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andrewGhazi committed Nov 26, 2024
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Expand Up @@ -128,7 +128,7 @@ e.g. a `matrix` of counts, a `data.frame` of sample metadata, a `data.frame` of
There are two main disadvantages to this type of "from scratch" approach:

1. It requires a substantial amount of manual bookkeeping to keep the different data components in sync. If you performed a QC step that removed dead cells from the count matrix, you also had to remember to remove that same set of cells from the cell-wise metadata. Did you filter out genes that did not display sufficient expression levels to be retained for further analysis? Then you also need to remember to filter the gene metadata table too.
2. All the downstream steps had to be "from scratch" as well. All the data munging, analysis, and visualization code will need to be customized to the idiosyncrasies of a given input set.
2. All the downstream steps have to be "from scratch" as well. All the data munging, analysis, and visualization code will need to be customized to the idiosyncrasies of a given input set.

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