Bioinformatics analysis codes built with R

Description

This project includes the code used in my manuscripts.

Geo.R for bulk-seq

• The GEOquery package downloads data from GEO. (Sometimes if you can't get down, you still need to manually download and read it)
• Limma package performs differential analysis.
• The DESeq2 package performs differential analysis.
• Construct a co expression map using the MEGENA package.
• The e1071 package implements mSVM-REF recognition and screening of key genes (the mSVM-REF function is a link point I written by Professor John Colby, and also refers to Professor Maryam's parallel code link point I, which has been improved)
• Glmnet package implementation for lasso regression screening
• The randomForest package implements random forest filtering.
• Venn package draws Wayne diagram.
• The prediction effect of pROC package test.
• CIBERSORT for immune infiltration analysis (function code point me).
• Some visualizations were performed using packages such as ggplot2 and Yu's aplot packages.

The manuscript has been published. If it is helpful to you, please cite it. (PMID: 36930329 click me)

scRNA.R for scRNA-seq and SMR

• The Seurat package (version 4.3.0) was used to pre-process the raw sequencing data, and dimensionality reduction techniques such as PCA and UMAP.
• Analysis of differentially expressed genes.
• Cell-to-cell contact analysis by CellChat.
• Regulatory network analysis by SCENIC.
• Single-cell trajectory analysis by Monocle3.
• SMR analysis.
• GEO cohor studies DEGs.
• and so on.

CAMR.R The content in R is Mendelian randomization of 21 risk factors and cardiac arrest using the TwoSampleMR package