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on page 1 showing 20 out of 209 results

    Mfuzz

Cite this (Mfuzz, RRID:SCR_000523)

URL: http://mfuzz.sysbiolab.eu/

Resource Type: Resource, software resource

Software package for noise-robust soft clustering of gene expression time-series data (including a graphical user interface).

  • From Current Category

Cite this (Insight Segmentation and Registration Toolkit, RRID:SCR_001149)

URL: http://www.itk.org

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

Open-source software toolkit for performing registration and segmentation in 2, 3, and more dimensions. This extensive suite of software tools for image analysis, developed through extreme programming methodologies, employs leading-edge algorithms for registering and segmenting multidimensional data. ITK is implemented in C++. ITK is cross-platform, using the CMake build environment to manage the compilation process. In addition, an automated wrapping process generates interfaces between C++ and interpreted programming languages such as Tcl, Java, and Python (using CableSwig). This enables developers to create software using a variety of programming languages. ITK's C++ implementation style is referred to as generic programming (i.e., using templated code). Such C++ templating means that the code is highly efficient, and that many software problems are discovered at compile-time, rather than at run-time during program execution. Because ITK is an open-source project, developers from around the world can use, debug, maintain, and extend the software. ITK uses a model of software development referred to as extreme programming. Extreme programming collapses the usual software creation methodology into a simultaneous and iterative process of design-implement-test-release. The key features of extreme programming are communication and testing. Communication among the members of the ITK community is what helps manage the rapid evolution of the software. Testing is what keeps the software stable. In ITK, an extensive testing process (using Dart) is in place that measures the quality on a daily basis. The ITK Testing Dashboard is posted continuously reflecting the quality of the software.

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    OLIN

Cite this (OLIN, RRID:SCR_001304)

URL: http://itb.biologie.hu-berlin.de/~futschik/software/R/OLIN/index.html

Resource Type: Resource, software resource

Software functions for normalization of two-color microarrays by optimised local regression and for detection of artifacts in microarray data.

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    CYCLE

Cite this (CYCLE, RRID:SCR_001328)

URL: http://itb.biologie.hu-berlin.de/~futschik/software/R/cycle/index.html

Resource Type: Resource, software resource

Software package for the identification of periodically expressed genes using Fourier analysis and the statistical assessment of significance using different background models.

  • From Current Category

Cite this (InterMine, RRID:SCR_001772)

URL: http://intermine.github.io/intermine.org/

Resource Type: Resource, software resource

An open source data warehouse system built for the integration and analysis of complex biological data that enables the creation of biological databases accessed by sophisticated web query tools. Parsers are provided for integrating data from many common biological data sources and formats, and there is a framework for adding data. InterMine includes a user-friendly web interface that works "out of the box" and can be easily customized for specific needs, as well as a powerful, scriptable web-service API to allow programmatic access to data.

  • From Current Category

Cite this (flowPhyto, RRID:SCR_002183)

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

Resource Type: Resource, software resource

An R package that performs aggregate statistics on virtually unlimited collections of raw flow cytometry files and provides a memory efficient, parallelized solution for analyzing high-throughput flow cytometric data.

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    SumsDB

Cite this (SumsDB, RRID:SCR_002759)

URL: http://sumsdb.wustl.edu/sums/

Resource Type: Resource, data analysis service, database, analysis service resource, production service resource, service resource, storage service resource, atlas, image repository, data repository, data or information resource

THIS RESOURCE IS NO LONGER IN SERVICE, documented on May 11, 2016. Repository of brain-mapping data (surfaces and volumes; structural and functional data) derived from studies including fMRI and MRI from many laboratories, providing convenient access to a growing body of neuroimaging and related data. WebCaret is an online visualization tool for viewing SumsDB datasets. SumsDB includes: * data on cerebral cortex and cerebellar cortex * individual subject data and population data mapped to atlases * data from FreeSurfer and other brainmapping software besides Caret SumsDB provides multiple levels of data access and security: * Free (public) access (e.g., for data associated with published studies) * Data access restricted to collaborators in different laboratories * Owner-only access for work in progress Data can be downloaded from SumsDB as individual files or as bundles archived for offline visualization and analysis in Caret WebCaret provides online Caret-style visualization while circumventing software and data downloads. It is a server-side application running on a linux cluster at Washington University. WebCaret "scenes" facilitate rapid visualization of complex combinations of data Bi-directional links between online publications and WebCaret/SumsDB provide: * Links from figures in online journal article to corresponding scenes in WebCaret * Links from metadata in WebCaret directly to relevant online publications and figures

  • From Current Category

Cite this (NanoStriDE, RRID:SCR_003407)

URL: http://nanostride.soe.ucsc.edu/

Resource Type: Resource, source code, data analysis service, production service resource, analysis service resource, service resource, software resource

Web application that accepts the raw count data produced by the NanoString nCounter analysis system, normalizes it according to guidelines provided by NanoString Technologies, performs differential expression analysis on the normalized data, and provides a heatmap of the results from the differential expression analysis.

  • From Current Category

    CHAoS

Cite this (CHAoS, RRID:SCR_005174)

URL: http://www.well.ox.ac.uk/~kgaulton/chaos.shtml

Resource Type: Resource, software resource

A Perl-based system for annotation of variants identified in high-throughput sequencing experiments. Functionality includes annotation of variants with information relating to population genetics, known transcripts, positional records, and sequence motif-based prediction. In addition, annotated variants can be summarized and extracted to facilitate downstream analysis. There is also basic support for gene-based biological annotation, and eventually will include tools for variant and genotype analysis and visualization.

  • From Current Category

Cite this (Biopieces, RRID:SCR_005783)

URL: http://www.biopieces.org

Resource Type: Resource, software resource, source code, software toolkit

A collection of bioinformatics tools that can be pieced together in a very easy and flexible manner to perform both simple and complex tasks. The Biopieces work on a data stream in such a way that the data stream can be passed through several different Biopieces, each performing one specific task: modifying or adding records to the data stream, creating plots, or uploading data to databases and web services. The Biopieces are executed in a command line environment where the data stream is initialized by specific Biopieces which read data from files, databases, or web services, and output records to the data stream that is passed to downstream Biopieces until the data stream is terminated at the end of the analysis. The advantage of the Biopieces is that a user can easily solve simple and complex tasks without having any programming experience. Moreover, since the data format used to pass data between Biopieces is text based, different developers can quickly create new Biopieces in their favorite programming language - and all the Biopieces will maintain compatibility. Finally, templates exist for creating new Biopieces in Perl and Ruby. There are currently ~190 Biopieces (March 2014).

  • From Current Category

Cite this (Predictive Networks, RRID:SCR_006110)

URL: https://compbio.dfci.harvard.edu/predictivenetworks//

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

A flexible, open-source, web-based application and data services framework that enables the integration, navigation, visualization and analysis of gene interaction networks. The primary goal of PN is to allow biomedical researchers to evaluate experimentally derived gene lists in the context of large-scale gene interaction networks. The PN analytical pipeline involves two key steps. The first is the collection of a comprehensive set of known gene interactions derived from a variety of publicly available sources. The second is to use these ''known'' interactions together with gene expression data to infer robust gene networks. The regression-based network inference algorithm creates a graph of gene interactions in which cycles may be present (but no self-loops). Based on information-theoretic techniques, a causal gene interaction network is inferred from both prior knowledge (interactions extracted from biomedical literature and structured biological databases) and gene expression data. A prediction model is fitted for each gene, given its parents, enabling assessment of the predictive ability of the network model.

  • From Current Category

Cite this (BrainSuite, RRID:SCR_006623)

URL: http://users.loni.ucla.edu/~shattuck/brainsuite/

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

Suite of image analysis tools designed to process magnetic resonance images (MRI) of the human head. BrainSuite provides an automatic sequence to extract genus-zero cortical surface mesh models from the MRI. It also provides a set of viewing tools for exploring image and surface data. The latest release includes graphical user interface and command line versions of the tools. BrainSuite was specifically designed to guide its users through the process of cortical surface extraction. NITRC has written the software to require minimal user interaction and with the goal of completing the entire process of extracting a topologically spherical cortical surface from a raw MR volume within several minutes on a modern workstation. The individual components of BrainSuite may also be used for soft tissue, skull and scalp segmentation and for surface analysis and visualization. BrainSuite was written in Microsoft Visual C using the Microsoft Foundation Classes for its graphical user interface and the OpenGL library for rendering. BrainSuite runs under the Windows 2000 and Windows XP Professional operating systems. BrainSuite features include: * Sophisticated visualization tools, such as MRI visualization in 3 orthogonal views (either separately or in 3D view), and overlayed surface visualization of cortex, skull, and scalp * Cortical surface extraction, using a multi-stage user friendly approach. * Tools including brain surface extraction, bias field correction, voxel classification, cerebellum removal, and surface generation * Topological correction of cortical surfaces, which uses a graph-based approach to remove topological defects (handles and holes) and ensure a tessellation with spherical topology * Parameterization of generated cortical surfaces, minimizing a harmonic energy functional in the p-norm * Skull and scalp surface extraction

  • From Current Category

Cite this (CD-HIT-OTU, RRID:SCR_006983)

URL: http://weizhong-lab.ucsd.edu/cd-hit-otu/

Resource Type: Resource, software resource

Data analysis service and software program that perform Operantional Taxonomic Units (OTUs) finding. It uses a three-step clustering for identifying OTUs. The first-step clustering is raw read filtering and trimming. The second step is error-free reads picking.. At the last step, OTU clustering is done at different distanct cutoffs (0.01, 0.02, 0.03... 0.12).

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    TDARACNE

Cite this (TDARACNE, RRID:SCR_000498)

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

Resource Type: Resource, software resource

Software package to infer gene regulatory networks from time-series measurements. The algorithm is expected to be useful in reconstruction of small biological directed networks from time course data.

  • From Current Category

    DEMI

Cite this (DEMI, RRID:SCR_002291)

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

Resource Type: Resource, software resource

R package for estimating differential expression from multiple indicators that capitalizes on the high number of concurrent measurements. It extends to various experimental designs and target categories (transcripts, genes, genomic regions) as well as small sample sizes.

  • From Current Category

Cite this (GenomicRanges, RRID:SCR_000025)

URL: http://www.bioconductor.org/packages/2.13/bioc/html/GenomicRanges.html

Resource Type: Resource, software resource

Software package that defines general purpose containers for storing genomic intervals as well as more specialized containers for storing alignments against a reference genome.

  • From Current Category

    flowCL

Cite this (flowCL, RRID:SCR_000046)

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

Resource Type: Resource, software resource

Software for semantic labelling of flow cytometric cell populations.

  • From Current Category

    flowBin

Cite this (flowBin, RRID:SCR_000051)

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

Resource Type: Resource, software resource

A software package to combine flow cytometry data that has been multiplexed into multiple tubes with common markers between them. It establishes common bins across tubes in terms of the common markers, then determines expression within each tube for each bin in terms of the tube-specific markers.

  • From Current Category

    metaSeq

Cite this (metaSeq, RRID:SCR_000056)

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

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

Software package for meta-analysis of RNA-Seq count data in multiple studies. The probabilities by one-sided NOISeq are combined by Fisher's method or Stouffer's method.

  • From Current Category

Cite this (RmiR.Hs.miRNA, RRID:SCR_000101)

URL: http://www.bioconductor.org/packages/release/data/annotation/html/RmiR.Hs.miRNA.html

Resource Type: Resource, software resource

Software package for various databases of microRNA Targets.

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