The descriptions of the popular methods for scRNA-seq pipelines
| Task | Tool (language) | Year | Description |
|---|---|---|---|
| General scRNA-seq | Seurat (R) | 2015∼2023 | A popular R package for the preprocessing and explorative downstream analysis of single-cell RNA sequencing data. Commonly, it is used with a variety of R-based package |
| General scRNA-seq | Scanpy (Python) | 2018 | A popular Python package for the preprocessing and explorative downstream analysis of single-cell RNA sequencing data. Commonly, it is used with a variety of Python-based package |
| Empty-drop identification | EmptyDrops (R) | 2019 | It estimates the background levels of RNA present in empty droplets, then identifies droplets containing cell that significantly deviate from the background |
| Ambient RNA identification | DecontX (Python) | 2020 | It utilizes Bayesian method to estimate the percentage of contaminating transcripts from ambient RNA, then removing contaminated transcripts in each cell data |
| Doublet identification | DoubletFinder (R) Scrublet (Python) | 2019 2019 | Generate artificial doublets using a nearest-neighbor algorithm, then identifies the doublets that are similar to artificial doublets |
| Normalization | SCtransform (R) | 2019 | It utilizes regularized negative binomial regression, which represent normalized data value without affected by technical issues |
| Visualization | t-SNE (R, Python) UMAP (R, Python) | 2008 2018 | Both are unsupervised non-linear dimensionality reduction method for visualization. UMAP has been rapidly overtaking t-SNE due to its superior ability to preserve large-scale structures |
| Differential expression testing | ROTSvoom (R) D3E (Python) Limma-trend (R) Wilcoxon rank-sum (R, Python) | 2020 | They are famous packages for differential expression testing, which show good performance after prefiltering lowly expressed genes. Wilcoxon rank-sum test is most widely used option |
| Pseudotime | Monocle3 (R) scTEP (R) | 2019 2023 | Monocle3 is the most popular package for pseudotime while scTEP is the most recently developed package, which may show better accuracy |
Abbreviations: scRNA-seq, single-cell RNA-sequencing; t-SNE, t-distributed stochastic neighbor embedding; UMAP, uniform manifold approximation and projection; scTEP, single-cell data trajectory inference method using ensemble pseudotime.
