WEBVTT

00:00.700 --> 00:02.600
In this video, I will present you

00:02.600 --> 00:05.500
the shinny application scMonitor, which is

00:05.500 --> 00:08.200
oriented to easily explore

00:08.200 --> 00:10.300
a previously processed seurat object.

00:11.600 --> 00:13.800
Firstly, you should select the file

00:13.800 --> 00:16.800
containing the seurat object.

00:16.800 --> 00:19.000
For now, the file format must be RDS.

00:19.700 --> 00:21.600
Depending on the object size and

00:21.600 --> 00:23.800
computer potency the loading

00:23.800 --> 00:25.000
will take more or less time.

00:26.200 --> 00:28.200
UMAP distribution that generates

00:28.400 --> 00:30.000
is the same that shows as default,

00:30.400 --> 00:33.400
usually clusters identified by seurat itself.

00:33.400 --> 00:37.200
We can group colors by any

00:37.200 --> 00:39.300
other variable that we have included in the

00:39.300 --> 00:42.600
metadata from the object specifying it in "GroupBy".

00:43.200 --> 00:45.500
Tipically, the sample origin or

00:45.500 --> 00:46.300
a manual annotation

00:46.300 --> 00:47.700
from the cell type.

00:48.800 --> 00:51.400
Distribution can also be divided by

00:51.400 --> 00:54.500
another variable selecting in "FacetBy".

00:54.500 --> 00:57.300
In this case, we are looking at

00:57.300 --> 00:59.900
the distribution of cell type

00:59.900 --> 01:01.000
by the sample origin.

01:02.800 --> 01:05.800
Another available visualization is to show expression

01:05.800 --> 01:08.100
for a group of genes separated by a white space

01:08.100 --> 01:10.400
over UMAP distribution.

01:11.300 --> 01:13.500
With the "Height" bar we can adjust

01:13.500 --> 01:15.500
the size in order to feel comfortable.

01:18.900 --> 01:22.700
Finally, we can create signatures in order to visualize

01:22.800 --> 01:25.200
their score from cells.

01:25.200 --> 01:27.300
One must indicate the signature name and

01:27.300 --> 01:29.800
on the box below specify the genes

01:29.800 --> 01:32.600
that are included. Once added, you can

01:32.600 --> 01:34.700
specify its name in the

01:34.700 --> 01:35.500
signatures box.