Hi , I would like to know if DeSeq2 can be used to analyze gene expression of Single cell RNA seq data? If DeSeq cannot be used which other package would be a suitable choice for my samples?

Thanks.

Funnily enough, there's a Bioconductor workflow for analyzing single-cell RNA-seq data:

https://www.bioconductor.org/help/workflows/simpleSingleCell/

... and you can also find relevant packages with the SingleCell tag:

http://www.bioconductor.org/packages/release/BiocViews.html#___SingleCell

... which should be enough to get you started.