pavlopouloslab/scala repository overview

Title: An interactive application for multimodal analysis of single cell next generation sequencing data

Overview:

Welcome to SCALA (v1.0)

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scRNA-seq data analysis:

• Seurat based standard analysis
  • QC
  • Normalization
  • Detection of highly variable genes
  • Dimensionality reduction
  • Clustering
  • Identification of marker genes
• Doublet detection (DoubletFinder)
• Cell cycle phase analysis (Seurat)
• Signature scoring (UCell)
• Automatic cluster annotation (CIPR)
• Functional enrichment analysis (gProfiler, Flame)
• Trajectory inference (slingshot)
• Ligand - Receptor analysis (NicheNetR)
• Gene Regulatory Network reconstruction (SCENIC, decoupleR + collecTRI)

scATAC-seq data analysis:

• ArchR based analysis
  • QC inspection
  • LSI
  • Dimensionality reduction
  • Clustering
  • Doublet detection
  • Inference of gene activity scores
  • Identification of marker genes
  • Identification of marker peaks
  • Motif enrichment analysis
  • Trajectory analysis
  • Integration with scRNA-seq data
  • GRNs
  • Visualization of tracks

Web Application: http://scala.fleming.gr/app/scala⁠

Code:https://github.com/PavlopoulosLab/SCALA⁠

Docker:https://hub.docker.com/r/pavlopouloslab/scala⁠

Please cite: ____________________________________________________________________________

https://doi.org/10.1016/j.csbj.2023.10.032⁠

How to run:

1. Pull the image to your machine:
2. docker pull pavlopouloslab/scala
3. Create a container for the image using a port of your choice, e.g. 3838:
4. docker run -p 3838:3838 -ti --rm pavlopouloslab/scala