dna-methylation

There are 122 repositories under dna-methylation topic.

  • brain-epigenomics

    Language:R3

  • TCGA-Pancreatic-carcinoma-workflow

    2

  • TDbasedUFE

    This is a R package that intends to perform all the features possible by tensor decomposition based unsupervised feature extraction

    Language:R5

  • DNA-Methylation

    R-based DNA methylation array data analysis workflow.

    Language:R5

  • CGi

    Takes output from DMRichR and performs statistical testing and visualization for CpG and genic annotation enrichments

    Language:R5

  • ARPEGGIO

    A SnakeMake workflow to analyse whole genome bisulfite sequencing data from allopolyploids.

    Language:Python5

  • mint

    A pipeline for the integration of DNA methylation and hydroxymethylation data

    Language:R5

  • RAMEN

    Regional Association of Methylation variability with the Exposome and geNome (RAMEN) is an R package whose goal is to identify Variable Methylated Regions (VMRs) in microarray DNA methylation data. Additionally, using Genotype (G) and Environmental (E) data, it can identify which G, E, G+E or GxE model better explains this variability.

    Language:R4

  • Kreibich_2023_5mC_at_enhancers

    Analysis of Single Molecule Footprinting (SMF) data for the analysis of DNA methylation, chromatin accessibility and TF binding. The repository contains all primary code to reproduce the main analyses for the publication "Single molecule footprinting identifies context-dependent regulation of enhancers by DNA methylation" (Kreibich et al., 2023)

    Language:R4
  • epialleleR

    epialleleR

    Fast, epiallele-aware methylation caller and reporter — an R/Bioconductor package

    Language:R4

  • Pan-B-cell-methylome

    Code accompanying the findings in Duran-Ferrer 2020, Nat Cancer. The epiCMIT mitotic clock calculator and a Pan B-cell tumor classifier algorithm are provided.

    Language:R4

  • Foragers_vs_Nurses

    Data and scripts from the manuscript: Gene expression and epigenetics reveal species-specific mechanisms acting upon common molecular pathways in the evolution of task division in bees

    Language:R4

  • BEclear

    Correction of batch effects in DNA methylation data

    Language:R4

  • PipiDABS

    PipiDABS: A Comprehensive and User-Friendly Pipeline for Downstream DNA Methylation Analysis of High-throughput Bisulfite Sequencing Data.

    Language:R4

  • WilsonDiseaseEpigenome

    Analysis scripts for identification and visualization of Wilson disease-associated DNA methylation changes in human liver and blood

    Language:R4

  • BSVF

    Bisulfite Sequencing Virus integration Finder

    Language:C4

  • MidlifeDementiaRisk

    DNA Methylation-based Prediction of Midlife Dementia Risk

    Language:R3

  • reffree_cell_mix_tutorial

    Example of an estimation of cell-type proportions using reference-free method (RefFreeEWAS)

    3

  • ART_methylation

    Meta-analysis of DNA methylation in ART

    Language:R3

  • methyvim

    :package: :microscope: R/methyvim: Targeted, Robust, and Model-free Differential Methylation Analysis

    Language:TeX3

  • forkedTF

    ForkedTF is an R-library that introduces Forked-PMW (FPMW) and Forked-Sequence Logos (F-Logos) to provide a more comprehensive depiction of the sequence affinity of a Transcription factor (TF) of interest, including its DNA sequence and DNA methylation level, along with a segregated list of partner TFs.

    Language:R2

  • idDMR

    idDMR - Identify Differentially Methylated Regions for microarray data

    Language:R2

  • LFS-Early-Cancer-Onset-Prediction

    DNA methylation predicts early onset of primary tumor in patients with Li-Fraumeni Syndrome

    Language:R2

  • CpelNano.jl

    DNA methylation landscape analysis for nanopore sequencing data.

    Language:Julia2

  • CUE

    CUE: CpG impUtation Ensemble for DNA Methylation Levels Across the HumanMethylation450 (HM450) BeadChip and HumanMethylation EPIC (HM850) BeadChip Platforms

    Language:HTML2

  • TFregulomeR-dev

    TFregulomeR reveals transcription factors’ context-specific features and functions

    Language:R2

  • TwistNext

    A NextFlow pipeline for Twist NGS DNA Methylation data analysis

    Language:Nextflow1

  • PARamrfinder

    PARamrfinder is a high performance parallel tool to predict allele-specific DNA methylation (ASM) in mammals in the absence of SNP data.

    Language:C++1

  • main_project

    Cancer prediction using DNA methylation

    Language:Jupyter Notebook1

  • Gene_Analysis

    Analysis of data from GEO

    Language:R1

  • nanopore

    Identification of epigenetic sites in MealyBugs using ONT Nanopore Sequencing

    Language:R1

  • DLBepigenetics

    Data analysis of DNA methylation EPIC array data in post-mortem brain tissue from DLB and control subjects.

    Language:R1

  • bs-ATLAS-seq

    bs-ATLAS-seq analysis scripts

    Language:Shell1

  • DNAMethyl

    Predicts the age of a person using the methylation frequencies of CpG sites in human blood/saliva samples.

    Language:Python1

  • Decitabine-treatment

    A multiomics approach reveals RNA dynamics promote cellular sensitivity to DNA hypomethylation

    Language:Jupyter Notebook1

  • Alveolar-Cell-Type-Deconvolution

    DNA methylome-based validation of induced sputum as an effective protocol to study lung immunity: construction of a classifier of pulmonary cell types

    Language:R1