Single-cell analysis
Bioconductor branch, http://bioconductor.org/packages/release/BiocViews.html#___SingleCell.
Abdelaal et al. A comparison of automatic cell identification methods for single-cell RNA sequencing data. Genome Biology (2019) 20:194, https://doi.org/10.1186/s13059-019-1795-z
Single cell RNA-seq data analysis bundle.
Popescu D-M et al. Decoding human fetal liver haematopoiesis. Nature https://doi.org/10.1038/s41586-019-1652-y.
BayesPrism
GitHub, https://github.com/Danko-Lab/BayesPrism
Chu, T., Wang, Z., Pe’er, D. & Danko, C.G. Cell type and gene expression deconvolution with BayesPrism enables Bayesian integrative analysis across bulk and single-cell RNA sequencing in oncology. Nature Cancer 3, 505-517 (2022).
CReSCENT
Fullname: CanceR Single Cell ExpressioN Toolkit
Availability: https://crescent.cloud/
Mohanraj, S., et al. (2020). "CReSCENT: CanceR Single Cell ExpressioN Toolkit." Nucleic Acids Research.
cytoSCAPE
GitHub: https://github.com/digitalcytometry/cytospace; Web: https://cytospace.stanford.edu/
DENDRO
https://github.com/zhouzilu/DENDRO
Zhou Z, et al. DENDRO: genetic heterogeneity profiling and subclone detection by single-cell RNA sequencing. Genome Biol 21, 10 (2020). https://doi.org/10.1186/s13059-019-1922-x
SCANPY
https://github.com/theislab/Scanpy
SCENIC
https://aertslab.org/#scenic and https://pyscenic.readthedocs.io/en/latest/.
scMAGeCK
https://bitbucket.org/weililab/scmageck/src/master/
Yang L, et al. scMAGeCK links genotypes with multiple phenotypes in single-cell CRISPR screens. Genome Biol 21, 19 (2020). https://doi.org/10.1186/s13059-020-1928-4
Seurat
Stuart T, et al. Comprehensive Integration of Single-Cell Data. Cell. 2019;177(7):1888–1902.e21. doi:10.1016/j.cell.2019.05.031
Signac
https://cloud.r-project.org/web/packages/Signac
Stuart, T., Srivastava, A., Madad, S., Lareau, C.A. & Satija, R. Single-cell chromatin state analysis with Signac. Nature Methods 18, 1333-1341 (2021).
souporcell
https://github.com/wheaton5/souporcell
Heaton H, et al. Souporcell: robust clustering of single-cell RNA-seq data by genotype without reference genotypes. Nat Methods (2020). https://doi.org/10.1038/s41592-020-0820-1
squidpy
Web: https://squidpy.readthedocs.io/en/latest/.
Palla, G. et al. Squidpy: a scalable framework for spatial omics analysis. Nature Methods (2022).