BOD2022 Workshop ScRNA - One cell at a time

A workshop to explore the current methods for processing and analysing scRNA-seq datasets. From the read count matrices to cell trajectories and other advanced insights.

Details

1h 30min duration K participants

Presenters

• Ana Luisa Falcão
• Diogo Macedo
• Mónica Fernandes

Curriculum

• Data Intake and Read Mapping
  • Cell Ranger Danger
• Preprocessing Read Counts
  • Quality Control
    • Count depth
    • Number of genes per barcode
  • Normalization
    • z-scores
  • Filtering
    • Highly expressed genes
  • Data Correction
    • Doublets prediction
    • Batch effect
  • Data Integration
• Analysing Read Counts
  • Visualization and Dimensionality Reduction
  • Clustering
    • Leiden Comunity
    • Inter group
    • Inter sample
  • Trajectory Inferance
    • DPT pseudeotime
  • Marker Genes
    • Dot Plot
    • Inter group
    • Inter sample

What to do before you join us

conda env create diodupmia/bodxi_scrna_workshop
source activate bodxi_scrna_workshop

conda env create -f bodxi_scrna_workshop.yml
source activate bodxi_scrna_workshop

Link for env

https://anaconda.org/diodupima/bodxi_scrna_workshop