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on page 1 showing 20 out of 211 results from 1 sources

Cite this (ABS: A Database of Annotated Regulatory Binding Sites From Orthologous Promoters, RRID:SCR_002276)

URL: http://genome.imim.es/datasets/abs2005/index.html

Resource Type: Resource, data or information resource, database

Public database of known binding sites identified in promoters of orthologous vertebrate genes that have been manually curated from bibliography. We have annotated 650 experimental binding sites from 68 transcription factors and 100 orthologous target genes in human, mouse, rat or chicken genome sequences. Computational predictions and promoter alignment information are also provided for each entry. For each gene, TFBSs conserved in orthologous sequences from at least two different species must be available. Promoter sequences as well as the original GenBank or RefSeq entries are additionally supplied in case of future identification conflicts. The final TSS annotation has been refined using the database dbTSS. Up to this release, 500 bps upstream the annotated transcription start site (TSS) according to REFSEQ annotations have been always extracted to form the collection of promoter sequences from human, mouse, rat and chicken. For each regulatory site, the position, the motif and the sequence in which the site is present are available in a simple format. Cross-references to EntrezGene, PubMed and RefSeq are also provided for each annotation. Apart from the experimental promoter annotations, predictions by popular collections of weight matrices are also provided for each promoter sequence. In addition, global and local alignments and graphical dotplots are also available.

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Cite this (AffyRNADegradation, RRID:SCR_000118)

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

Resource Type: Resource, software resource

Software package that helps with the assessment and correction of RNA degradation effects in Affymetrix 3' expression arrays. The parameter d gives a robust and accurate measure of RNA integrity. The correction removes the probe positional bias, and thus improves comparability of samples that are affected by RNA degradation.

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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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Cite this (Annotation Ontology, RRID:SCR_002862)

URL: http://code.google.com/p/annotation-ontology/

Resource Type: Resource, ontology, data or information resource, controlled vocabulary

A vocabulary for performing several types of annotation - comment, entities annotation (or semantic tags), textual annotation (classic tags), notes, examples, erratum... - on any kind of electronic document (text, images, audio, tables...) and document parts. AO is not providing any domain ontology but it is fostering the reuse of the existing ones for not breaking the principle of scalability of the Semantic Web.

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Cite this (ArrayExpress (R), RRID:SCR_000120)

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

Resource Type: Resource, software resource

Software to access the ArrayExpress Repository at EBI and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet

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Cite this (arrayMvout, RRID:SCR_001317)

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

Resource Type: Resource, software resource

Software package that supports the application of diverse quality metrics to AffyBatch instances, summarizing these metrics via PCA, and then performing parametric outlier detection on the PCs to identify aberrant arrays with a fixed Type I error rate.

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Cite this (ArrayPlex, RRID:SCR_000312)

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

Resource Type: Resource, software resource

An open source software that integrates various forms of microarray data from diverse annotation and primary data sources. This software provides a programmatic framework (API set) that will be used for collaborative development and deploys an easy to maintain client-server architecture.

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Cite this (ARRmNormalization, RRID:SCR_001292)

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

Resource Type: Resource, software resource

Software package to perform the Adaptive Robust Regression method (ARRm) for the normalization of methylation data from the Illumina Infinium HumanMethylation 450k assay.

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Cite this (Baby Brain Toolkit, RRID:SCR_009440)

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

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

Software toolkit developed for the fbrain project that consists of several image processing tools: image reconstruction, image denoising, image segmentation, tractography etc., for a better understanding of fetal brain development.

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Cite this (beadarray, RRID:SCR_001314)

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

Resource Type: Resource, software resource

Software package to read bead-level data (raw TIFFs and text files) output by BeadScan as well as bead-summary data from BeadStudio. Methods for quality assessment and low-level analysis are provided.

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Cite this (beadarraySNP, RRID:SCR_001281)

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

Resource Type: Resource, software resource

Software package for importing data from Illumina SNP experiments and performing copy number calculations and reports.

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Cite this (BeadDataPackR, RRID:SCR_001310)

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

Resource Type: Resource, software resource

Software that provides functionality for the compression and decompression of raw bead-level data from the Illumina BeadArray platform.

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    BEDTools

Cite this (BEDTools, RRID:SCR_006646)

URL: https://github.com/arq5x/bedtools2

Resource Type: Resource, software resource

A powerful toolset for genome arithmetic allowing one to address common genomics tasks such as finding feature overlaps and computing coverage. Bedtools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF. While each individual tool is designed to do a relatively simple task (e.g., intersect two interval files), quite sophisticated analyses can be conducted by combining multiple bedtools operations on the UNIX command line.

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Cite this (Biologic Stylus, RRID:SCR_002991)

URL: http://biologicstylus.sourceforge.net/

Resource Type: Resource, software resource, software application, simulation software, source code

Biologic Stylus is Biologic Institute's Stylus simulation software suite. Programming Language: C++, Python

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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).

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    BMIQ

Cite this (BMIQ, RRID:SCR_003446)

URL: https://code.google.com/p/bmiq/

Resource Type: Resource, software resource

Software using a beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data.

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    BRAIN

Cite this (BRAIN, RRID:SCR_003018)

URL: http://bioconductor.org/packages/release/bioc/html/BRAIN.html

Resource Type: Resource, software resource

Software package for calculating aggregated isotopic distribution and exact center-masses for chemical substances (in this version composed of C, H, N, O and S).

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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

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    breseq

Cite this (breseq, RRID:SCR_010810)

URL: https://code.google.com/p/breseq/

Resource Type: Resource, software resource

A computational pipeline for finding mutations relative to a reference sequence in short-read DNA re-sequencing data intended for haploid microbial genomes.

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Cite this (CAMERA - Collection of annotation related methods for mass spectrometry data, RRID:SCR_002466)

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

Resource Type: Resource, software resource

A Bioconductor package integrating algorithms to extract compound spectra, annotate isotope and adduct peaks, and propose the accurate compound mass even in highly complex data.

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