component	version	role
FastQC	0.12.1	Week 1 read QC
Cutadapt	5.2	Week 1 adapter trimming
Bowtie2	2.5.5	Week 1 alignment
SAMtools	1.24	BAM processing and validation
Picard	3.4.0	Duplicate handling and insert-size QC
bedtools	2.31.1	Blacklist and consensus interval operations
MACS3	3.0.2	Week 1 teaching peak call
MultiQC	1.25	Week 1 focused QC report
featureCounts	2.1.1	Paired-fragment counting
R	4.5.2	Differential analysis runtime
DESeq2	1.50.2	Donor-aware differential accessibility
apeglm	1.32.0	Log2 fold-change shrinkage
vsn	3.78.1	Variance-stabilizing diagnostics dependency
ggplot2	4.0.3	Figures
pheatmap	1.0.13	Sample-distance heatmap
GENCODE	Release 50	GRCh38 primary-assembly annotation
g:Profiler	e114_eg62_p19_27110d83	Exploratory enrichment database build
HOMER	5.1	Exploratory motif enrichment
IGV	2.19.8	Exploratory locus-level visual QC
Java	21.0.12	IGV runtime