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109 lines
2.1 KiB
109 lines
2.1 KiB
WEBVTT
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00:00.700 --> 00:02.600
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In this video, I will present you
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00:02.600 --> 00:05.500
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the shinny application scMonitor, which is
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00:05.500 --> 00:08.200
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oriented to easily explore
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00:08.200 --> 00:10.300
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a previously processed seurat object.
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00:11.600 --> 00:13.800
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Firstly, you should select the file
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containing the seurat object.
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00:16.800 --> 00:19.000
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For now, the file format must be RDS.
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00:19.700 --> 00:21.600
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Depending on the object size and
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00:21.600 --> 00:23.800
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computer potency the loading
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00:23.800 --> 00:25.000
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will take more or less time.
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00:26.200 --> 00:28.200
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UMAP distribution that generates
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00:28.400 --> 00:30.000
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is the same that shows as default,
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00:30.400 --> 00:33.400
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usually clusters identified by seurat itself.
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00:33.400 --> 00:37.200
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We can group colors by any
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00:37.200 --> 00:39.300
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other variable that we have included in the
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00:39.300 --> 00:42.600
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metadata from the object specifying it in "GroupBy".
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00:43.200 --> 00:45.500
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Tipically, the sample origin or
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00:45.500 --> 00:46.300
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a manual annotation
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00:46.300 --> 00:47.700
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from the cell type.
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00:48.800 --> 00:51.400
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Distribution can also be divided by
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00:51.400 --> 00:54.500
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another variable selecting in "FacetBy".
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00:54.500 --> 00:57.300
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In this case, we are looking at
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00:57.300 --> 00:59.900
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the distribution of cell type
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00:59.900 --> 01:01.000
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by the sample origin.
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01:02.800 --> 01:05.800
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Another available visualization is to show expression
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01:05.800 --> 01:08.100
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for a group of genes separated by a white space
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01:08.100 --> 01:10.400
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over UMAP distribution.
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01:11.300 --> 01:13.500
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With the "Height" bar we can adjust
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01:13.500 --> 01:15.500
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the size in order to feel comfortable.
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01:18.900 --> 01:22.700
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Finally, we can create signatures in order to visualize
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01:22.800 --> 01:25.200
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their score from cells.
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01:25.200 --> 01:27.300
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One must indicate the signature name and
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on the box below specify the genes
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01:29.800 --> 01:32.600
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that are included. Once added, you can
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specify its name in the
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01:34.700 --> 01:35.500
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signatures box.
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