bio-methylation-methylkit
methylKit Analysis
Read Bismark Coverage Files
library(methylKit)
file_list <- list('sample1.bismark.cov.gz', 'sample2.bismark.cov.gz',
'sample3.bismark.cov.gz', 'sample4.bismark.cov.gz')
sample_ids <- c('ctrl_1', 'ctrl_2', 'treat_1', 'treat_2')
treatment <- c(0, 0, 1, 1) # 0 = control, 1 = treatment
meth_obj <- methRead(
location = as.list(file_list),
sample.id = as.list(sample_ids),
treatment = treatment,
assembly = 'hg38',
context = 'CpG',
pipeline = 'bismarkCoverage'
More from gptomics/bioskills
bioskills
Installs 425 bioinformatics skills covering sequence analysis, RNA-seq, single-cell, variant calling, metagenomics, structural biology, and 56 more categories. Use when setting up bioinformatics capabilities or when a bioinformatics task requires specialized skills not yet installed.
104bio-single-cell-batch-integration
Integrate multiple scRNA-seq samples/batches using Harmony, scVI, Seurat anchors, and fastMNN. Remove technical variation while preserving biological differences. Use when integrating multiple scRNA-seq batches or datasets.
5bio-epitranscriptomics-merip-preprocessing
Align and QC MeRIP-seq IP and input samples for m6A analysis. Use when preparing MeRIP-seq data for peak calling or differential methylation analysis.
5bio-data-visualization-multipanel-figures
Combine multiple plots into publication-ready multi-panel figures using patchwork, cowplot, or matplotlib GridSpec with shared legends and panel labels. Use when combining multiple plots into publication figures.
5bio-data-visualization-specialized-omics-plots
Reusable plotting functions for common omics visualizations. Custom ggplot2/matplotlib implementations of volcano, MA, PCA, enrichment dotplots, boxplots, and survival curves. Use when creating volcano, MA, or enrichment plots.
5bio-read-qc-fastp-workflow
All-in-one read preprocessing with fastp including adapter trimming, quality filtering, deduplication, base correction, and HTML report generation. Use when preprocessing Illumina data and wanting a single fast tool instead of separate Cutadapt, Trimmomatic, and FastQC steps.
5