A Minimal Book Example
1
Introduction
2
How to run RIMA
2.1
Install RIMA and Set Up the Running Environment
2.2
Download pre-built references
2.3
Prepare input files
2.4
Running RIMA
2.5
Output
3
Pre-processing of bulk RNA-seq data
3.1
Read Alignment
3.2
Quality Control
3.3
Gene quantification
3.4
Batch effect removal
3.5
Video demo of RIMA
4
Differential gene analysis
4.1
Differential gene expression using DESeq2
4.1.1
Inputs of DESeq2
4.2
Different gene expression analysis
4.2.1
Running DESeq2 without batch effect
4.2.2
Running DESeq2 with batch effect
4.2.3
Output from DESeq2
4.2.4
Volcano Plot(s)
4.3
Gene set enrichment analysis (GSEA)
4.4
Single sample gene set enrichment analysis (ssGSEA)
5
Immune Analysis
6
Immune repertoire
6.1
TRUST4
6.1.1
TRUST4 output
6.2
BCR cluster calculation
6.3
Clonotypes per kilo-reads (CPK)
6.4
TCR and BCR entropy and Clonality
6.5
Fraction of reads mapped to TCR and BCR
6.6
Somatic hypermutation rate of BCR
6.7
Ig isotype frequency
6.8
Cohort analysis
6.9
Video demo
7
Immune Infiltration
7.0.1
Cibersort
7.0.2
TIMER
7.0.3
quanTIseq
7.0.4
xCell
7.0.5
EPIC
7.0.6
MCP-counter
7.1
Running the immune_infiltration_cohort module
7.2
immune_infiltration_cohort Output
7.3
Additonal comparisons across cell type and across samples
7.3.1
Comparison across cell type
7.3.2
Comparison across samples
7.4
Video demo
8
Immune Response
8.1
Characterizing the TME and T cell functionality
8.2
TIDE
8.2.1
Config.yaml sections relevant to TIDE
8.2.2
Cold and hot tumors
8.2.3
T cell dysfunction
8.2.4
T cell exclusion
8.2.5
Normalization
8.2.6
Running TIDE
8.3
Microsatelite instability (MSI)
8.4
Response comparison analysis of biomarkers
8.5
Video demo
9
HLA Typing
9.1
Identify HLA type
9.2
Video demo
10
Fusion
10.1
Fusion calling
10.2
Remove fusion homology
10.3
Comparison within phenotype
11
Microbiome
11.1
Centrifuge
11.2
Microial classfication from RNA-seq data
11.3
Video demo
11.3.1
We have prepared the RIMA reference folder with the current version we used. You can directly download from Iris server:
12
Steps to make your own custom reference files for RIMA pipeline
12.0.1
Reference fasta
12.0.2
Gene annotation file (gtf)
12.0.3
build STAR index
12.0.4
RSeQC reference files
12.0.5
build salmon index
12.0.6
GMT file for gene set analysis
12.0.7
STAR-Fusion genome resource lib
12.0.8
Centrifuge index
12.0.9
TRUST4 reference files
Published with bookdown
Tutorial of RNA-seq tumor immunity analysis
Chapter 5
Immune Analysis
Here is a review of existing methods.