wgbs

There are 2 repositories under wgbs topic.

• sns

  igordot / sns

  Analysis pipelines for genomic sequencing data

  bioinformaticsrna-seqwgswesilluminasequencingatac-seqwgbsrrbsanalysisgenomicsdnapipelinenyu
  Language:Shell 66

• sajuukLyu / Protocols-4pub

  Multi-omics analysis protocols by Lyu.

  rna-seqatac-seqwgbschip-seq
  Language:HTML 51

• 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)

  bioinformaticsdna-methylationwgbscpgbiostatisticsdmrsworkflowrrbsem-seqtidyversewhole-genome-bisulfite-sequencing
  Language:R 42

• jlab-code / MethylStar

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

  bismarkdna-methylationgenomemethylationpipelinewgbs
  Language:Python 35

• ENCODE-DCC / wgbs-pipeline

  ENCODE whole-genome bisulfite sequencing (WGBS) pipeline

  bioinformaticswgbsmethylationngspipeline
  Language:Python 31

• 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)

  bioinformaticswgbscpgdna-methylationalignmentwhole-genome-bisulfite-sequencingslurmbismark-cytosine-report
  Language:Shell 23

• hhg7 / defiant

  Differential methylation: Easy, Fast, Identification and ANnoTation

  bisulfite-sequencingdifferentially-methylated-elementsmethylationdmrrrbswgbs
  Language:Shell 18

• benoukraflab / TFregulomeR-old

  TFregulomeR reveals transcription factors’ context-specific features and functions

  transcription-factor-binding-sitedna-methylationchip-seqwgbscofactor
  Language:R 16

• itsvenu / ALPS

  AnaLysis routines for ePigenomicS data - 🏫 Bioconductor project

  epigenomicsdata-analysischip-seqatac-seqwgbsdatavizrstatsbioconductor
  Language:R 16

• waterlandlab / CluBCpG

  Cluster-based analysis of CpG methylation

  cpg-methylationwgbsbioinformatics
  Language:Python 13

• lulizou / boostme

  R package to impute methylation within WGBS using machine learning

  wgbsimputationmachine-learningdna-methylation-predictionxgboost
  Language:R 12

• twlab / methylGrapher

  Methylation analysis pipeline for Genome Graph

  alignmentgenome-graphmethylationwgbs
  Language:Python 11

• cemordaunt / comethyl

  An R package for weighted region comethylation network analysis

  whole-genome-bisulfite-sequencingwgbsdna-methylationcomethylation-network-analysiswgcnar-package
  Language:R 8

• cemordaunt / DMRfinder

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

  whole-genome-bisulfite-sequencingwgbsdna-methylationpipelinedmrs
  Language:R 8

• DKFZ-ODCF / AlignmentAndQCWorkflows

  The DKFZ alignment workflow plugin originally developed at the eilslabs

  workflowbwawgbsquality-controlalignmentfastq-filesroddywesbwa-membam-filesconda-environment
  Language:Python 7

• seb-mueller / snakemake-bisulfite

  Pipeline for BS-Seq data based on snakemake

  bismarkbisulfite-sequencingcondadna-methylationem-seqepigeneticspipelinesnakemakesnakemake-bisulfitewgbs
  Language:Python 6

• cemordaunt / WilsonDiseaseEpigenome

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

  whole-genome-bisulfite-sequencingwgbsdna-methylationdmrswilson-disease
  Language:R 4

• LieberInstitute / BiocMAP

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

  wgbsnextflow
  Language:HTML 3

• luuloi / Meth10X

  Whole Genome Bisulfite Sequencing Alignment pipeline

  wgbsworkflowpipelinenomeseq
  Language:Shell 3

• andrewdavidsmith / transferase

  The transferase system for retrieving methylome data from methbase

  dna-methylationepigeneticsepigenomicsmethylomebisulfitebisulfite-sequencingmethyl-seqmethylationmethylation-analysiswgbs
  Language:C++ 2

• 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

  wgbsslimsrsyncmd5summergesequencingfastqdnamethylation
  Language:Shell 2

• huishenlab / Biscuit_Snakemake_Workflow

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

  methylationwgbs
  Language:Python 2

• linquynus / TFregulomeR-dev

  TFregulomeR reveals transcription factors’ context-specific features and functions

  dna-methylationchip-seqwgbscofactortranscription-factor-binding-site
  Language:R 2

• YoannPa / Computational_Epigenomics

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

  epigenomicswgbsdataprocessingbioinformaticsmethylationcomputational-epigenomicsbeta-valuescoverage450khuman-methylation-450k
  Language:HTML 2

• 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".

  wgbswhole-genome-bisulfite-sequencingdmrdifferentially-methylated-regionsrtidyversebioconductorbioinformatics
  Language:R 1

• 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

  bioconductorbioconductor-packagedatadna-methylationwgbsbisulfite-sequencingbloodflowsort
  Language:R 1

• 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

  whole-genome-bisulfite-sequencingwgbsdna-methylationdmrsautism
  Language:R 0

• cemordaunt / WilsonDiseaseThioredoxin

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

  whole-genome-bisulfite-sequencingwgbsdna-methylationdmrswilson-diseaserna-seqgene-expression
  Language:R 0

• 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

  open-access-datamotifmethylationwgbstf-binding
  Language:Jupyter Notebook 0
• iscream

  huishenlab / iscream

  Make fast and memory efficient BED file queries, summaries, and matrices.

  rcppwgbsbedtabix
  Language:R 0

• tangilim / Age-Realted_CpGs_ZF_JD

  Code for DNA methylation extraction, age-related CpG site identification, data manipulation, genomic annotation, statistical analyses and plots include in submitted paper on sex chromosome-mediated aging methylomes in female heterogametic species

  ageingbirdsdnamecologywgbs
  Language:R 0

• aryeelab / tcgaWGBSData.hg19

  tcgawgbshg19sequencing
  Language:R

• christacaggiano / snakemake_WGBS

  Using Snakemake to implement ENCODE WGBS pipeline

  wgbsmethylationsnakemakepythonbismark
  Language:Python

• CompEpigen / methrix_docs

  Documentation for methrix R package

  dna-methylationwgbs
  Language:HTML

• hmyh1202 / WGBS

  A Whole-genome Bisulfite Sequencing(WGBS) pipline

  wgbsngspipeline

• labbcb / methseq

  Automation tool for high-throughput sequencing DNA methylation data

  wgbsem-seqwdlcromwell
  Language:WDL