Suites of Bioinformatic Tools for Basic Scientists

 

SWAN Pathway Analysis

Pre-print of SWAN is available on bioRxiv. Overviews of concepts and math are available on YouTube.

Start Here: SWAN Data Groomer

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

SWAN Single Pathway Analysis

Deep-dive into interesting pathways with striking visual outputs from SWAN analysis
​

SWAN Pan-Pathway Analysis

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

SWAN TCGA CNAlysis Atlas

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

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

PCA Calculator
​and Plotter

Groups data in an unbiased manner based on principal components, a measure of data variation.

Two-Sample Statistics Calculator

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

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

FairSubset

  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.