recountmethylation - Access and analyze public DNA methylation array data compilations
Resources for cross-study analyses of public DNAm array data from NCBI GEO repo, produced using Illumina's Infinium HumanMethylation450K (HM450K) and MethylationEPIC (EPIC) platforms. Provided functions enable download, summary, and filtering of large compilation files. Vignettes detail background about file formats, example analyses, and more. Note the disclaimer on package load and consult the main manuscripts for further info.
Last updated 24 days ago
dnamethylationepigeneticsmicroarraymethylationarrayexperimenthub
6.45 score 9 stars 9 scripts 220 downloadslute - Framework for cell size scale factor normalized bulk transcriptomics deconvolution experiments
Provides a framework for adjustment on cell type size when performing bulk transcripomics deconvolution. The main framework function provides a means of reference normalization using cell size scale factors. It allows for marker selection and deconvolution using non-negative least squares (NNLS) by default. The framework is extensible for other marker selection and deconvolution algorithms, and users may reuse the generics, methods, and classes for these when developing new algorithms.
Last updated 24 days ago
rnaseqsequencingsinglecellcoveragetranscriptomicsnormalization
5.38 score 2 stars 3 scripts 104 downloads