Shiny app for visualisation of three timepoints from the Yang 2019 data
RNA
Home
Sample select
Quality checks
GRN inference
Differential expression
Volcano and MA plots
DE Summary
Enrichment
Cross plot
Expression patterns
Welcome to bulkAnalyseR!
An accessible, interactive pipeline for analysing and sharing bulk sequencing results
Tutorial
Vignette describing the different panels in this app and how to use them:
https://core-bioinformatics.github.io/bulkAnalyseR/articles/bulkAnalyseR.html
GitHub
Latest stable version, bug reports and feature requests:
https://github.com/Core-Bioinformatics/bulkAnalyseR
Manuscript
For a more detailed overview of the app functionality:
https://www.biorxiv.org/content/10.1101/2021.12.23.473982v1
Our website
Wellcome MRC - Cambridge Stem Cell Institute Core Bioinformatics Group:
https://www.corebioinf.stemcells.cam.ac.uk/bulkAnalyseR
Created by
Ilias Moutsopoulos, Eleanor Williams, and Irina Mohorianu
Use the selected samples!
Select all
Deselect all
Select using metadata column:
srr
timepoint
0h
12h
36h
Jaccard Similarity Index Heatmap
Show annotations
srr
timepoint
# of (most abundant) genes
Show JSI values
File name for JSI plot download
Download JSI Plot
Principal Component Analysis
Group by
srr
timepoint
# of (most abundant) genes
Show sample labels
Show ellipses around groups
File name for PCA plot download
Download PCA Plot
MA plots
Genes to highlight:
Show guidelines
Sample 1
SRR7624365
SRR7624366
SRR7624371
SRR7624372
SRR7624375
SRR7624376
Sample 2
SRR7624365
SRR7624366
SRR7624371
SRR7624372
SRR7624375
SRR7624376
Other genes to highlight:
File name for MA plot download
Download MA Plot
Scatter plots
Sample 1
SRR7624365
SRR7624366
SRR7624371
SRR7624372
SRR7624375
SRR7624376
Sample 2
SRR7624365
SRR7624366
SRR7624371
SRR7624372
SRR7624375
SRR7624376
Genes to highlight:
File name for scatter plot download
Download Scatter Plot
Density plots
Group by
srr
timepoint
File name for density plot download
Download Density Plot
Violin plots
Colour by
srr
timepoint
Apply log transformation to expression
File name for violin plot download
Download Violin Plot
Individual gene expression
Genes to include:
Apply log transformation to expression
File name for bar plot download
Download Bar Plot
Number of networks:
1
2
3
4
Metadata column to use:
timepoint
Samples for GRN #1:
0h
12h
36h
Samples for GRN #2:
0h
12h
36h
Samples for GRN #3:
0h
12h
36h
Samples for GRN #4:
0h
12h
36h
Target genes:
Start GRN inference
Connections to plot:
File name for plot download
Select plot to download:
1
2
3
4
Download Plot
Metadata column to use:
timepoint
Condition 1:
0h
12h
36h
Condition 2:
0h
12h
36h
DE pipeline:
edgeR
DESeq2
logFC threshold
Adjusted p-value threshold
Start DE
File name for download
Download Table
Gene selection
Select genes of interest by clicking on the corresponds rows in the table
Reset row selection
Select top 50 genes
Type of plot:
Volcano
MA
Other genes to highlight:
File name for plot download
Download Plot
Gene heatmap
Heatmap values
Expression
Log2 Expression
Z-score
Show annotations
srr
timepoint
Additional genes to include:
If no genes are selected in the DE panel or here then the top 50 DE genes are chosen.
File name for heatmap plot download
Download Heatmap Plot
Principal Component Analysis on DE genes
Group by
srr
timepoint
Show sample labels
Show ellipses around groups
File name for PCA plot download
Download PCA Plot
Select data sources
GO:BP
GO:MF
GO:CC
KEGG
REAC
TF
MIRNA
CORUM
HP
HPA
WP
Start enrichment analysis
File name for data download
Download Data
File name for plot download
Download Plot
Metadata column to use for comparison #1:
timepoint
DE comparison #1 Condition 1:
0h
12h
36h
DE comparison #1 Condition 2:
0h
12h
36h
DE pipeline for comparison #1:
edgeR
DESeq2
Metadata column to use for comparison #2:
timepoint
DE comparison #2 Condition 1:
0h
12h
36h
DE comparison #2 Condition 2:
0h
12h
36h
DE pipeline for comparison #2:
edgeR
DESeq2
logFC threshold
Adjusted p-value threshold
Start DE
File name for download
Download Table
Genes to highlight:
File name for plot download
Download Plot
Metadata column to use:
timepoint
Series of states to use
Unused states
0h
12h
36h
Number of standard deviations from the mean to use for interval overlap:
1
2
3
4
5
6
7
8
9
10
Calculate expression patterns
Pattern to plot
File name for download
Download grouped expression table
Download values
Expression
Log2 Expression
Mean Scaled
Z-score
Heatmap values
Expression
Log2 Expression
Mean Scaled
File name for line plot download
Download Line Plot
Heatmap values
Expression
Log2 Expression
Z-score
File name for heatmap plot download
Download Heatmap Plot