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https://github.com/cortex-lab/Kilosort

Software tool that implements an integrated template matching framework for detecting and clustering spikes from multi-channel electrophysiological recordings.

Proper citation: KiloSort (RRID:SCR_016422) Copy   

•   Source: SciCrunch Registry

http://starbase.sysu.edu.cn/index.php

Web based tool to visualize, analyze, discover and download of large-scale functional genomics data. Used for analysis of the CLIP-Seq and Degradome-Seq data sets, exploration of miRNA–target interactions and decoding RNA interaction networks from CLIP-Seq (HITS-CLIP, PAR-CLIP, iCLIP, CLASH) data. To show RNA-RNA and protein-RNA interaction networks in developmental, physiological and pathological processes.

Proper citation: Starbase V2.0 (RRID:SCR_016303) Copy   

•   Source: SciCrunch Registry

https://fractalis.lcsb.uni.lu/

Software as a scalable open-source service for platform-independent interactive visual analysis of biomedical data. It is a service and a library that work in tandem to equip existing platforms with visual analytical capabilities for explorative data analysis.

Proper citation: Fractalis (RRID:SCR_016362) Copy   

•   Source: SciCrunch Registry

https://github.com/lanagarmire/lilikoi

Software tool as an R package for personalized pathway-based classification modeling using metabolomics data. Provides personalized pathway deregulation measurements (PDS scores) and offers a standardized classification model for biomarker prediction.

Proper citation: lilikoi (RRID:SCR_016361) Copy   

•   Source: SciCrunch Registry

https://www.pbcconsortium.org/

Portal to provide a repository for beta-cell data, to connect researchers from different backgrounds interested in contributing data, models and/or ideas for new insights into beta-cell biology. Used to understand beta-cell biology and diabetes through a cross-disciplinary approach for the assembly of spatiotemporal multi-scale whole cell models of human pancreatic beta-cells.

Proper citation: The Pancreatic Beta-Cell Consortium (RRID:SCR_016328) Copy   

•   Source: SciCrunch Registry

http://fmri.uib.no/index.php?option=com_content&view=article&id=53&Itemid=78

Software package as a set of Matlab tools which allow the correction of fMRI-related gradient artifacts from EEG data. Designed to work within the EEGLAB environment, providing a GUI to remove fMRI gradient artifacts from the EEG. Can also be used from the Matlab command line, providing expert users with the ability to use them in custom scripts.

Proper citation: The Bergen fMRI Toolbox Plugin for EEGLab (RRID:SCR_016335) Copy   

•   Source: SciCrunch Registry

http://cole-trapnell-lab.github.io/monocle-release/docs/

Software package for analyzing single cell gene expression, classifying and counting cells, performing differential expression analysis between subpopulations of cells, and reconstructing cellular trajcectories. Works well with very large single-cell RNA-Seq experiments containing tens of thousands of cells or more. Used in computational analysis of gene expression data in single cell gene expression studies to profile transcriptional regulation in complex biological processes and highly heterogeneous cell populations.

Proper citation: Monocle2 (RRID:SCR_016339) Copy   

•   Source: SciCrunch Registry

https://github.com/KM-Lab/Electrographic-Seizure-Analyzer

Software to automate analysis of electrographic seizures based on EEG or LFP data, featuring customizable thresholds and parameters for event detection and parameter setting.

Proper citation: Electrographic Seizure Analyzer (RRID:SCR_016344) Copy   

•   Source: SciCrunch Registry

http://jvenn.toulouse.inra.fr/app/example.html

JavaScript plug-in software application for web environments to analyze data. It is an interactive Venn diagram viewer.Used for comparing lists with Venn Diagrams. It handles up to six input lists and presents results using classical or Edwards-Venn layouts. User interactions can be controlled and customized.

Proper citation: jVenn (RRID:SCR_016343) Copy   

•   Source: SciCrunch Registry

https://github.com/jkrijthe/Rtsne

Software as R wrapper for Van der Maaten's Barnes-Hut implementation of t-Distributed Stochastic Neighbor Embedding. Used for high-dimentional data visualisation.

Proper citation: Rtsne (RRID:SCR_016342) Copy   

•   Source: SciCrunch Registry

https://amp.pharm.mssm.edu/biojupies/

Software as an open source web server that automatically generates RNA-seq data analysis of jupyter notebooks. It allows creation and containment of documents that have live code, visualizations and narrative text.

Proper citation: BioJupies (RRID:SCR_016346) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/bioc/html/MAST.html

Software as an open source package for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data.

Proper citation: MAST (RRID:SCR_016340) Copy   

•   Source: SciCrunch Registry

https://redivis.com

Commercial collaborative research platform for hosting and analyzing datasets.Data platform for academic research. Redivis provides organizations with central hub where researchers can easily discover, access, and analyze their data.

Proper citation: Redivis (RRID:SCR_023111) Copy   

•   Source: SciCrunch Registry

https://californiacoastalatlas.net/

Resource designed to publish information and data about California coast reflecting current scientific understanding and data for the purpose of informing public policy and advancing the understanding of coastal processes.

Proper citation: California Coastal Atlas (RRID:SCR_024554) Copy   

•   Source: SciCrunch Registry

http://mouse.brain-map.org/static/atlas

Allen Mouse Brain Atlas includes full color, high resolution anatomic reference atlas accompanied by systematic, hierarchically organized taxonomy of mouse brain structures. Enables interactive online exploration of atlas and to provide deeper level of 3D annotation for informatics analysis and viewing in Brain Explorer 3D viewer.

Proper citation: Allen Mouse Brain Reference Atlas (RRID:SCR_002978) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/package=wavethresh

Software R package to perform 1, 2 and 3D real and complex-valued wavelet transforms, nondecimated transforms, wavelet packet transforms, nondecimated wavelet packet transforms, multiple wavelet transforms, complex-valued wavelet transforms, wavelet shrinkage for various kinds of data, locally stationary wavelet time series, nonstationary multiscale transfer function modeling, density estimation.

Proper citation: wavethresh (RRID:SCR_024311) Copy   

•   Source: SciCrunch Registry

http://pmap.burnham.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23, 2022. A database of proteolytic pathways. Its goal is to contribute to the scientific community and the understanding of proteolysis by providing better tools and data to researchers and medical researchers.

Proper citation: PMAP (RRID:SCR_000740) Copy   

•   Source: SciCrunch Registry

https://wiki.nci.nih.gov/display/cageneindex/Cancer+Gene+Index+End+User+Documentation

THIS RESOURCE IS NO LONGER IN SERVICE, documented on November 17, 2016. A database of genes that have been experimentally associated with human cancer diseases and/or pharmacological compounds, the evidence of these associations, and relevant annotations on the data.

Proper citation: Cancer Gene Index (RRID:SCR_001117) Copy   

•   Source: SciCrunch Registry

https://epd.expasy.org/epd/

EPDnew databases are the result of merging Eukaryotic Promoter Database, EPD, promoters within house analysis of promoter specific high throughput data for selected organisms only. EPDnew is a set of species specific databases of experimentally validated promoters.

Proper citation: EPDnew (RRID:SCR_002485) Copy   

•   Source: SciCrunch Registry

http://nirlweb.duhs.duke.edu/

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. Neuropsychiatric Imaging Research Laboratory (NIRL) analyze magnetic resonance images to research numerous psychiatric disorders including depression, bipolar disorder, and post traumatic stress disorder. NIRL also develop new methods for MR image processing to improve quality and reliability of research in the field of neuroimaging. The laboratory computer resources include Sun MicroSystems SPARC workstations, Windows PCs, over 3 terabytes of online hard disk space, and a web server system. The lab has a site filtered anonymous ftp server system for data transfer. There are individual offices for visiting fellows and analysts for image processing as well as shared work-study rooms and conference facilities.

Proper citation: Duke University Medical Center Neuropsychiatric Imaging Research Laboratory (RRID:SCR_007124) Copy   

•   Source: SciCrunch Registry