Detailed User Guide

Data Management

• Import Data
• Search for Data
• View Collection Details
• View Sample Details
• Annotate Samples
• View Data Object Details
• Manage Data

Data Analysis

• Run Bioinformatic Tools and Pipelines
• Pipelines Overview
• In Detail: CUT & RUN
• In Detail: General RNA-Seq analysis pipeline (STAR)
• In Detail: General RNA-Seq analysis pipeline (featureCounts)
• In Detail: General RNA-Seq analysis pipeline (Salmon)
• In Detail: General 3’ mRNA-Seq pipeline
• In Detail: CHIP-seq pipeline
• In Detail: ATAC-seq pipeline
• In Detail: WGBS pipeline
• In Detail: Variant Detection in Data Obtained with Swift Biosciences Kits

Data Visualization

• Visualize: Genome Browser
• Visualize: Sample Comparison
• Visualize: Gene Expression
• Visualize: Differential Expression
• Visualize: Heat Map
• Visualize: Pathway Analysis
• Sample Basket
• Gene Basket
• Gene Set Basket