Learn how to analyze RNA-Seq & Single Cell data using Partek Flow bioinformatics software in this user training series.

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Partek Flow Basic Components (90 mins)
30 March, 1pm

  • How to transfer files to Flow server
  • Import data to a project: – fastq, bam, bcl, .txt, .h5, seurat object – GEO project, URL, Basespace
  • Sample attribute management
  • Project management: – Task log, sharing, task details – Project and data export – Importing and re-using pipelines
  • Library file management
  • Gene list management
  • Orphaned files cleaning

Bulk RNA-Seq Data Analysis (60 min)
1 April, 1pm

  • QA/QC
  • Trimming bases and filtering reads
  • Alignment
  • Quantification
  • Filtering features and normalization
  • Differential analysis
  • Alternative splicing detection
  • Biological interpretation
  • Data visualization: PCA scatterplot, volcano plot, heatmap, dot plot, chromosome view etc.

scRNA-Seq Data Analysis: Basic Functions for a Single Sample (60 mins)
6 April, 1pm

  • Single cell QA/QC – QC cells and filter – QC features and filter
  • Normalization methods
  • Dimension reduction methods- PCA, tSNE, UMAP
  • Clustering analysis- Graph-based clustering- K-means clustering
  • Cell type classification in Data Viewer
  • Visualization: scatterplot, violin plot
  • Trajectory analysis

scRNA-Seq Data Analysis: Advanced Functions for Multiple Samples (60 mins)
8 April, 1pm

  • Batch removal methods
  • Differential analysis
  • Sample composition analysis
  • Pseudo bulk analysis
  • Visualization: dot plot, box plot, violin plot, volcano plot, heatmap, bubble map, bar chart, pie chart
  • Spatial transcriptome
  • CITE-Seq data analysis