Description

Estimation and removal of cell free mRNA contamination in droplet based single cell RNA-seq data.

The filtered counts are preprocessed with Seurat (LogNormalize, PCA, kNN graph, clustering) to provide cluster assignments to SoupX, which then estimates per-cluster contamination and adjusts counts. The adjusted counts are written to the output H5AD as an ambient layer.

Input

Name
Description
Pattern

0 ()

1 ()

2 ()

npcs (integer)

Number of principal components for Seurat PCA (also controls FindNeighbors dims = 1:npcs).

cluster_algorithm (integer)

Seurat FindClusters algorithm identifier passed to FindClusters(algorithm = ...). Valid values:

  • 1: louvain
  • 2: louvain_multilevel
  • 3: slm
  • 4: leiden

Output

Name
Description
Pattern

0 ()

0 ()

Tools

soupx Documentation

Estimation and removal of cell free mRNA contamination in droplet based single cell RNA-seq data

https://github.com/constantAmateur/SoupXdoi: 10.1093/gigascience/giaa151License: MIT
Authors