Curator Dashboard

Software tool for species tree reconstruction from multi-copy gene family trees.Used for estimating unrooted species tree given set of unrooted gene trees and is statistically consistent under the multi-species coalescent model. ASTRAL-pro extends ASTRAL to allow multi-copy genes. ASTRAL-Pro 2, ultrafast and memory efficient version of ASTRAL-Pro that adopts placement based optimization algorithm for significantly better scalability without sacrificing accuracy.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software R package offers multitude of analysis and visualization modules that are commonly used in cancer genomic studies, including driver gene identification, pathway, signature, enrichment, and association analyses. Maftools requires somatic variants in Mutation Annotation Format (MAF) and is independent of larger alignment files.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Web server for the global and local quality estimation of 3D protein models

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tool for accurate prediction of contacts and long range hydrogen bonding in proteins.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

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