Curator Dashboard

Software reproducible genomics analysis pipelines with GNU Guix. Used for analysis of RNA sequencing, chromatin immunoprecipitation sequencing, bisulfite-treated DNA sequencing, and single-cell resolution RNA sequencing. All pipelines process raw experimental data and generate reports containing publication-ready plots and figures, with interactive report elements and standard observables.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software package dedicated to phylogenetic sampling. Used to sample sequence alignment according to its corresponding phylogenetic tree.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software suite of tools to build and search generalized profiles.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software Python program to discover optimal partitioning schemes for DNA sequences.Used for simultaneously choosing partitioning schemes and models of molecular evolution for phylogenetic analyses of DNA, protein, and morphological data.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tool for multiple sequence alignment based on profile consistency. Used to construct multiple sequence alignment given set of protein sequences.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software interface for running PDB2PQR web service. Used to prepare structures for further calculations by reconstructing missing atoms, adding hydrogens, assigning atomic charges and radii from specified force fields, and generating PQR files.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software Java program for calculating patristic distances and graphically comparing the components of genetic change.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software to align the core genome of hundreds to thousands of bacterial genomes. Input can be both draft assemblies and finished genomes, and output includes variant (SNP) calls, core genome phylogeny and multi-alignments. Parsnp leverages contextual information provided by multi-alignments surrounding SNP sites for filtration/cleaning, in addition to existing tools for recombination detection/filtration and phylogenetic reconstruction.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software library provides suite of data structures, algorithms, and utilities for PacBio C++ applications.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software Python program to search for pathogen nucleic acid sequences in NGS datasets.Used for pathogen identification in metagenomic and clinical next generation sequencing samples.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software wrapper to speed up downloading process by dividing the work into multiple threads.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software miRSeq data alignment workflow. Used to integrate genetic information to assess the impact of variants on miRNA expression. Used for integrating genome wide genotype data into miRNA sequence alignment analysis.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Open source software network communication interface for image guided interventions.Provides plug-and-play unified real-time communications in operating rooms for image-guided interventions, where imagers, sensors, surgical robots,and computers from different vendors work cooperatively to ensure seamless data flow among those components and enable a closed loop process of planning, control, delivery, and feedback.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Open source software framework that includes the necessary building blocks for surgical simulations, such as native device support, haptic feedback, graphics, discrete collision detection and physics simulation. Developers can refactor the physics engine, swap models, ODE solvers, or linear system solvers.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software as neural network based method that focuses on identification of unstructured loops. Trained to distinguish between very long contiguous segments with non-regular secondary structure and well-folded proteins. Trained on predicted information rather than on experimental data.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Open source lightweight DICOM server for medical imaging.Vendor neutral archive to automate and optimize imaging flows. Can be extended with plugins that provide solutions for teleradiology, digital pathology, or enterprise ready databases.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Open source software for electronic health records and medical practice management solution.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tool for detecting natural selection and recombination in DNA or RNA sequences.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software to count cell colonies and other circular objects. Used to facilitate enumeration of colony forming unit.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software package for analysing NGS data in DNA metabarcoding context. Used to filter and edit sequences while taking into account taxonomic annotation to set up tailor-made analysis pipelines for broad range of DNA metabarcoding applications, including biodiversity surveys or diet analyses.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth