Skip to content
/ scout Public

Tools for Single-Cell mRNA-seq (sc RNA-seq) Analysis

License

MIT license
0 stars 0 forks Branches Tags Activity
Star
Notifications You must be signed in to change notification settings

lutrarutra/scout

BranchesTags

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 

History

61 Commits
figures
figures
 
 
scout
scout
 
 
.gitignore
.gitignore
 
 
LICENSE
LICENSE
 
 
README.md
README.md
 
 
environment.yml
environment.yml
 
 
matplotlib.ipynb
matplotlib.ipynb
 
 
pipeline.ipynb
pipeline.ipynb
 
 
setup.py
setup.py
 
 

Repository files navigation

scout - reproducible single-cell data analysis with interactive visualisations.

scRNA-data is handled with ScanPy, plots made with Plotly.

Pipeline: Colab

Quality Control Violins

alt text

Mitochondrial Scatter Plot

alt text

Dispersion Plot

alt text

PCA Projection

alt text

PCA Correlation Circle

alt text

PCA Explained Correlation (w.r.t. categorical variables)

alt text

PCA Explained Variance

alt text

UMAP Projection

alt text

Trimap Projection

alt text

3D Projection (Looks better live)

alt text

DE Volcano

alt text

Heatmap

alt text

alt text

GSEA Volcano

alt text

Additional plots for Matplotlib (old stuff)

Volcano Plot

alt text

P-value & Marker Score Distributions

alt text

Marker Score

alt text

Clustered Heatmap i.e. Clustermap

alt text

GSEA Volcano

alt text

Sorted Heatmap

alt text

How to use?

  1. conda env create -f environment.yml
  2. conda activate scout
  3. pip install -e .
  4. import scout

About

Tools for Single-Cell mRNA-seq (sc RNA-seq) Analysis

Resources

Readme

License

MIT license
Activity

Stars

0 stars

Watchers

1 watching

Forks

0 forks
Report repository

Releases

No releases published

Packages

 
 
 

Languages