cfDNAReferences

cfDNAReferences is a tiny database for cell free DNA analysis. We collected frequently used genome markers/features for our python wrapped pipeline cfDNApipe, which contains many integrated algorithms for cell free DNA analysis.

Note: hg38 is released now.

Blacklist

From Boyle-Lab.

ChromSizes

Chromatin size file from UCSC.

CpGisland

CpGisland file from UCSC.

CytoBand

cytoBand information from UCSC.

Gaps

Genome gaps file from UCSC。

OCF Markers

Data for OCF Analysis in cfDNApipe, please see this paper.

Plasma Deconvolution Markers

These are markers for plasma DNA methylation deconvolution algorithm, please see this paper.

refFlat File

refFlat annotation from UCSC.

access-5kb-mappable file

From cnvkit.