Natian and Ryabhatta
1
Introduction
1.1
Overview
1.1.1
Single-cell/Single nucleus RNA seq technologies
1.1.2
Alignment of sequencing reads
1.1.3
Post alignment processing
1.2
Seurat and Monocle
1.3
Need for Ryabhatta and Natian
2
Download and Installation
2.1
No install, ready-to-use app.
2.2
Version that requires installation.
2.3
Reporting issues
3
Video manuals
4
💫 💫 💫 Natian 💫 💫 💫
5
Processing work flows
6
First run
6.1
Ready-to-use apps
6.2
Installation version
6.3
Opening screen
7
Types of input data
7.1
10x Cell Ranger output
7.2
Gene count matrix output
7.3
Gene expression omnibus (GEO)
7.4
Partially processed Seurat objects
8
Adding Meta data
8.1
Individual category of meta data and the actual value added to the Seurat object
8.2
Add meta data from a file
8.3
Load meta data from column name
9
Quality control options
10
Regressing cell cycle signal (Optional)
11
Normalization, Finding variable genes, Scaling data, and Principal component analysis
12
Dimensionality reduction and clustering cells
12.1
Repeating dimensionality reduction
12.2
Upload dimensionality reduction
13
Finding markers for clusters
13.1
Markers
13.2
Threshold for change
13.3
minimum percentage expression
13.4
Number of markers to display
13.5
Find only positive markers
13.6
Markers table and Switch to marker’s view
14
Getting cell IDs from reference
15
Integration of Seurat objects
16
Download Session notes
17
Saving current file
18
🌕 🌕 🌕 Ryabhatta 🌕 🌕 🌕
19
Analytical steps possible using Ryabhatta
20
First run
20.1
Ready-to-use apps
20.2
Installation and run app
20.3
Open screen
21
Loading data
21.1
Load .rds/.RDS file
21.2
Load .RData file
21.3
Load .RObj
22
Rename Seurat object
23
Remove Seurat object
24
Quick action buttons
24.1
Switch between tSNE and UMAP
24.2
Display number of UMIs per cell
24.3
Display number of genes per cell
24.4
Overlay meta information
24.5
Split based on meta information
24.6
Assign meta information as identity
24.7
Assign Identity as meta information
24.8
Download the plot
24.9
Reset Dim plot
25
Display settings
25.1
Show labels on the plots
25.2
Show axes on the plots
25.3
Change plot features like point size, point color
25.4
format Dimensionality reduction graph
25.5
format the expression plots
26
Cell count per cluster/condition
27
Enter gene names to visualize
28
Load gene names from a text file
29
Selecting meta data category
30
Plotting options
30.1
Violin plot
30.2
Heatmaps
30.3
Dot plots
30.4
Ridge plots
30.5
Feature plots
30.6
ExpressO plots
30.7
Download expression plot
30.8
Download source data
31
Editing meta data
31.1
Combine meta data
31.2
Change meta data name
31.3
Split on meta
32
Analyze Individual Clusters
33
Select genes based on expression
34
Interactive feature plots for manual selection
35
Monocle Pseudotime analysis
36
Identity tracking and changing
37
Cell cyle scores
38
Saving Seurat objects
References
Published with bookdown
User manual for Ryabhatta and Natian
User manual for Ryabhatta and Natian
Sathiya N Manivannan
2022-04-11
A descriptive manual to use Natian and Ryabhatta