myExperiment - Content

LONI Pipeline

Uploader

Pipeline

Download

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...

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

Credits: Pipeline

LONI Pipeline

Uploader

Pipeline

Microsatellite-based Ancestry and Parentag... (1)

Download

GENEPOP is genetics software package that does the following types of analyses: Hardy Weinberg Exact Tests Linkage Disequilibrium Population Differentiation Nm estimates Basic Information, Fis and gene diversities Fst & other correlations File Conversion Additional Miscellaneous Utilities Problems addressed by this GENEPOP workflow This specific GENEPOP workflow computes the following: Testing : Hardy-W...

Created: 2011-04-05 | Last updated: 2011-07-14

Credits: Pipeline

LONI Pipeline

Uploader

Pipeline

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

Download

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

LONI Pipeline

Uploader

Pipeline

PLINK Association workflow (1)

Download

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...

Created: 2011-04-05 | Last updated: 2011-07-14

Credits: Pipeline

LONI Pipeline

Uploader

Pipeline

GWASS Impute (1)

Download

Genome-wide Association Study Software (GWASS) package provides genomics tools facilitating the analysis of genome-wide association studies. These tools were used in the design and analysis of the 7 genome-wide association studies carried out by the Wellcome Trust Case-Control Consortium (WTCCC) IMPUTE2 is a GWASS program for phasing observed genotypes and imputing missing genotypes. It includes basic and advanced functions. URL: http://www.loni.ucla.edu/twiki/bin/view/CCB/Pipe...

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

Credits: Pipeline

LONI Pipeline

Uploader

Pipeline

mrFAST Indexing and Mapping (1)

Download

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

LONI Pipeline

Uploader

Pipeline

EMBOSS-Matcher Pipeline Workflow (1)

Download

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...

Created: 2011-04-05 | Last updated: 2011-07-14

Credits: Pipeline

LONI Pipeline

Uploader

Pipeline

Bioinformatics BLAST processing Workflow (1)

Download

This is a simple workflow demonstrating a sequence Basic Local Alignment Search Tool (BLAST). This workflow shows an example of a common bioinformatics pipeline workflow using tools from several different institutions. This workflow starts by formatting the NCIBI/NCBI Escherichia coli (E. coli) database, creating a database-index table, using a FASTA query instructions to create a filtering file, and finally running miBLAST, an efficient Basic Local Alignment Search Tool (BLAST) for batc...