Curator Dashboard

International project to analyze mouse and human hematopoiesis, and provide a tractable system with clear clinical significance and importance to NIDDK. Collection of information from the flood of epigenomic data on hematopoietic cells as catalogs of validated regulatory modules, quantitative models for gene regulation, and a guide for translation of research insights from mouse to human.

• Resource
• dkNET
• 8 years ago - submitted by Ko-Wei Lin

Project to ethically obtain and evaluate human kidney biopsies from participants with Acute Kidney Injury (AKI) or Chronic Kidney Disease (CKD), create a kidney tissue atlas, define disease subgroups, and identify critical cells, pathways, and targets for novel therapies. Used to develop the next generation of software tools to visualize and understand the various components of kidney diseases and to optimize data collection. Multi site collaboration comprised of patients, clinicians, and investigators from across the United States.

• Resource
• dkNET
• 8 years ago - submitted by Ko-Wei Lin

Software tool as clustering method designed for high dimensional single cell data. Algorithmically defines phenotypes in high dimensional single cell data. Used for large scale analysis of single cell heterogeneity.

• Resource
• SciCrunch
• 8 years ago - submitted by Edyta Vieth

Software tool for simulating the mucosal immune responses to Helicobacter pylori infection in stomach.

• Resource
• SciCrunch
• 8 years ago - submitted by Josep Bassaganya-Riera

Software as a cross platform gene expression visualization tool. Extensible viewer for microarray data in the PCL or CDT format. Interactive display of clustered gene expression data. Java application for visualizing large data matrices. It can load a dataset, cluster it, browse it, customize its appearance and export it into a figure.

• Resource
• SciCrunch
• 8 years ago - submitted by Edyta Vieth

Software tool to identify metagenomic sequences of phages, chromosomes or plasmids. Used for identifying phages and plasmids from metagenomic fragments using deep learning., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

• Resource
• SciCrunch
• 8 years ago - submitted by Zhencheng Fang

Software Python package for neuroimaging data. Framework to design and train neural network architectures. Used in medical imaging community to ensure consistent performance of networks across variable users, institutions, and scanners.

• Resource
• RRID-Legacy
• 8 years ago - submitted by Andrew Beers

Web tool for gene expression profiling, meta-analysis and systems understanding. Used for statistical, visual and network-based meta-analysis of gene expression data.

• Resource
• RRID-Legacy
• 8 years ago - by Anonymous

Software application for matching a single candidate protein sequence and its modifications against a set of mass spectrometric observations. Used to analyze top-down mass spectrometry data.

• Resource
• SciCrunch
• 8 years ago - submitted by Paul Thomas

Organization dedicated to analysis of protein molecules by mass spectrometry, with a focus on intact protein measurements. Biomedical projects originated from clinical and basic research programs that utilize both targeted and untargeted analyses. Used for the development of new technology, training and dissemination of proteomics methods to laboratories and scientists.

• Organization
• SciCrunch
• 8 years ago - submitted by Paul Thomas

Molecular computing based on XNA-built alphabets.

• Resource
• RRID-Legacy
• 8 years ago - submitted by Oleg Gradov

Software tool to analyze Flow or mass cytometry data using a Self-Organizing Map. Used to obtain an overview of how all markers are behaving on all cells, and to detect subsets that might be missed otherwise.

• Resource
• SciCrunch
• 8 years ago - submitted by Edyta Vieth

Software for burst analysis of freely diffusing single-molecule Förster Resonance Energy Transfer (smFRET) experiments to study cellular processes at the molecular scale. Used for single and multi-spot single-molecule FRET (smFRET) data.

• Resource
• SciCrunch
• 8 years ago - submitted by Edyta Vieth

Software tool for automated processing, analysis, and visualization of data acquired by single molecule localization microscopy methods such as PALM and STORM. ImageJ interactive and modular plugin for SMLM data analysis and super-resolution imaging.

• Resource
• SciCrunch
• 8 years ago - submitted by Edyta Vieth

Software tools for analyzing co-localization single-molecule spectroscopy image data.

• Resource
• RRID-Legacy
• 8 years ago - by Anonymous

Matlab based scripts for load, save, make, reslice, view and edit both Neuroimaging Informatics Technology Initiative (NIfTI) and ANALYZE data on any platform.

• Resource
• SciCrunch
• 8 years ago - submitted by Ka Tsun Ng

Software tool as a combined strategy to identify junction reads from back spliced exons and intron lariats. Computational pipeline to precisely identify junction reads from Circularized Exons. Used to identify circular RNAs (circRNAs and ciRNAs).

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• SciCrunch
• 8 years ago - submitted by Edyta Vieth

Software tool for single molecule Molecular Inversion Probes data analysis. This is a stand-alone perl script. Except that this is dependent on the samtools, no installation required.

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• SciCrunch
• 8 years ago - submitted by Edyta Vieth

Software customizable toolbox for parameter estimation in MathWorks MATLAB. Offers scalable algorithms for optimization, uncertainty and identifiability analysis which do not depend on any problem-specific assumptions.

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• SciCrunch
• 8 years ago - submitted by Edyta Vieth

Web tool for CRISPR/Cas9 target prediction. Identifies and ranks all candidate sgRNA target sites according to their off-target quality and displays full documentation.

• Resource
• SciCrunch
• 8 years ago - submitted by Edyta Vieth