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on page 1 showing 20 out of 310 results from 1 sources

Cite this (3D Interactive Chemical Shift Imaging, RRID:SCR_002581)

URL: https://www.nitrc.org/projects/threedicsi/

Resource Type: Resource, software resource, software application, data processing software

A user-friendly and comprehensive software program for multi-dimensional CSI data visualization, spectral processing, localization, quantification and multi-variate analysis.

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Cite this (ABC (Atlas Based Classification), RRID:SCR_005981)

URL: http://www.nitrc.org/projects/abc

Resource Type: Resource, software resource, image analysis software, workflow software, data processing software, software application

A comprehensive processing pipeline developed and used at University of North Carolina and University of Utah for brain MRIs. The processing pipeline includes image registration, filtering, segmentation and inhomogeneity correction. The tool is cross-platform and can be run within 3D Slicer or as a stand-alone program. The image segmentation algorithm is based on the EMS software developed by Koen van Leemput.

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Cite this (aCGH.Spline, RRID:SCR_002927)

URL: http://cran.r-project.org/src/contrib/Archive/aCGH.Spline/

Resource Type: Resource, software resource

An R package for array comparative genomic hybridization (aCGH) dye bias normalization.

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    ADaCGH2

Cite this (ADaCGH2, RRID:SCR_001981)

URL: http://www.bioconductor.org/packages/release/bioc/html/ADaCGH2.html

Resource Type: Resource, software resource

Software for analysis and plotting of array comparative genomic hybridization (CGH) data. It allows usage of Circular Binary Segementation, wavelet-based smoothing (both as in Liu et al., and HaarSeg as in Ben-Yaacov and Eldar), HMM, BioHMM, GLAD, CGHseg. Most computations are parallelized (either via forking or with clusters, including MPI and sockets clusters) and use ff for storing data.

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    aLFQ

Cite this (aLFQ, RRID:SCR_005925)

URL: http://cran.r-project.org/web/packages/aLFQ/

Resource Type: Resource, software resource

An R-package for estimating absolute protein quantities from label-free liquid chromatography tandem mass spectrometry (LC-MS/MS) proteomics data. It supports the commonly used absolute label-free protein abundance estimation methods (TopN, iBAQ, APEX, NSAF and SCAMPI) for LC-MS/MS proteomics data, quantifying on either MS1-, MS2-levels or spectral counts together with validation algorithms to enable automated data analysis and error estimation. Specifically, they used Monte-carlo cross-validation and bootstrapping for model selection and imputation of proteome-wide absolute protein quantity estimation.

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    AliView

Cite this (AliView, RRID:SCR_002780)

URL: https://github.com/AliView

Resource Type: Resource, software resource

Software for aligning viewing and editing dna / aminiacid sequences, intuitive, fast and leightweight. It has been designed to meet the requirements of next generation sequencing era phylogenetic datasets.

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Cite this (AltAnalyze - Alternative Splicing Analysis Tool, RRID:SCR_002951)

URL: http://www.altanalyze.org/

Resource Type: Resource, software resource, software application

Software application for microarry, RNA-Seq and metabolomics analysis. For splicing sensitive platforms (RNA-Seq or Affymetrix Exon, Gene and Junction arrays), it will assess alternative exon (known and novel) expression along protein isoforms, domain composition and microRNA targeting. In addition to splicing-sensitive platforms, it provides comprehensive methods for the analysis of other data (RMA summarization, batch-effect removal, QC, statistics, annotation, clustering, network creation, lineage characterization, alternative exon visualization, gene-set enrichement and more). AltAnalyze can be run through an intuitive graphical user interface or command-line and requires no advanced knowledge of bioinformatics programs or scripting. Alternative regulated exons can be subsequently visualized in the context of proteins, domains and microRNA binding sites with the Cytoscape Plugin DomainGraph.

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    AmiGO

Cite this (AmiGO, RRID:SCR_002143)

URL: http://amigo.geneontology.org/

Resource Type: Resource, data analysis service, database, analysis service resource, software application, production service resource, service resource, software resource, data or information resource

Official Web-based tools for searching and browsing the Gene Ontology database, which consists of a controlled vocabulary of terms covering biological concepts, and a large number of genes or gene products whose attributes have been annotated using GO terms. It can be accessed online at the main installation or deployed locally. The Gene Ontology project is a major bioinformatics initiative with the aim of standardizing the representation of gene and gene product attributes across species and databases. AmiGO can be used to:
* search for a gene or gene product, or a list of gene or gene products, and view the GO term associations
* perform a sequence identity BLAST search and view the GO term associations for the genes or proteins returned
* search for GO terms and view the genes or gene products they are annotated to
* browse the GO ontology and view terms
* the slimmer tool can be used to map the granular annotations of the query set of genes to one or more high-level
* term enrichment tool is used to discover what a set of genes may have in common by examining annotations and finding significant shared GO terms.
* GOOSE is for advanced users who want to run custom SQL queries against the GO database.

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    AMILab

Cite this (AMILab, RRID:SCR_009525)

URL: http://amilab.org

Resource Type: Resource, software resource, software application, data processing software

An opensource software for image analysis, processing and visualization. It provides convenient visualization tools for 2D and 3D images and it is highly extensible through its own scripting language. At visualization level, AMILab includes a 2D/3D image viewer, a 3D polygon viewer based on OpenGL, a 2D Curve viewer to visualize 2D curves, histograms and color/opacity transfer functions, and a GPU-enabled raycasting script for Volume Rendering based on VTK. The software includes an automatic C++ wrapping system which permits fast development of new visualization tools and image processing algorithms. This wrapping system currently wraps about 200 classes from wxwidgets library and about 100 classes from VTK.

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    Amplicon

Cite this (Amplicon, RRID:SCR_003294)

URL: http://sourceforge.net/projects/amplicon/

Resource Type: Resource, software resource

Software tool for designing PCR primers on aligned groups of DNA sequences. The most important application is the design of "group-specific" PCR primer sets that amplify a DNA region from a given taxonomic group but do not amplify orthologous regions from other taxonomic groups. It is written in Python 2.3 and Tkinter 8.4. The current script was created for Windows and an executable is available. Future versions of the script should be able to run on Linux and Mac

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    Apollo

Cite this (Apollo, RRID:SCR_001936)

URL: http://gmod.org/wiki/Apollo

Resource Type: Resource, software resource, software application

A standalone Java application with a GUI (graphical user interface) for editing genome annotations. Like GBrowse, it allows users to scroll and zoom in on areas of interest in a sequence; authorized users can edit annotations and write the changes back to the underlying database. Apollo can run off GFF3 or a Chado database, and it can also integrate with remote services, such as BLAST and Primer BLAST analyses.

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Cite this (APSampler, RRID:SCR_000042)

URL: http://code.google.com/p/apsampler/

Resource Type: Resource, software resource

A software tool that allows multi-locus and multi-level association analysis of genotypic and phenotypic data.

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    AutoSeg

Cite this (AutoSeg, RRID:SCR_009438)

URL: http://www.nitrc.org/projects/autoseg/

Resource Type: Resource, software resource, image analysis software, data processing software, software application

A novel C++ based application developped at UNC-Chapel Hill that performs automatic brain tissue classification and structural segmentation. AutoSeg is designed for use with human and non-human primate pediatric, adolescent and adult data. AutoSeg uses a BatchMake pipeline script that includes the main steps of the framework entailing N4 bias field correction, rigid registration to a common coordinate image, tissue segmentation, skull-stripping, intensity rescaling, atlas-based registration, subcortical segmentation and lobar parcellation, regional cortical thickness and intensity statistics. AutoSeg allows efficient batch processing and grid computing to process large datasets and provides quality control visualizations via Slicer3 MRML scenes.

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    Babel

Cite this (Babel, RRID:SCR_004307)

URL: http://taylorlab.ucsf.edu/software_data.html

Resource Type: Resource, software resource, software application, data analysis software, data processing software

Software that implements babel routines for identifying unusual ribosome protected fragment counts given mRNA counts

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    BamView

Cite this (BamView, RRID:SCR_004207)

URL: http://bamview.sourceforge.net/

Resource Type: Resource, software resource, source code

A free interactive display of read alignments in BAM data files that can be launched with Java Web Start or downloaded. This interactive Java application for visualizing the large amounts of data stored for sequence reads which are aligned against a reference genome sequence can be used in a number of contexts including SNP calling and structural annotation. It has been integrated into Artemis so that the reads can be viewed in the context of the nucleotide sequence and genomic features. The source code is available as part of the Artemis code which can be downloaded from GitHub.

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Cite this (Basic4Cseq, RRID:SCR_002836)

URL: http://www.bioconductor.org/packages/release/bioc/html/Basic4Cseq.html

Resource Type: Resource, software resource

An R/Bioconductor package for basic filtering, analysis and subsequent near-cis visualization of 4C-seq data. Virtual fragment libraries can be created for any BSGenome package, and filter functions for both reads and fragments and basic quality controls are included. Fragment data in the vicinity of the experiment's viewpoint can be visualized as a coverage plot based on a running median approach and a multi-scale contact profile.

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Cite this (BD FACSDiva Software, RRID:SCR_001456)

URL: http://www.bdbiosciences.com/instruments/software/facsdiva/index.jsp

Resource Type: Resource, software resource, commercial organization

A collection of tools for flow cytometer and application setup, data acquisition, and data analysis that help streamline flow cytometry workflows. It provides features to help users integrate flow systems into new application areas, including index sorting for stem cell and single-cell applications, as well as automation protocols for high-throughput and robotic laboratories.

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    BEAT

Cite this (BEAT, RRID:SCR_002387)

URL: http://www.bioconductor.org/packages/devel/bioc/html/BEAT.html

Resource Type: Resource, software resource

Software that implements all bioinformatics steps required for the quantitative, high-resolution analysis of DNA methylation patterns from bisulfite sequencing data.

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    BiGGR

Cite this (BiGGR, RRID:SCR_002854)

URL: http://www.bioconductor.org/packages/release/bioc/html/BiGGR.html

Resource Type: Resource, software resource

Software package that provides an interface to simulate metabolic reconstruction from the BiGG database and other metabolic reconstruction databases. The package facilitates flux balance analysis (FBA) and the sampling of feasible flux distributions. Metabolic networks and estimated fluxes can be visualized with hypergraphs.

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Cite this (BioSig: An Imaging Bioinformatics System for Phenotypic Analysis, RRID:SCR_008428)

URL: http://biosig.sourceforge.net/

Resource Type: Resource, data processing software, software library, software application, software resource, software toolkit, image processing software

An open source software library for processing of electroencephalogram (EEG) and other biomedical signals like electroencephalogram (EEG), electrocorticogram (ECoG), electrocardiogram (ECG), electrooculogram (EOG), electromyogram (EMG), respiration, and so on. Biosig contains tools for quality control, artifact processing, time series analysis, feature extraction, classification and machine learning, and tools for statistical analysis. Many tools are able to handle data with missing values (statistics, time series analysis, machine learning). Another feature is that more then 40 different data formats are supported, and a number of converters for EEG,, ECG and polysomnography are provided. Biosig has been widely used for scientific research on EEG-based BraiN-Computer Interfaces (BCI), sleep research, and ECG and HRV analysis. It provides software interfaces several programming languages (C, C++, Matlab/Octave, Python), and it provides also an interactive viewing and scoring software for adding, and editing of annotations, markers and events.

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