Thewhey-Brian / Singe-cell_Toolkits

Notes for toolkits of single-cell analysis

Singe-cell_Toolkits

Notes for toolkits of single-cell analysis

Package

R Package

• HDF5Array (https://www.bioconductor.org/packages/devel/bioc/manuals/HDF5Array/man/HDF5Array.pdf)
• rhdf5 (https://bioconductor.org/packages/release/bioc/vignettes/rhdf5/inst/doc/rhdf5_cloud_reading.html)
• Seurat (Using "@" to access the Seurat object; https://satijalab.org/seurat/articles/essential_commands.html)
• SeuratDisk
• uwot
• umap

Python Package

• scipy
• scanpy
• anndata (https://anndata.readthedocs.io/en/latest/)

Collected Data List

https://github.com/Thewhey-Brian/Singe-cell_Toolkits/blob/main/scData_list.xlsx

Useful Links

• https://satijalab.org/seurat/articles/pbmc3k_tutorial.html

Some Awesome References

• https://github.com/crazyhottommy/scRNAseq-analysis-notes
• https://github.com/mdozmorov/scRNA-seq_notes
• https://github.com/martinjzhang/scDRS