methylGSA - Gene Set Analysis Using the Outcome of Differential Methylation
The main functions for methylGSA are methylglm and methylRRA. methylGSA implements logistic regression adjusting number of probes as a covariate. methylRRA adjusts multiple p-values of each gene by Robust Rank Aggregation. For more detailed help information, please see the vignette.
Last updated 5 months ago
dnamethylationdifferentialmethylationgenesetenrichmentregressiongeneregulationpathwaysenrichmentgeneralized-linear-modelslogistic-regressionmethylationontologyshiny
10 stars 6.78 score 211 dependenciesRNAAgeCalc - A multi-tissue transcriptional age calculator
It has been shown that both DNA methylation and RNA transcription are linked to chronological age and age related diseases. Several estimators have been developed to predict human aging from DNA level and RNA level. Most of the human transcriptional age predictor are based on microarray data and limited to only a few tissues. To date, transcriptional studies on aging using RNASeq data from different human tissues is limited. The aim of this package is to provide a tool for across-tissue and tissue-specific transcriptional age calculation based on GTEx RNASeq data.
Last updated 5 months ago
rnaseqgeneexpressionbiological-ageelastic-netgene-expressiongenotype-tissue-expressionpredictionregularized-regressionrna-seq
6 stars 5.08 score 160 dependenciesNBAMSeq - Negative Binomial Additive Model for RNA-Seq Data
High-throughput sequencing experiments followed by differential expression analysis is a widely used approach to detect genomic biomarkers. A fundamental step in differential expression analysis is to model the association between gene counts and covariates of interest. NBAMSeq a flexible statistical model based on the generalized additive model and allows for information sharing across genes in variance estimation.
Last updated 5 months ago
rnaseqdifferentialexpressiongeneexpressionsequencingcoveragedifferential-expressiongene-expressiongeneralized-additive-modelsgeneralized-linear-modelsnegative-binomial-regressionsplines
2 stars 4.78 score 84 dependencies