Curator Dashboard

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.

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• SciCrunch
• 8 years ago - submitted by Edyta Vieth

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

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• 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.

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

A combined strategy to identify circular RNAs (circRNAs and ciRNAs) (Zhang et al., Complementary Sequence-Mediated Exon Circularization, Cell (2014), 159:134-147) ; CIRCexplorer is a combined strategy to identify junction reads from back spliced exons and intron lariats.; http://yanglab.github.io/CIRCexplorer/

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• SciCrunch
• 8 years ago - submitted by Edyta Vieth

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.

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• SciCrunch
• 8 years ago - submitted by Edyta Vieth

Software R package of multivariate methods for the exploration and integration of biological datasets with a focus on variable selection. Used to analyse data from high throughput sequencing technologies and spectral imaging., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 8 years ago - submitted by Edyta Vieth

Software R package for multivariate analysis and feature selection of omics data. Used for visualization, regression, classification, and feature selection of omics data where the number of variables exceeds the number of samples and with multicollinearity among variables.

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• SciCrunch
• 8 years ago - submitted by Edyta Vieth

Metal binding site validation server. Used for systematic inspection of the metal-binding architectures in macromolecular structures. The validation parameters that CMM examines cover the entire binding environment of the metal ion, including the position, charge and type of atoms and residues surrounding the metal.

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• SciCrunch
• 8 years ago - submitted by Edyta Vieth

Software interactive perl/tk application which can read common sequence alignment formats which the user can then alter, embellish, markup etc to produce the kind of sequence figure commonly found in biochemical articles. Extensible WYSIWYG protein sequence alignment editor for publication quality figures.

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• SciCrunch
• 8 years ago - submitted by Edyta Vieth

Collection of text files providing specific annotations for human single nucleotide polymorphisms (SNPs), namely whether they are predicted to abolish, create or change the affinity of one or several transcription factor (TF) binding sites. Used to investigate the molecular mechanisms underlying regulatory variation in the human genome. SNP2TFBS is also accessible over a web interface, enabling users to view the information provided for an individual SNP, to extract SNPs based on various search criteria, to annotate uploaded sets of SNPs or to display statistics about the frequencies of binding sites affected by selected SNPs.

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• dkNET
• 8 years ago - submitted by Maryann Martone

Software R package for statistical analysis and visualization of functional profiles for genes and gene clusters.

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• RRID-Legacy
• 8 years ago - by Anonymous

Software tool for analysis of RNA-Seq experiments for which transcript abundances have been quantified with kallisto. Used for the differential analysis of gene expression data that utilizes bootstrapping in conjunction with response error linear modeling to decouple biological variance from inferential variance.

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• RRID-Legacy
• 8 years ago - by Anonymous

Software package for interpreting gene expression data. Used for interpretation of a large-scale experiment by identifying pathways and processes.

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• SciCrunch
• 8 years ago - submitted by Edyta Vieth

Open source software suite environment for nonlinear statistical modeling enabling model development, numerical stability, computation, and accuracy parameter estimates. Language built around the AUTODIF Library, a C++ language extension which transparently implements reverse mode automatic differentiation.

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• SciCrunch
• 8 years ago - submitted by Edyta Vieth

Korea University is a private research university in Seoul, South Korea. Established in 1905, Korea University is one of the nation's oldest and most prominent institutions of higher education. The student body consists of over 20,000 undergraduate students and over 10,000 graduate students. Korea University consists of the Seoul Campus, Sejong Campus and three auxiliary hospitals (Anam Hospital, Guro Hospital, Ansan Hospital).

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• SciCrunch
• 8 years ago - submitted by Edyta Vieth

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 18,2023. Software package to capture, process, measure, analyze and share images and data.

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• RRID-Legacy
• 8 years ago - by Anonymous

Software package as a growth curve automatic processing pipeline in Matlab.

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• SciCrunch
• 8 years ago - submitted by Kang Kang