Table 4 Cell-agreement matrix (C) of each method compared to RainDrop for different datasets. Datasets are ordered by genome and size. Columns of the matrices show the average value of genes present (left) or absent (right) in cells calculated by RainDrop. Rows show the average gene count present (top) or absent (bottom) in cells calculated by CellRanger (Alevin)
From: RainDrop: Rapid activation matrix computation for droplet-based single-cell RNA-seq reads
Method | \(C_{neurons\_900}\) | \(C_{neuron\_9k}\) | \(C_{t\_4k}\) | Cpbmc8k |
|---|---|---|---|---|
Alevin | \(\left [\begin {array}{ll}2197&56 \\ 12&28788\end {array}\right ]\) | \(\left [\begin {array}{ll}2151&42 \\ 15&28846\end {array}\right ]\) | \(\left [\begin {array}{ll}965&39 \\ 6&32528\end {array}\right ]\) | \(\left [\begin {array}{ll}1321&60 \\ 6&32151\end {array}\right ]\) |
CellRanger | \(\left [\begin {array}{ll}2205&31 \\ 14&28802\end {array}\right ]\) | \(\left [\begin {array}{ll}2160&21 \\ 15&28856\end {array}\right ]\) | \(\left [\begin {array}{ll}937&5 \\ 8&32588\end {array}\right ]\) | \(\left [\begin {array}{ll}1281&6 \\ 10&32240\end {array}\right ]\) |
Reference used | mm10-3.0.0 | mm10-3.0.0 | GRCh38-3.0.0 | GRCh38-3.0.0 |