deconvR - Simulation and Deconvolution of Omic Profiles
This package provides a collection of functions designed for analyzing deconvolution of the bulk sample(s) using an atlas of reference omic signature profiles and a user-selected model. Users are given the option to create or extend a reference atlas and,also simulate the desired size of the bulk signature profile of the reference cell types.The package includes the cell-type-specific methylation atlas and, Illumina Epic B5 probe ids that can be used in deconvolution. Additionally,we included BSmeth2Probe, to make mapping WGBS data to their probe IDs easier.
Last updated
dnamethylationregressiongeneexpressionrnaseqsinglecellstatisticalmethodtranscriptomicsbioconductor-packagedeconvolutiondna-methylationomics
6.33 score 11 stars 26 scripts 471 downloadsmethylTFR - Quantification of DNA Methylation Signatures in TFBS
methylTFR is an extensive R package designed specifically for analyzing DNA methylation signatures within transcription factor binding sites (TFBS) across diverse genomic annotations. It enhances methylation analysis by calculating a bias-corrected 'deviation' in methylation levels, leveraging GC bias distribution and frequency data. This package offers a variety of functions that facilitate the motif activity exhibiting diverse methylation patterns across distinct samples or cells.
Last updated
softwarednamethylationsinglecellstatisticalmethodgeneregulationepigeneticstranscriptionsequencingwholegenomedifferentialmethylationmotifannotationmotifdiscoverycoverage
3.90 score 7 scriptsmethylTFRAnnotationHg38 - methylTFR Annotations for hg38
Precomputed transcription factor binding sites, motif GC frequency tables and a genome-wide GC distribution for use with the methylTFR package. Binding sites are genome-wide motif matches extended to the footprint window methylTFR reads across; the GC tables record how each motif's sites distribute over genome-wide GC quintiles, which is what allows a deviation score to be corrected for sequence composition. The data are hosted on AnnotationHub and retrieved on first use; this package provides the accessors and the documentation.
Last updated
annotationdataannotationhubfunctionalannotationsequenceannotationhomo_sapiens
3.29 score 13 scriptsmethylTFRAnnotationMm10 - methylTFR Annotations for mm10
Precomputed transcription factor binding sites, motif GC frequency tables and a genome-wide GC distribution for use with the methylTFR package. Binding sites are genome-wide motif matches extended to the footprint window methylTFR reads across; the GC tables record how each motif's sites distribute over genome-wide GC quintiles, which is what allows a deviation score to be corrected for sequence composition. The data are hosted on AnnotationHub and retrieved on first use; this package provides the accessors and the documentation.
Last updated
annotationdataannotationhubfunctionalannotationsequenceannotationmus_musculus
3.18 score 3 scripts