Curator Dashboard

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

Software package for analysis of geometrical and topological properties of periodic structures including crystals, networks, tilings.ToposPro was tailored to process large samples of crystallographic data and to find correlations between structure parameters.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software free desktop Windows application for the management and analysis of microbiology laboratory data with a particular focus on antimicrobial resistance surveillance developed and supported by the WHO Collaborating Centre for Surveillance of Antimicrobial Resistance at the Brigham and Women's Hospital in Boston, Massachusetts. WHONET, available in 44 languages, supports local, national, regional, and global surveillance efforts in over 2,300 hospital, public health, animal health, and food laboratories in over 130 countries worldwide.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software versatile open source tool for metagenomics. Used for processing and preparing metagenomics, genomics and population genomics nucleotide sequence data.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tool to process micrograph images for particle size.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software R package that examines the role of unmeasured confounding in mediation analysis allowing for normally distributed or Bernoulli distributed exposures, outcomes, mediators, measured confounders, and unmeasured confounders. Umediation also accommodates multiple measured confounders, multiple unmeasured confounders, and allows for mediator exposure interaction on the outcome. Enables to simulate unmeasured confounding in mediation analysis in order to see how the results of the mediation analysis would change in the presence of unmeasured confounding.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Instrument control and data acquisition software for Agilent Seahorse XFe96 and XFe24 analyzers with Windows 10 64-bit OS only. Experiment design, instrument control, data analysis, and file management software. Software provides intuitive interface with predefined assay templates and streamlined experimental design for simplified metabolic analysis.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Scientific image acquisition software. Software allows color and monochrome cameras to capture high quality images and videos from their microscope or lens system.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tool for image acquisition.Supports ProgRes microscope cameras and delivers optimal image quality and reproducible results.Included with all of Jenoptik ProgRes microscope cameras.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software for analysing complex statistical models using Markov chain Monte Carlo methods.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tool to simultaneously build gene and species trees when gene families have undergone duplications and losses. Can analyze thousands of gene families in dozens of genomes simultaneously.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software package provides functions for finding parameters that minimize or maximize objectives while satisfying constraints. Toolbox includes solvers for linear programming, mixed integer linear programming, quadratic programming, second order cone programming, nonlinear programming, constrained linear least squares, nonlinear least squares, nonlinear equations.

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