Curator Dashboard

The Black Dog Institute is dedicated to understanding, preventing and treating mental illness. We are about creating a world where mental illness is treated with the same level of concern, immediacy and seriousness as physical illness; where scientists work to discover the causes of illness and new treatments, and where discoveries are immediately put into practice through health services, technology and community education.

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• RRID-Legacy
• 9 years ago - by Anonymous

Disease portal for Hepatitis that provides information about causes, symptoms, treatments, and other characteristics of Hepatitis. This webpage is curated by Verywell, a health and wellness organization.

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• SciCrunch
• 9 years ago - submitted by Isabella Froman

Oncotopix Discovery is a comprehensive solution powered for whole slide image analysis of tissue sections, TMA slides across any image analysis application. Simple to program also for scientists without an IT background.

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• RRID-Legacy
• 9 years ago - by Anonymous

Implements an algorithm to conduct advanced gene set enrichment analysis on the results of genomics experiments. Simillion C, Liechti R, Lischer HE, Ioannidis V, Bruggmann R. Avoiding the pitfalls of gene set enrichment analysis with SetRank. BMC bioinformatics. 2017;18(1):151. doi: 10.1186/s12859-017-1571-6.

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• RRID-Legacy
• 9 years ago - by Anonymous

The main purpose of Cufflinks.cuffmerge is to merge together several Cufflinks assemblies, making it easier to produce an assembly GTF file suitable for use with Cufflinks.cuffdiff. Cufflinks.cuffmerge also runs Cuffcompare in the background and automatically filters out transcribed fragments (transfrags) that are likely to be artifacts. Trapnell C, Hendrickson D,Sauvageau S, Goff L, Rinn JL, Pachter L. Differential analysis of gene regulation at transcript resolution with RNA-seq. Nature Biotechnology. 2013;31:46-53.

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• RRID-Legacy
• 9 years ago - by Anonymous

Software package for differential gene expression analysis based on the negative binomial distribution. Used for analyzing RNA-seq data for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates.

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• RRID-Legacy
• 9 years ago - by Anonymous

Sequence analysis software for rt-qPCR analysis. It establishes standard curves, calculates delta delta Ct and automatically determines the ideal threshold setting for each run.

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• RRID-Legacy
• 9 years ago - submitted by Keiji Honda

Software toolkit for analyzing and visualizing data of single cell qPCR/RNA-seq. It offers methods for identifying gene expression and mutation patterns at the single-cell level and is designed for use with Biomark and C1 systems.

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• RRID-Legacy
• 9 years ago - submitted by Keiji Honda

A web interface for the scoring of biomedical digital objects by user evaluation according to the FAIR data principles: Findability, Accessibility, Interoperability, and Reusability. Prototype currently available at: http://amp.pharm.mssm.edu/fairshake

• SciCrunch
• 9 years ago - submitted by Anita Bandrowski

ARCHS4 provides access to gene counts from HiSeq 2000 and HiSeq 2500 platforms for human and mouse experiments from GEO and SRA. The website enables downloading of the data in H5 format for programmatic access as well as a 3-dimensional view of the sample and gene spaces. Search features allow browsing of the data by meta data annotation, ability to submit your own up and down gene sets, and explore matching samples enriched for annotated gene sets. Selected sample sets can be downloaded into a tab separated text file through auto-generated R scripts for further analysis. Reads are aligned with Kallisto using a custom cloud computing platform. Human samples are aligned against the GRCh38 human reference genome, and mouse samples against the GRCm38 mouse reference genome.

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• SciCrunch
• 9 years ago - submitted by Anita Bandrowski

Software tool for aggregation and analysis of gene expression signatures from related studies.Used to aggregate and analyze gene expression signatures extracted from GEO by crowd using GEO2Enrichr. Used to view aggregated report that provides global, interactive views, including enrichment analyses, for collections of signatures from multiple studies sharing biological theme.

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• SciCrunch
• 9 years ago - submitted by Anita Bandrowski

Clustergrammer is a web-based tool for visualizing and analyzing high-dimensional data as interactive and shareable hierarchically clustered heatmaps. Clustergrammer enables intuitive exploration of high-dimensional data and has several optional biology-specific features.

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• SciCrunch
• 9 years ago - submitted by Anita Bandrowski

Software resource that allows students or the general public find variants that may be significantly associated with some disease. CREEDS also visualizes and analyzes gene expression signatures.

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• dkNET
• 9 years ago - submitted by Anita Bandrowski

A biobank is a repository that stores and manages biological samples known as biospecimens for use in research. The Precision Medicine Initiative (PMI) Cohort Program biobank has been awarded to Mayo Clinic in Rochester, Minnesota. The biobank will support the collection, analyses, storage and distribution of biospecimens for research use. Data from laboratory analyses of biospecimens will be combined with an array of other lifestyle and health information provided by volunteers to help researchers continue to unravel individual differences that contribute to disease and response to treatments.

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• dkNET
• 9 years ago - submitted by Anita Bandrowski

This engine presents case-control association results from the UK Biobank hospital in-patient health-related outcomes summary information data (Data-Field 41202); computational grouping of phenotypes with cancer (Category 100092) registry, death registry data (Category 100093), algorithmically-defined outcomes (Category 42), and verbal questionnaire data (Category 100071); and manually curated grouping of phenotypes.

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• dkNET
• 9 years ago - submitted by Anita Bandrowski

Funding program for Precision Medicine genome sequencing from the National Institutes of Health, NHBLI.

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• dkNET
• 9 years ago - submitted by Anita Bandrowski

Consortium of researchers aiming to characterize the genetic basis of type 2 diabetes with a principal focus on samples of European descent. DIAGRAM also features a database of DIAGRAM publications and diabetes-related research data.

• dkNET
• 9 years ago - submitted by Anita Bandrowski

Collection of genome-wide transcriptional expression data from cultured human cells treated with bioactive small molecules and simple pattern-matching algorithms. camp aims to enable the discovery of functional connections between drugs, genes and diseases through the transitory feature of common gene-expression changes., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• RRID-Legacy
• 9 years ago - by Anonymous

Software for detection and reporting of spindle or slow oscillation events, simple automatic EMG artifacts, and their co-occurance or respective matching non-events. SpiSOP was designed to process large data quanta at once and multiple datasets in parallel.

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• RRID-Legacy
• 9 years ago - by Anonymous

MATLAB Toolbox for presenting stimuli and recording responses with precise timing. It also provides additional utilities for the manipulation of sound, keyboard, mouse, joystick, serial port, parallel port, subject responses and physiological monitoring hardware.

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• RRID-Legacy
• 9 years ago - by Anonymous