Packages

The packages used in the GEMMA data analysis

Description	Package	Version
Data import	GEOquery	2.52.0
Batch correction	Sva (ComBat)	3.32.1
Preprocessing, normalization, statistical analysis	Limma	3.40.6
Preprocessing, normalization	Minfi	1.30.0
GC-correction	ArrayTV	1.22.0
Segmenting copy number data	DNAcopy	1.58.0
Copy number calling	CNVkit (Python)	0.9.6
Genome sequences	BSgenome.Hsapiens.UCSC.hg18	1.3.1
Coordinate liftover	Rtracklayer	1.44.4
Annotation	annotatr	1.10.0
Annotation	Org.Hs.eg.db	3.8.2
Illumina identifiers	lumiHumanIDMapping	1.10.1
Identify Methylated Regions	DMRcate	1.20.0
Venn diagram -visualization	VennDiagram	1.6.2
Summarizing copy number data	CNVRanger	1.0.3
Visualize copy number data	GenVisR	1.16.1
Representation of genomic intervals	GenomicRegions	1.36.1
Data integration	MixOmics	6.8.5
Pathway analysis	ReactomePA	1.28.0
Gene set enrichment analysis	gage	2.34.0
Visualizing intersections	VennDiagram	1.6.20
Enrichment visualizations	enrichplot	1.4.0
Gene relevance based on multiple evidences in complex networks: https://www.itb.cnr.it/mnd
[Snippets]

PRS construction
PRS-CS |https://github.com/getian107/PRScs| infers posterior SNP effect sizes under continuous shrinkage (CS) priors using GWAS summary statistics and an external LD reference panel
PLINK2