Statistics

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Intro to Data Mining

Very useful flowchart of how to handle different Exploratory Data Analysis

Network Analysis & Annotation

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NetworkAnalyst.ca

A dynamic network analysis website for gene, expression and multi-experiment meta-analysis.
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g:Profiler

A bioinformatics toolkit for characterizing gene lists from high-throughput genomic data
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DAVID

One of the most popular and free pathway and network analysis website.

Misc

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OMIC tools

Workflow for genomic, transcriptomic, proteomic, and metabolic data analysis