README.md

In Louisahadj/Lentiviral_barcoding: A RShiny application for the visualization and analysis of single cell lineage-tracing data

CellDestiny: A RShiny application for the visualization and analysis of single cell lineage-tracing data

AIM :

CellDestiny is a user-friendly R Shiny application that allow you to easly vizualise and analyze all your single cell lineage-tracing data (lentiviral barcoding, integration site gene therapy, CRISPR gene therapy, etc.).

It is composed of two parts:

1. QC (quality control)
2. Analysis

The QC part enables the user to check for PCR artefacts through sample duplicates comparison and to check for repeat usage of barcodes accross individuals.

The analysis part enables to explore cleaned data (with merged duplicates) by ploting several type of graphs highlighting different biological insights.

After ploting, plot images and their corresponding matrix can be downloaded.

INSTALLATION:

1) Download zip file

* click on the green button "Code" above and "Download ZIP"

2) Unzip the folder 3) Go into it and double click on the Rproject: CellDestiny.Rproj. An R or Rstudio window will open.

Write on the R console :

library(lentiviralBarcoding)
Launch_myApp()

### Getting started

To use the app, install as written above and click on the load data button in the load section on the right (( add picture))

INPUTS FORMAT

Sample names and metdata

To use the app, you need two input files: 1. the count matrix with samples by column and cell identifier (i.e. barcodes) by row 2. the corresponding metadata, listing all sample variables

To do so, you need write sample names rigorously as they have to describe your samples.

For example, if you have four samples, two composed of Tcell and two others composed of Bcell both in two conditions, treatead with EPO and without.

Then you could write your sample names as:

sample 1: LT_EPO
sample 2: LT_noEPO
sample 3: LB_EPO
sample 4: LB_noEPO

Your metadata file must then be:

cellType | treatment
---------------------
LT       | EPO
LB       | noEPO

What is important here is that: 1. all columns must contain the list of all values (i.e. LT, LB) of variables (i.e. cellType) used in you sample names. Order of metadata columns must be the same as sample variables. 2. all values have to be written in the extact same way than in names (i.e. becarefull to uppercases and wite spaces) 3. an underscore ("_") has to be used only for variable name separator and must not be find in value names

QC versus analysis matrices

QC matrix and its corresponding metadata must contain duplicates infromation which must not be the case in the analysis part because sample duplicates have been checked and merged.

Case above representing inputs for the analysis part, its QC matrix sample names will then be:

sample 1 duplicate 1: LT_EPO_a
sample 1 duplicate 2: LT_EPO_b
sample 2 duplicate 1: LT_noEPO_a
sample 2 duplicate 2: LT_noEPO_b
sample 3 duplicate 1: LB_EPO_a
sample 3 duplicate 2: LB_EPO_b
sample 4 duplicate 1: LB_noEPO_a
sample 4 duplicate 2: LB_noEPO_b

And its metadata:

cellType | treatment | duplicate
--------------------------------
LT       | EPO       | a
LB       | noEPO     | b

Concrete examples can be found in the directory dataTest/LentiviralBarcodingData/.

LICENSE

This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License.

Louisahadj/Lentiviral_barcoding documentation built on April 7, 2022, 11:29 p.m.