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Suites of Bioinformatic Tools for Basic Scientists

 

SWAN Pathway Analysis

Publication of SWAN is available on Pubmed, Nucleic Acids Research, and as a pre-print.
Overviews of concepts and math are available on YouTube. A printable manual is linked below.
Data usage disclaimer for SWAN: data entered into this system should be limited to public data
swan_manual.pdf
File Size: 1380 kb
File Type: pdf
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Start Here: SWAN Data Groomer

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Transform data output from vendors and core facilities into a format amenable to pathway analysis

SWAN Single Pathway Analysis

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Deep-dive into interesting pathways with striking visual outputs from SWAN analysis
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SWAN Pan-Pathway Analysis

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Central pathway analysis software: Shifted Weighted Annotation Network analysis. Performs automated analysis over a large number of pathways

SWAN TCGA CNAlysis Atlas

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Pan-pathway SWAN analysis results for TCGA cancer datasets, plus summary data for each cancer type

Simple Statistics Apps

Easy to use Apps to generate standard scientific statistics

Power Calculator

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Simple calculator to determine sample size or power, using t-test distribution.  Simulates data for verification.

PCA Calculator
​and Plotter
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Groups data in an unbiased manner based on principal components, a measure of data variation.

Two-Sample Statistics Calculator

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Compare two sets of data using t-test or Wilcoxon rank-sum (aka Mann-Whitney U test).  Graph the data along with p-value.

Other Published Apps

CAIRN
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 Navigate CNAs along specific loci or gene(s), using custom or TCGA data.
​See publication for more information.

FairSubset

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  Determines which consistent N subset of data retain the average and standard deviation of original data.  Helps with single-datum plots and replicate normalization. ​See publication for more information.

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