igordot/sns

Analysis pipelines for genomic sequencing data

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andrewdavidsmith/transferase

The transferase system for retrieving methylome data from methbase

Language: C++ - Size: 3.63 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 2 - Forks: 0

LieberInstitute/BiocMAP

Our typical analysis steps for WGBS data, starting from FASTQ reads and ending with the construction of bsseq objects. Created using nextflow

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huishenlab/Biscuit_Snakemake_Workflow Fork of vari-bbc/Biscuit_Snakemake_Workflow

Snakemake Workflow For Running Biscuit https://github.com/huishenlab/biscuit

Language: Python - Size: 3.06 MB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 2 - Forks: 8

twlab/methylGrapher

Methylation analysis pipeline for genome graph

Language: Python - Size: 9.83 MB - Last synced at: 10 days ago - Pushed at: about 1 month ago - Stars: 12 - Forks: 0

huishenlab/iscream

Reading and manipulating WGBS data

Language: R - Size: 5.81 MB - Last synced at: 14 days ago - Pushed at: 14 days ago - Stars: 0 - Forks: 1

dcolinmorgan/mili_benchmark

mix of python, bash and R functions, scripts and notebooks to benchmark the use of methylation as proxy to infer TF binding

Language: Jupyter Notebook - Size: 128 MB - Last synced at: 3 months ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

ben-laufer/DMRichR

A R package and executable for the preprocessing, statistical analysis, and downstream testing and visualization of differentially methylated regions (DMRs) from CpG count matrices (Bismark cytosine reports)

Language: R - Size: 4.62 MB - Last synced at: 6 months ago - Pushed at: over 1 year ago - Stars: 39 - Forks: 23

CompEpigen/methrix_docs

Documentation for methrix R package

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ben-laufer/CpG_Me

A whole genome bisulfite sequencing (WGBS) pipeline for the alignment and QC of DNA methylation that goes from from raw reads (FastQ) to a CpG count matrix (Bismark cytosine reports)

Language: Shell - Size: 1.01 MB - Last synced at: 6 months ago - Pushed at: about 3 years ago - Stars: 20 - Forks: 11

ENCODE-DCC/wgbs-pipeline

ENCODE whole-genome bisulfite sequencing (WGBS) pipeline

Language: Python - Size: 310 MB - Last synced at: about 1 year ago - Pushed at: over 3 years ago - Stars: 24 - Forks: 13

cemordaunt/DMRfinder

A pipeline to identify differentially-methylated regions from whole-genome bisulfite sequencing data

Language: R - Size: 7.85 MB - Last synced at: 9 months ago - Pushed at: about 5 years ago - Stars: 6 - Forks: 4

DKFZ-ODCF/AlignmentAndQCWorkflows

The DKFZ alignment workflow plugin originally developed at the eilslabs

Language: Python - Size: 5.22 MB - Last synced at: 4 months ago - Pushed at: over 1 year ago - Stars: 7 - Forks: 5

cemordaunt/comethyl

An R package for weighted region comethylation network analysis

Language: R - Size: 33.5 MB - Last synced at: 9 months ago - Pushed at: over 1 year ago - Stars: 7 - Forks: 2

waterlandlab/CluBCpG

Cluster-based analysis of CpG methylation

Language: Python - Size: 9.7 MB - Last synced at: 10 months ago - Pushed at: over 1 year ago - Stars: 10 - Forks: 6

itsvenu/ALPS

AnaLysis routines for ePigenomicS data - 🏫 Bioconductor project

Language: R - Size: 2.09 MB - Last synced at: over 1 year ago - Pushed at: almost 2 years ago - Stars: 15 - Forks: 3

linquynus/TFregulomeR-dev

TFregulomeR reveals transcription factors’ context-specific features and functions

Language: R - Size: 7.36 MB - Last synced at: over 1 year ago - Pushed at: about 3 years ago - Stars: 2 - Forks: 3

YoannPa/Computational_Epigenomics

This repository contains data and functions related to computational epigenomics data analysis.

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jlab-code/MethylStar

A fast and robust pre-processing pipeline for bulk or single-cell whole-genome bisulfite sequencing (WGBS) data.

Language: Python - Size: 2.96 MB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 29 - Forks: 6

christacaggiano/snakemake_WGBS

Using Snakemake to implement ENCODE WGBS pipeline

Language: Python - Size: 116 KB - Last synced at: almost 2 years ago - Pushed at: over 6 years ago - Stars: 0 - Forks: 1

lulizou/boostme

R package to impute methylation within WGBS using machine learning

Language: R - Size: 8.81 MB - Last synced at: almost 2 years ago - Pushed at: about 2 years ago - Stars: 9 - Forks: 3

sajuukLyu/Protocols-4pub

Multi-omics analysis protocols by Lyu.

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benoukraflab/TFregulomeR-old

TFregulomeR reveals transcription factors’ context-specific features and functions

Language: R - Size: 7.26 MB - Last synced at: almost 2 years ago - Pushed at: about 3 years ago - Stars: 15 - Forks: 3

hhg7/defiant

Differential methylation: Easy, Fast, Identification and ANnoTation

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ben-laufer/PCB-Placenta-and-Brain

Analyses for the manuscript "Prenatal PCB exposure alters a shared neurodevelopmental DNA methylation profile in mouse placenta and fetal brain".

Language: R - Size: 59.6 KB - Last synced at: 6 months ago - Pushed at: almost 4 years ago - Stars: 1 - Forks: 0

cemordaunt/WilsonDiseaseEpigenome

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

Language: R - Size: 111 KB - Last synced at: 9 months ago - Pushed at: almost 6 years ago - Stars: 4 - Forks: 0

seb-mueller/snakemake-bisulfite

Pipeline for BS-Seq data based on snakemake

Language: Python - Size: 1.06 MB - Last synced at: about 2 years ago - Pushed at: about 3 years ago - Stars: 5 - Forks: 0

labbcb/methseq 📦

Automation tool for high-throughput sequencing DNA methylation data

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luuloi/Meth10X

Whole Genome Bisulfite Sequencing Alignment pipeline

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cemordaunt/AutismCordBloodMethylation

Analysis of DNA methylation data by whole-genome bisulfite sequencing in umbilical cord blood from ASD and TD subjects in the MARBLES and EARLI studies

Language: R - Size: 311 KB - Last synced at: 9 months ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 1

ben-laufer/FASTQ_Me

An example script of how to download WGBS data from SLIMS, check md5sums, merge lanes, and submit a project to CpG_Me

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stephaniehicks/FlowSorted.Blood.WGBS.BLUEPRINT

A Bioconductor ExperimentHub data package for flow sorted purified whole blood cell types measured using DNA methylation on WGBS platform from BLUEPRINT

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cemordaunt/WilsonDiseaseThioredoxin

Analysis of DNA methylation and gene expression for thioredoxin system genes in Wilson disease

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aryeelab/tcgaWGBSData.hg19

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