El. knyga: Computational Epigenomics and Epitranscriptomics

DNA methylation data analysis using Msuite.- Interactive DNA methylation
arrays analysis with ShinyÉPICo.- Predicting Chromatin Interactions from DNA
Sequence using DeepC.- Integrating single-cell methylome and transcriptome
data with MAPLE.- Quantitative comparison of multiple chromatin
immunoprecipitation-sequencing (ChIP-seq) experiments with spikChIP.- A Guide
To MethylationToActivity: A Deep-Learning Framework That Reveals Promoter
Activity Landscapes from DNA Methylomes In Individual Tumors.- DNA
modification patterns filtering and analysis using DNAModAnnot.- Methylome
imputation by methylation patterns.- Sequoia: a framework for visual analysis
of RNA modifications from direct RNA sequencing data.- Predicting
pseudouridine sites with Porpoise.- Pseudouridine Identification and
Functional Annotation with PIANO.- Analyzing mRNA epigenetic sequencing data
with TRESS.- Nanopore Direct RNA Sequencing Data Processing and Analysis
Using MasterOfPores.- Data Analysis Pipeline for Detection and Quantification
of Pseudouridine () in RNA by HydraPsiSeq.- Analysis of RNA sequences and
modifications using NASE.- Mapping of RNA modifications by direct Nanopore
sequencing and JACUSA2.