Bioconductor核心包

# 安装Bioconductor
if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
# 安装Bioconductor包
BiocManager::install("DESeq2")
BiocManager::install("edgeR")
BiocManager::install("Biostrings")
# Biostrings：序列处理
library(Biostrings)
dna <- DNAString("ATGCGCTAGCTA")
complement(dna)
reverseComplement(dna)
translate(dna)
# 计算GC含量
letterFrequency(dna, "GC") / length(dna)
# 读取FASTA文件
fasta_file <- readDNAStringSet("sequences.fasta")
width(fasta_file)  # 序列长度
alphabetFrequency(fasta_file)  # 碱基频率
# DESeq2：差异表达分析（简要示例）
library(DESeq2)
# countData: 基因计数矩阵（行是基因，列是样本）
# colData: 样本信息
# dds <- DESeqDataSetFromMatrix(countData = counts, 
#                               colData = sample_info,
#                               design = ~ condition)
# dds <- DESeq(dds)
# results <- results(dds)