Which pipeline is better for the pre-processing of the single-cell transcriptomics dataset?

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4.7 years ago

B- for bioinformatics ▴ 30

Hi I have planned to analyze some scRNA seq dataset.

The first will do pre-processing in Seurat, thereafter shift into Scanpy

Does it recommendable? or there are any alternative ways?

rna-seq RNA-Seq • 1.1k views

ADD COMMENT • link 4.6 years ago by B- for bioinformatics ▴ 30

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Why python is such a hard requirement?

ADD REPLY • link 4.7 years ago by lakhujanivijay 5.8k

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Hi what did you mean?

ADD REPLY • link 4.7 years ago by B- for bioinformatics ▴ 30

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Why are you looking for a pipeline to work specifically with Python? why can't you just use Seurat ?

ADD REPLY • link 4.7 years ago by lakhujanivijay 5.8k

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If you have to use python for downstream analysis, why not do pre-processing in scanpy from the very beginning?

ADD REPLY • link 4.6 years ago by shoujun.gu ▴ 350

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