Curator Dashboard

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

Software DICOM library which provides user-friendly C++11 and Python API for different parts of the DICOM standard.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Online predictor of NOn-Regular Secondary Structure for disordered regions in protein. Used to predict long regions with no regular secondary structure. Upon user submission of protein sequence, NORSp will analyse the protein about its secondary structure, and presence of transmembrane helices and coiled-coil then return e-mail to user about the presence and position of disordered regions.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tool as alignment program for protein sequence-to-sequence alignments based on the standard Needleman-Wunsch dynamic programming algorithm.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tool as tree drawing program to draw any phylogenetic tree expressed in Newick phylogenetic tree format (e.g., the format used by the PHYLIP package).Used for rooting the unrooted trees obtained from parsimony, distance or maximum likelihood tree-building methods.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software provides access to NCBI's suite of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from Unix terminal window. Search terms are entered as command-line arguments. Individual operations are connected with Unix pipes to construct multi-step queries. Selected records can then be retrieved in variety of formats.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software workflow manager that enables development of portable and reproducible workflows.Supports deploying workflows on variety of execution platforms including local, HPC schedulers, AWS Batch, Google Cloud Life Sciences, and Kubernetes. Provides support to manage workflow dependencies through built-in support for Conda, Spack, Docker, Podman, Singularity, Modules, and more.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software tool for automated structrual variation detection from long-read sequencing using state-of-the-art tools. NextSV3 uses Minimap2 to do read mapping and uses two state-of-the-art SV callers (Sniffles and cuteSV) to do SV calling.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software alignment program that can align pairs of sequences using logarithmic and affine gap penalties.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth