Workflows

[untitled] (1)

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This workflow allows the user to search for processes that are involved with a certain gene. Using microarray-files (CEL-files), consisting of wild type and KO mice to which a stimulant is induced, the user can get an idea of the processes involved. (This is done using the global test and the literature weighted global test.) The results are then given as a text-file. Warning: workflow is not working (needs some revisions), all input is currently hardcoded! (You will have to change the file...

Created: 2011-04-26 | Last updated: 2011-04-26

Credits: Dennis Leenheer

Direct Hippocampal Mapping (1)

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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 ...

Created: 2011-04-06 | Last updated: 2011-04-06

Credits: Pipeline

Integrated Mapping and Assembly with Quali... (1)

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This workflow contains the first step of a genomics data analysis protocol designed and implemented by Federica Torri, Fabio Macciardi and Ivo Dinov to process large number of sequence data outputted by the Illumina sequencing pipeline. See Step II analysis (GATK/QC/Cleaning) here. This protocol is implemented using the LONI Pipeline environment and includes the following types of computational resources: Mapping and Assembly with Qualities (MAQ) Sequence Alignment and Mapping t...

Created: 2011-04-05 | Last updated: 2011-04-05

Credits: Pipeline

mrFAST Indexing and Mapping (1)

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This page contains a number of bioinformatics workflows based on the mrFAST sequence analysis package. This page describes Pipeline bioinformatics modules from the mrFAST suite.   mrFAST (micro-read Fast Alignment Search Tool) is mapper designed to map short reads to reference genome with a special emphasis on the discovery of structural variation and segmental duplications. mrFAST maps short reads with respect to user defined error threshold, including indels up to 6 bp. This manu...

Created: 2011-04-05 | Last updated: 2011-04-05

Credits: Pipeline