Curator Dashboard

Software for macromolecular model building, model completion and validation, and protein modelling using X-ray data. Coot displays maps and models and allows model manipulations such as idealization, rigid-body fitting, ligand search, Ramachandran plots, non-crystallographic symmetry and more. Source code is available.

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• SciCrunch
• 11 years ago - by Anonymous

Software genomic C++ library of reusable code for bioinformatics projects.Provides core collection of data structures, trying to avoid unnecessary code dependencies of other heavy libraries, while minimizing build time.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. Software tools for meta-analysis in the presence of hierarchical (and/or sampling) dependence, including with gene expression studies.

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• SciCrunch
• 13 years ago - by Anonymous

A package for statistical relative quantification of proteins and peptides in global, targeted, and data-independent proteomics. It handles shotgun, label-free, and label-based Selected Reaction Monitoring, as well as SWATH/DIA (Data Independent Acquisition) experiments. MSStats provide functionality for data processing and visualization, model-based statistical analysis, and model-based sample size calculations.

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• SciCrunch
• 11 years ago - submitted by James Go

Software tool as de novo assembler designed to assemble virus genomes that have no repeat sequences,using Illumina read pairs sequenced from mixed populations at extremely high and variable depth.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software package using Hidden Markov Models for characterizing chromosomal alterations in high throughput SNP arrays.

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• SciCrunch
• 13 years ago - by Anonymous

A study to determine whether vitamin D supplementation is safe and effective in delaying the onset of type 2 diabetes in people at risk for the disease and to gain a better understanding of how vitamin D affects glucose metabolism.

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• dkNET
• 11 years ago - submitted by Ko-Wei Lin

Software Perl wrapper for the Fast Artificial Neural Network library

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software package providing a general framework for the simulation of ChIP-seq data. Although currently focused on nucleosome positioning the package is designed to support different types of experiments.

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• SciCrunch
• 13 years ago - by Anonymous

Software used for detection of lesions in patients with multiple sclerosis. It provides an automated method for segmenting incident lesion voxels and allows for sensitive and specific detection of lesion incidence that can be applied to large collections of images. Using the explicit form of the statistical model, SuBLIME can be adapted to cases when more or fewer imaging sequences are available.

• RRID-Legacy
• 11 years ago - by Anonymous

Software Java library of data structures and algorithms.Provides some basic data structures and algorithms used by SplitsTree, Dendroscope and MEGAN.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Light-weight software package for normalization and visualization of microarray data using only basic R data types. Software can be used standalone, be utilized in other packages, or be wrapped up in higher-level classes.

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• SciCrunch
• 13 years ago - by Anonymous

A program for cluster analysis by fitting a mixture of Gaussians. KlustaKwik works by implementing a hard EM algorithm with unconstrained covariance matrices. It was designed for the specific problem of spike sorting of multi-electrode arrays, but can be used for any application.

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• RRID-Legacy
• 11 years ago - submitted by Jessica Cabotaje

Functions available from this module select the top n elements from a list using several common orderings and custom key extraction procedures.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software package that implements the Bayesian Estimation of Temporal Regulation algorithm to identify differentially expressed genes in microarray time-course data.

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• SciCrunch
• 13 years ago - by Anonymous

A data analysis pipeline for the Methyl-MAPS method.

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• SciCrunch
• 13 years ago - by Anonymous

Software high performance reflective language and system supporting both equational and rewriting logic specification and programming for wide range of applications.Supports equational specification and programming, rewriting logic computation.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

A multivariate quality assessment software for microarrays based on quality control (QC) reports. The Mahalanobis distance of an array's quality attributes is used to measure the similarity of the quality of that array against the quality of the other arrays. Then, arrays with unusually high distances can be flagged as potentially low-quality.

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• SciCrunch
• 13 years ago - by Anonymous

A community encyclopaedia that links brain research concepts with data, models and literature from around the world. It is an open project where users can participate and contribute to the global research community.

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• NIF
• 11 years ago - submitted by Maryann Martone

Software basecaller for Oxford Nanopore Technologies sequencing data. Oxford Nanopore Basecaller.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth