EpiDISH - Epigenetic Dissection of Intra-Sample-Heterogeneity
EpiDISH is a R package to infer the proportions of a priori known cell-types present in a sample representing a mixture of such cell-types. Right now, the package can be used on DNAm data of blood-tissue of any age, from birth to old-age, generic epithelial tissue and breast tissue. Besides, the package provides a function that allows the identification of differentially methylated cell-types and their directionality of change in Epigenome-Wide Association Studies.
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dnamethylationmethylationarrayepigeneticsdifferentialmethylationimmunooncology
10.49 score 57 stars 5 dependents 304 scripts 1.6k downloads
tricycle - tricycle: Transferable Representation and Inference of cell cycle
The package contains functions to infer and visualize cell cycle process using Single Cell RNASeq data. It exploits the idea of transfer learning, projecting new data to the previous learned biologically interpretable space. We provide a pre-learned cell cycle space, which could be used to infer cell cycle time of human and mouse single cell samples. In addition, we also offer functions to visualize cell cycle time on different embeddings and functions to build new reference.
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singlecellsoftwaretranscriptomicsrnaseqtranscriptionbiologicalquestiondimensionreductionimmunooncology
7.06 score 31 stars 82 scripts 950 downloads