pertpy

DecontX — R/Bioconductor method in the celda package for estimating and removing ambient RNA contamination from droplet-based single-cell RNA-seq data. Uses a Bayesian Dirichlet mixture model over cel

1 shared topic • 1 shared operation

scater — Bioconductor single-cell RNA-seq QC and visualization toolkit built on SingleCellExperiment. Use when user needs per-cell QC metrics with addPerCellQCMetrics, adaptive MAD-based outlier detec

1 shared topic • 1 shared operation

scDblFinder — Bioconductor R package for detecting doublets in single-cell RNA-seq data using simulation-based classification with gradient boosting. Identifies neotypic and heterotypic doublets in dr

1 shared topic • 1 shared operation

Seurat — comprehensive R toolkit for single-cell genomics enabling QC, normalization (LogNormalize, SCTransform), feature selection, dimensionality reduction (PCA, UMAP, t-SNE), graph-based clustering

1 shared topic • 1 shared operation

Signac — R toolkit for single-cell chromatin accessibility analysis built on Seurat. Processes scATAC-seq data from 10x Genomics and other platforms. Handles fragment files, performs TF-IDF normalizat

1 shared topic • 1 shared operation