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on page 1 showing 20 out of 557 results

    (at)Note

Cite this ((at)Note, RRID:SCR_005342)

URL: http://darwin.di.uminho.pt/anote2/wiki/index.php/Main_Page

Resource Type: Resource, software resource, software application, text-mining software

THIS RESOURCE IS NO LONGER AVAILABLE. Documented September 18, 2017. Text Mining platform that copes with major Information Retrieval and Information Extraction tasks and promotes multi-disciplinary research. It aims to provide support to three different usage roles: biologists, text miners and application developers. The workbench supports the retrieval, processing and annotation of documents as well as their analysis at different levels.

  • From Current Category

    3DBar

Cite this (3DBar, RRID:SCR_008896)

URL: http://www.3dbar.org

Resource Type: Resource, production service resource, analysis service resource, reference atlas, software resource, service resource, atlas, data or information resource

Software package for reconstructing three-dimensional models of brain structures from 2-D delineations using a customizable and reproducible workflow. 3dBAR also works as an on-line service (http://service.3dbar.org) offering a variety of functions for the hosted datasets: * downloading reconstructions of desired brain structures in predefined quality levels in various supported formats as well as created using customizable settings, * previewing models as bitmap thumbnails and (for webGL enabled browsers) interactive manipulation (zooming, rotating, etc.) of the structures, * downloading slides from available datasets as SVG drawings. 3dBAR service can also be used by other websites or applications to enhance their functionality. * Operating System: Linux * Programming Language: Python * Supported Data Format: NIfTI-1, Other Format, VRML

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    A5-miseq

Cite this (A5-miseq, RRID:SCR_012148)

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

Resource Type: Resource, software resource

Software that produces high quality microbial genome assemblies on a laptop computer without any parameter tuning. A5-miseq does this by automating the process of adapter trimming, quality filtering, error correction, contig and scaffold generation, and detection of misassemblies. Unlike the original A5 pipeline, A5-miseq can use long reads from the Illumina MiSeq, use read pairing information during contig generation, and includes several improvements to read trimming.

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    ABACUS

Cite this (ABACUS, RRID:SCR_013039)

URL: http://www.dei.unipd.it/~sambofra/abacus.html

Resource Type: Resource, software resource

An Algorithm based on a BivAriate CUmulative Statistic to identify SNPs significantly associated with a disease within predefined sets of SNPs such as pathways or genomic regions.

  • From Current Category

Cite this (AbMining ToolBox, RRID:SCR_000090)

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

Resource Type: Resource, software resource

Python scripts to analyze antibody libraries sequenced by next generation sequencing methods (454, Ion Torrent, MiSeq).

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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.

  • From Current Category

Cite this (ABS filter, RRID:SCR_005328)

URL: http://updepla1srv1.epfl.ch/waszaks/absfilter/

Resource Type: Resource, software resource

R package for identification and removal of low-complexity sites in allele-specific analysis of ChIP-seq data.

  • From Current Category

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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    ACID

Cite this (ACID, RRID:SCR_010470)

URL: http://www.diffusiontools.com/

Resource Type: Resource, software resource, software toolkit

Academic software toolkit for pre-processing of diffusion MRI data, estimation of DTI indices and spatially normalisation of DTI index maps, which fully integrates into the batch system of SPM8. These tools are made for users familiar with the underlying statistical, mathematical and image processing concepts. The ACID toolbox provides the option to write the estimated diffusion tensor in the format of the DTI and Fibertools Software Package.

  • From Current Category

    ACME

Cite this (ACME, RRID:SCR_001464)

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

Resource Type: Resource, software resource

A set of tools for analysing tiling array ChIP/chip, DNAse hypersensitivity, or other experiments that result in regions of the genome showing enrichment. It does not rely on a specific array technology (although the array should be a tiling array), is very general (can be applied in experiments resulting in regions of enrichment), and is very insensitive to array noise or normalization methods. It is also very fast and can be applied on whole-genome tiling array experiments quite easily with enough memory.

  • From Current Category

Cite this (ACT: Artemis Comparison Tool, RRID:SCR_004507)

URL: http://www.sanger.ac.uk/resources/software/act/

Resource Type: Resource, software resource

A free tool for displaying pairwise comparisons between two or more DNA sequences. It can be used to identify and analyze regions of similarity and difference between genomes and to explore conservation of synteny, in the context of the entire sequences and their annotation. It is based on the software for Artemis, the genome viewer and annotation tool. ACT runs on UNIX, GNU/Linux, Macintosh and MS Windows systems. It can read complete EMBL and GENBANK entries or sequences in FASTA or raw format. Other sequence features can be in EMBL, GENBANK or GFF format.

  • From Current Category

    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.

  • From Current Category

    ADJUST

Cite this (ADJUST, RRID:SCR_009526)

URL: http://www.unicog.org/pm/pmwiki.php/MEG/RemovingArtifactsWithADJUST

Resource Type: Resource, software resource

A completely automatic algorithm for artifact identification and removal in EEG data. ADJUST is based on Independent Component Analysis (ICA), a successful but unsupervised method for isolating artifacts from EEG recordings. ADJUST identifies artifacted ICA components by combining stereotyped artifact-specific spatial and temporal features. Features are optimised to capture blinks, eye movements and generic discontinuities. Once artifacted IC are identified, they can be simply removed from the data while leaving the activity due to neural sources almost unaffected.

  • From Current Category

    ADTEx

Cite this (ADTEx, RRID:SCR_012059)

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

Resource Type: Resource, software resource

A software tool for copy number variation (CNV) detection for whole-exome data from paired tumour/matched normal samples.

  • From Current Category

    AffyPipe

Cite this (AffyPipe, RRID:SCR_002032)

URL: https://github.com/nicolazzie/AffyPipe

Resource Type: Resource, software resource

An open-source software pipeline for Affymetrix Axiom genotyping workflow.

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    affyPLM

Cite this (affyPLM, RRID:SCR_001319)

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

Resource Type: Resource, software resource

Software for fitting probe-level models and tools using these models. Probe-level models (PLM) based quality assessment tools.

  • From Current Category

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.

  • From Current Category

    AHA

Cite this (AHA, RRID:SCR_012090)

URL: https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/AHA

Resource Type: Resource, software resource

Contigs from a draft assembly generated by a different assembler can be joined using PacBio long reads.

  • From Current Category

    AHEAD

Cite this (AHEAD, RRID:SCR_008890)

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

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

Open-source turnkey software for automatic hippocampus segmentation. Its primary use is for delineating hippocampus in T1-weighted MRI images. AHEAD is developed by Jung W. Suh, Hongzhi Wang, Sandhitsu Das, Brian Avants, Philip Cook, John Pluta and Paul Yushkevich, and colleagues at the Penn Image Computing and Science Laboratory (PICSL) at the University of Pennsylvania.

  • From Current Category

    ALCHEMY

Cite this (ALCHEMY, RRID:SCR_005761)

URL: http://alchemy.sourceforge.net/

Resource Type: Resource, software resource, source code

ALCHEMY is a genotype calling algorithm for Affymetrix and Illumina products which is not based on clustering methods. Features include explicit handling of reduced heterozygosity due to inbreeding and accurate results with small sample sizes. ALCHEMY is a method for automated calling of diploid genotypes from raw intensity data produced by various high-throughput multiplexed SNP genotyping methods. It has been developed for and tested on Affymetrix GeneChip Arrays, Illumina GoldenGate, and Illumina Infinium based assays. Primary motivations for ALCHEMY''s development was the lack of available genotype calling methods which can perform well in the absence of heterozygous samples (due to panels of inbred lines being genotyped) or provide accurate calls with small sample batches. ALCHEMY differs from other genotype calling methods in that genotype inference is based on a parametric Bayesian model of the raw intensity data rather than a generalized clustering approach and the model incorporates population genetic principles such as Hardy-Weinberg equilibrium adjusted for inbreeding levels. ALCHEMY can simultaneously estimate individual sample inbreeding coefficients from the data and use them to improve statistical inference of diploid genotypes at individual SNPs. The main documentation for ALCHEMY is maintained on the sourceforge-hosted MediaWiki system. Features * Population genetic model based SNP genotype calling * Simultaneous estimation of per-sample inbreeding coefficients, allele frequencies, and genotypes * Bayesian model provides posterior probabilities of genotype correctness as quality measures * Growing number of scripts and supporting programs for validation of genotypes against control data and output reformating needs * Multithreaded program for parallel execution on multi-CPU/core systems * Non-clustering based methods can handle small sample sets for empirical optimization of sample preparation techniques and accurate calling of SNPs missing genotype classes ALCHEMY is written in C and developed on the GNU/Linux platform. It should compile on any current GNU/Linux distribution with the development packages for the GNU Scientific Library (gsl) and other development packages for standard system libraries. It may also compile and run on Mac OS X if gsl is installed.

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