/imdev/

A software application of RExcel that integrates R into Excel as an embedded additon for omics tasks and analysis. It can be used specifically for tasks concerning multivariate data visualization, exploration, and analysis. imDev has interactive modules for dimensional reduction, prediction, feature selection, analysis of correlation, and generation of networked structures, all of which provide an integrated environment for systems level analysis of multivariate data.

Proper citation: imDEV (RRID:SCR_014674) Copy   

•   Source: SciCrunch Registry

https://github.com/ChristophRau/wMICA

Weighted implementation of Maximal Information Component Analysis, a co-expression network analysis algorithm for analysis of large interconnected networks and the identification of modules of similarly-acting nodes within the larger network.

Proper citation: wMICA (RRID:SCR_015490) Copy   

•   Source: SciCrunch Registry

https://neurophysics.ucsd.edu/software.php

Matlab-based routines for the detection and clustering of putative single units from a multi-unit time series, along with quality metrics. This sofwtare was developed by the David Kleinfeld Laboratory at UC San Diego.

Proper citation: UltraMegaSort 2000 (RRID:SCR_015857) Copy   

•   Source: SciCrunch Registry

https://sourceforge.net/projects/icacompass/

Algorithm for MATLAB and the EEGLAB toolbox that enables the automatic detection of independent components from an ICA that represent event-related brain potentials. It performs automatic Independent Component (IC) selection with respect to the contributions of the ICs to a certain ERP.

Proper citation: COMPASS (RRID:SCR_015874) Copy   

•   Source: SciCrunch Registry

http://gps.biocuckoo.org/

Software that detects kinase-specific phosphorylation sites. GPS provides a platform able to perform its prediction based on a group-based phosphorylation scoring algorithm. It allows users to query multiple protein sequences through a batch prediction mode.

Proper citation: GPS (RRID:SCR_016374) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=Boruta

Algorithm that performs feature selection. It finds relevant features by comparing original attributes' importance with importance achievable at random, estimated using their permuted copies (shadows).

Proper citation: Boruta (RRID:SCR_016234) Copy   

•   Source: SciCrunch Registry

https://github.com/NuttyLogic/EpigeneticPacemaker

Python implementation of conditional expectation maximization algorithm that estimates epigenetic landscapes and state of individuals and may be used to study nonlinear epigenetic aging. Fast conditional expectation maximization algorithm used to model epigenetic states associated with phenotype of interest. Can model non linear epigenetic trait associations directly without transformation of phenotype of interest.

Proper citation: Epigenetic Pacemaker (RRID:SCR_018158) Copy   

•   Source: SciCrunch Registry

https://atagousa.corecommerce.com/PAL-10S-p358.html

Digital hand held pocket refractometer that measures urine specific gravity. It has measurement temperature of 10 to 35 C and sample volume of 0.3ml.

Proper citation: Atago: PAL-10S Pocket Refractometer (RRID:SCR_018439) Copy   

•   Source: SciCrunch Registry

https://github.com/vinguyenle/k-FLBPCM-method

Software tool as novel k-FLBPCM method for detecting morphologically similar crops and weeds based on combination of contour masks and Local Binary Pattern operators.

Proper citation: k-FLBPCM method (RRID:SCR_017973) Copy   

•   Source: SciCrunch Registry

https://github.com/yhoogstrate/dr-disco

Software tool fo detecting genomic breakpoints of fusion transcripts in random hexamer RNA-seq data. Used for detection of exonic, intronic and intergenic fusion transcripts and their genomic breakpoints in poly(A)+ and rRNA-minus RNA sequencing data.

Proper citation: Dr. Disco (RRID:SCR_021739) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/FilterFFPE/

Software R package to find and filter artificial chimeric reads specifically generated in next generation sequencing process of formalin fixed paraffin embedded tissues. These artificial chimeric reads can lead to large number of false positive structural variant calls. Artifact chimeric read filter to improve SV detection in FFPE samples.

Proper citation: FilterFFPE (RRID:SCR_021086) Copy   

•   Source: SciCrunch Registry

http://www.informatics.jax.org/genes.shtml

Searchable database of mouse genes, DNA segments, cytogenetic markers and QTLs. MGI provides access to integrated data on mouse genes and genome features, from sequences and genomic maps to gene expression and disease models.

Proper citation: Genes, Genome Features and Maps (RRID:SCR_017524) Copy   

•   Source: SciCrunch Registry

http://www.informatics.jax.org/phenotypes.shtml

Enables comparative phenotype analysis, searches for human disease models, and hypothesis generation by providing access to spontaneous, induced, and genetically engineered mutations and their strain-specific phenotypes.

Proper citation: Phenotypes and Mutant Alleles (RRID:SCR_017523) Copy   

•   Source: SciCrunch Registry

http://www.cuilab.cn/transmir

Collection of transcription factor microRNA regulations. TransmiR v2.0 manually curated TF-miRNA regulations from publications during 2013-2017 and included ChIP-seq-derived TF-miRNA regulation data.

Proper citation: TransmiR (RRID:SCR_017499) Copy   

•   Source: SciCrunch Registry

https://jcr.clarivate.com/JCRLandingPageAction.action

Web tool with systematic, objective means to critically evaluate journals, with quantifiable, statistical information based on citation data. Provides information about academic journals in natural sciences and social sciences, including impact factors in database integrated with Web of Science. Sourced from Web of Science Core Collection,citation index on Web of Science platform.

Proper citation: Journal Citation Reports (RRID:SCR_017656) Copy   

•   Source: SciCrunch Registry

http://biocc.hrbmu.edu.cn/CellMarker/

Database provides cell markers for various cell types in tissues of human and mouse. Manually curated resource of cell markers in human and mouse. Provides user-friendly interface for browsing, searching and downloading markers of diverse cell types of different tissues. Summarized marker prevalence in each cell type is graphically presented., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: CellMarker (RRID:SCR_018503) Copy   

•   Source: SciCrunch Registry