Curator Dashboard

Software R package for multiple imputation of missing data in multilevel modeling.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software R package for choosing univariate class intervals for mapping or other graphics purposes.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software drawing R package designed for Manhattan plot of genomic analysis.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tool for peptide retention time prediction using deep learning. Supports peptide retention prediction for tryptic peptides, MHC bound peptides and PTM peptides.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software R package to estimate genomic copy number profiles at average genomic resolution of 5 Mb from read depth in high throughput single cell RNA sequencing data.Used for inference of genomic copy number and subclonal structure of human tumors from high-throughput single cell RNAseq data.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software R package enables creation of Ridgeline plots in 'ggplot2'

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software R package implements generalized estimating equations for parameters in mean, scale, and correlation structures, through mean link, scale link, and correlation link. Can handle clustered categorical responses. Used for fitting marginal generalized linear models to clustered data.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software R package provides access to all of the capabilities of DAGitty web application for drawing and analysing Directed Acyclic Graphs within the R platform for statistical computing. Used for graphical analysis of structural causal models.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tool that offers analysis of CRISPR editing data. Used for inference of CRISPR edits from Sanger trace data.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software R package to estimate generalized additive mixed models.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Web application as E-value calculator that compute E-values for variety of outcome measures, including risk ratios, odds ratios, rate ratios, risk differences, hazard ratios, and standardized mean differences.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software pipeline for estimating species trees from multi copy gene trees.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software to automate repetitive analysis steps and is widely considered the industry standard for NCA, TK, and PK/PD modeling. Used as non-compartmental analysis (NCA), pharmacokinetic/pharmacodynamic (PK/PD), and toxicokinetic (TK) modeling tool.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software pipeline designed to enable rapid and intuitive interpretation of genome editing experiments. Used for analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Web server predicts functional impact of amino-acid substitutions in proteins, such as mutations discovered in cancer or missense polymorphisms. Functional impact is assessed based on evolutionary conservation of affected amino acid in protein homologs., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software package for simulation of multiple gene families evolving under incomplete lineage sorting, gene duplication and loss, horizontal gene transfer, all three potentially leading to species tree/gene tree discordance and gene conversion. Used for phylogenomic simulation of gene, locus, and species trees.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tool as computational predictor of mammalian m(6)A site. Used for prediction of mammalian N6-methyladenosine (m6A) sites based on sequence-derived features.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tool for analysis of short time series gene expression data. Java program for clustering, comparing, and visualizing short time series gene expression data from microarray experiments. Allows to identify significant temporal expression profiles and genes associated with these profiles and to compare behavior of these genes across multiple conditions. STEM is fully integrated with the Gene Ontology.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tool for acquisition and analysis, visualization and analysis of RI tomograms. Used to color code the image according to the refractive index and identify various types of quantitative data.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Open source, species and gene tree reconciliation software. Software integrated phylogenetic tool, from sequences to reconciliations. Used to correct, rearrange and reroot gene trees with regard to given species tree.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth