| Software | SOURCE | IDENTIFIER |
|---|---|---|
| annadata | pypi | https://github.com/theislab/anndata |
| CellRanger v6.1.1 | 10x Genomics | http://10xgenomics.com |
| ggplot | bioconductor | https://ggplot2.tidyverse.org |
| ggpubr | bioconductor | https://github.com/kassambara/ggpubr |
| gseapy-0.10.7 | pypi | https://pypi.org/project/gseapy |
| harmonypy | pypi | https://github.com/slowkow/harmonypy |
| kallistobustools-0.24.4 | pypi |
https://github.com/pachterlab/kb_python
Modular, efficient and constant-memory single-cell RNA-seq preprocessing. Nat Biotechnol 39, 813–818 (2021). |
| scanpy v1.7.2 | bioconda | https://github.com/theislab/scanpy |
| scirpy v0.7.0 | bioconda | https://github.com/icbi-lab/scirpy |
| scrublet v0.2.3 | pypi | https://github.com/swolock/scrublet |
| statannot | pypi | https://pypi.org/project/statannot |
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