Workflows

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Type: LONI Pipeline
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Workflow EMBOSS-Matcher Pipeline Workflow (1)

Created: 05/04/11 @ 21:34:49 | Last updated: 14/07/11 @ 01:52:02

Credits: User Pipeline

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This page contains a number of bioinformatics workflows based on the advanced EMBOSS informatics package. This page describes as Pipeline modules several bioinformatics tools from the EMBOSS suite and demonstrates the construction of a couple of integrated pipeline workflows (end-to-end bioinformatics solutions via the LONI Pipeline). Matcher finds the best local alignments between two sequences. It can be used to compare two sequences looking for local sequence similarities using a ri...

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Original Uploader

Workflow Automated Image Registration (1)

Created: 06/04/11 @ 00:35:21 | Last updated: 06/04/11 @ 00:35:26

Credits: User Pipeline

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This is a simple registration workflow. The structural MRI images are aligned to a standard brain image by using AIR registration tools. To build this workflow follow the steps mentioned on the following pages. URL: http://www.loni.ucla.edu/Software/AIR Try this Pipeline Workflow Now!

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Workflow First Level within subject fMRI processing (1)

Created: 06/04/11 @ 01:41:51 | Last updated: 14/07/11 @ 00:33:54

Credits: User Pipeline

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Overview - fMRI-FEAT workflow This is a simple with-in subject fMRI analysis workflow. It takes 3D fMRI images and structural images of a subject and performs FSLmerge, BET (if the data is not already skull stripped) and first level FEAT processing.   Problem addressed by this workflow FSLMerge, BET and FEAT first level analysis can be performed using this workflow on one or more subjects that require the same processing. The design FSF file is generate using the FSL FEAT inte...

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Workflow BayesAss+ estiamtion of populations migrat... (1)

Created: 08/03/12 @ 18:30:18

Credits: User Pipeline

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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BayesAss+ is a program that estimates recent migration rates between populations using MCMC. It also estimates each individual’s immigrant ancestry, the generation in which immigration occurred (i.e. the individual can be assigned as an immigrant from a specific population, a non-immigrant, or the offspring of an immigrant and a non-immigrant), the population (as opposed to the sample) allele frequencies, inbreeding (F) values within each population, and genotypes at any locus wit...

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Workflow PLINK Association workflow (1)

Created: 05/04/11 @ 21:57:41 | Last updated: 14/07/11 @ 01:00:17

Credits: User Pipeline

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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PLINK is an open-source genome association analysis (GWAS) suite of tools providing a range of basic, large-scale computationally-efficient analyses. PLINK may be used for analysis of genotype/phenotype data, but requires some outside data-preprocessing (e.g., study design and planning, generating genotype or CNV calls from raw data). Support for visualization, annotation and storage of results is provided via gPLINK and Haploview.   The PLINK Association workflow provides testi...

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Workflow Minimum Deformation Template (MDT) Atlasin... (1)

Created: 06/04/11 @ 00:51:59 | Last updated: 14/07/11 @ 00:56:12

Credits: User Pipeline

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This pipeline present the redesigned automated workflow for constructing the Minimum Distance Template (MDT) atlas for a given population, based on one specific image modality (e.g., sMRI). There will be two specific validation examples based on 100+ ICBM subjects: Quantitative: The ICBM data will be registered to the MDT, NRU and ICBM 462 atlases and mean displacement stats across all subjects will be reported for each voxel. The distributions of these mean displacement magnitud...

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Workflow BATWING (1)

Created: 25/08/11 @ 19:39:58 | Last updated: 25/08/11 @ 19:57:37

Credits: User Pipeline

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Batwing reads in multi-locus haplotype data, and model and prior distri- bution specifications, and uses a Markov chain Monte Carlo (MCMC) method based on coalescent theory to generate approximate random samples from the posterior distributions of parameters such as mutation rates, effective population sizes and growth rates, and times of population splitting events. It also generates approximate posterior samples of the entire genealogical tree underly- ing the sample, including the tree hei...

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Workflow Global Shape Analysis Workflow (1)

Created: 06/04/11 @ 00:18:59 | Last updated: 06/04/11 @ 00:19:03

Credits: User Pipeline

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow takes raw un-skull-stripped volumes in multiple groups/populations, or a Study-Design, and generates a scene file containing the models of the ROIs where the groups are different. It also reports the global 56 regional p-values. Problem addressed by this workflow   Identifying the group differences between 2 populations in the global shapes of 56 cortical and sub-cortical ROIs. This workflow also generates DX models of all 56 ROIs which can be viewed as a scene in Sh...

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Workflow Direct Hippocampal Mapping (1)

Created: 06/04/11 @ 01:35:39 | Last updated: 06/04/11 @ 01:35:45

Credits: User Pipeline

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Overview - Direct Hippo Mapping The workflow takes volumetric masks of hippocampi from two groups, generates surfaces from each mask, and maps these surfaces to a hippocampal atlas. It also computes thickness and displacement feature on the surfaces and evaluates the statistical significance of the differences between the two groups with respect to these measurements.   Problem addressed by this workflow Automatically establishing correspondences between points on hippocampal ...

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Original Uploader

Workflow Migrate Pipeline Workflow (1)

Created: 08/03/12 @ 18:15:30

Credits: User Pipeline

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Migrate estimates effective population sizes and past migration rates between n population assuming a migration matrix model with asymmetric migration rates and different subpopulation sizes. Migrate uses maximum likelihood or Bayesian inference to jointly estimate all parameters.     Workflow Usage & Specifications Migrate can use the following data types: •Sequence data using Felsenstein's 84 model with or without site rate variation, •Single nucleotide poly...

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