Benchmarking-Ploidy-Estimation-Tools

Tools and Usage Examples for Ploidy Estimation in Benchmarking Studies

Bulk DNA-seq

ASCAT: https://github.com/VanLoo-lab/ascat

CNAnorm: https://github.com/sheffield-bioinformatics-core/cox_ctdna_cnv ;https://bioconductor.org/packages/release/bioc/manuals/CNAnorm/man/CNAnorm.pdf

ABSOLUTE: https://github.com/ShixiangWang/DoAbsolute

absCNseq: https://github.com/seqanswers/absCNseq

PyLOH: https://github.com/uci-cbcl/PyLOH

TITAN: https://github.com/gavinha/TitanCNA/tree/master/scripts/snakemake

Sequenza: https://bitbucket.org/sequenzatools/sequenza/src/chemins/

FACETS: https://github.com/dariober/cnv_facets

Sclust: https://www.nature.com/articles/nprot.2018.033#Sec10

PURPLE: https://github.com/hartwigmedical/hmftools/tree/master/purple

Accucopy: https://github.com/polyactis/Accucopy

HMMcopy: https://github.com/shahcompbio/single_cell_pipeline

Ginkgo: https://github.com/robertaboukhalil/ginkgo

AneuFinder: https://bioconductor.org/packages/release/bioc/vignettes/AneuFinder/inst/doc/AneuFinder.pdf

SCOPE: https://bioconductor.org/packages/devel/bioc/vignettes/SCOPE/inst/doc/SCOPE_vignette.html

SeCNV: https://github.com/deepomicslab/SeCNV

rcCAE: https://github.com/zhyu-lab/rccae

CNVeil: https://github.com/maiziezhoulab/CNVeil

scAbsolute: https://github.com/markowetzlab/scDNAseq-workflow

Name		Name	Last commit message	Last commit date
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Bulk DNA-seq.md		Bulk DNA-seq.md
README.md		README.md
scDNA-seq.md		scDNA-seq.md