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Preprocess Normalization #43

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minhtran1309 opened this issue Oct 23, 2019 · 0 comments
Open

Preprocess Normalization #43

minhtran1309 opened this issue Oct 23, 2019 · 0 comments

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@minhtran1309
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minhtran1309 commented Oct 23, 2019

Hi,
I found two repositories for st_analysis and quite confused which one is the latest and updated one.
Anyway, my issue is that I want to make use of several RNA-seq count matrix, but there is no function that could perform TMM normalization or Sum Factors normalization from this repo.
Whereas, the other repo which has been updated for 2 years, does have those function I need. However, most library modules are outdated and no longer be supported like py2ri().
For example:

n_cells = len(counts.columns)
pandas2ri.activate()
r_counts = pandas2ri.py2ri(counts)
scran = RimportLibrary("scran")
multicore = RimportLibrary("BiocParallel")
multicore.register(multicore.MulticoreParam(multiprocessing.cpu_count()-1))
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