• RNA-Seq data analysis
  • 01_fastqc
  • 02_trimming
  • 03_quantification_salmon
  • 04_alignment_Rsubread
  • 05_duplicates_analysis_dupRadar
  • 06_differential_gene_expression_limma_voom
  • 07_differential_gene_expression_dream
  • 08_differential_transcript_usage_isoforSwitchAnalyzeR
  • 09_GSEA_analysis

RNA-Seq data analysis

This repository contain code for RNA-Seq data analysis.

01_fastqc

Quality check using FASTQC.

02_trimming

Quality control using TrimGalore.

03_quantification_salmon

Pseudoalignment with salmon.

04_alignment_Rsubread

Alignment using Rsubread.

05_duplicates_analysis_dupRadar

Assesment of PCR duplicates using dupRadar.

06_differential_gene_expression_limma_voom

Differential gene expression using limma-voom pipeline from limma package.

07_differential_gene_expression_dream

Differential gene expression using dream pipeline.

08_differential_transcript_usage_isoforSwitchAnalyzeR

Differential transcrip usage analysis using DEXseq and isoform switching analysis using IsoformSwitchAnalyzeR.

09_GSEA_analysis

Functional analysis (GSEA) using fGSEA package.