Computational Cancer Biology and Epigenomics

Pinned Repositories

ATACseq_workflows
Workflows for processing of ATAC-seq Data based on the Common Workflow Language (CWL)
Language:Common Workflow Language4 3 10
BasicR
Language:HTML3 4 02
ChIPseq_workflows
Workflows for processing of ChIP-seq, ChIPmentation, and Cut&Run data based on the Common Workflow Language
Language:Common Workflow Language8 3 12
DecompPipeline
Large automated pipeline for running the MeDeCom
Language:HTML4 4 86
ezASCAT
Conveniently perform ASCAT copy-number analysis from Tumor-Normal or Tumor only BAM files in R
Language:R10 3 12
figeno
Tool for plotting sequencing data along genomic coordinates.
Language:Python235 6 157
methrix
An R :package: for fast and flexible DNA methylation analysis
Language:R27 8 2510
methylbert
A Transformer-based model for read-level DNA methylation pattern identification and tumour deconvolution
Language:Jupyter Notebook13 2 40
methylseq_simulation
Read-level methylome simulator
Language:Python4 2 00
WGBS_workflows
WGBS pipeline based on CWL
Language:Common Workflow Language2 4 01

Computational Cancer Biology and Epigenomics's Repositories

CompEpigen/figeno
Tool for plotting sequencing data along genomic coordinates.
Language:Python235 6 157
CompEpigen/methrix
An R :package: for fast and flexible DNA methylation analysis
Language:R27 8 2510
CompEpigen/methylbert
A Transformer-based model for read-level DNA methylation pattern identification and tumour deconvolution
Language:Jupyter Notebook13 2 40
CompEpigen/ezASCAT
Conveniently perform ASCAT copy-number analysis from Tumor-Normal or Tumor only BAM files in R
Language:R10 3 12
CompEpigen/DecompPipeline
Large automated pipeline for running the MeDeCom
Language:HTML4 4 86
CompEpigen/methylseq_simulation
Read-level methylome simulator
Language:Python4 2 00
CompEpigen/BasicR
Language:HTML3 4 02
CompEpigen/wf_WGS
Nextflow workflow to process WGS data
Language:Python3 1 00
CompEpigen/cutandrun_SRSF2_Wagner2023
Language:Python2 1 00
CompEpigen/SeqDeconv_Pipeline
Sequencing-based deconvolution pipeline examples
2 3 00
CompEpigen/ChIP_downstream_analysis
Language:HTML1 4 10
CompEpigen/KBH_thesis_work
Thesis project for KBH
Language:Python1 3 22
CompEpigen/Nanopore_workflows
Language:Common Workflow Language1 4 01
CompEpigen/pubARID1A
This repository contains the code and data for the research paper of the ARID1A project conducted in the Cancer Epigenomics Division, German Cancer Research Center (DKFZ).
Language:R1
CompEpigen/pyjacker
Language:Python1 1 01
CompEpigen/scMethrix
An R 📦 for fast and flexible scDNA methylation analysis
Language:R1 4 12
CompEpigen/WGS_pipeline
Language:Python1 1 00
CompEpigen/bed-beta
More extensive tools for bayesian epiallele detection (beta version)
Language:R1 0
CompEpigen/BS_Benchmarking_CWL
Language:Common Workflow Language3 0
CompEpigen/CancerEpigenomicsTutorial
Yearly tutorial for the Cancer Biology M.Sc. students
Language:R2 01
CompEpigen/Decomp_web
Supplementary resources website for the paper "Reference-free deconvolution of complex DNA methylation data - a detailed protocol"
Language:HTML3 01
CompEpigen/denbi_kpi_tracking
Utilities for tracking KPIs for de.NBI.
Language:Python2 0
CompEpigen/digital_sorter
Language:R
CompEpigen/dxm
Deconvolution of Methylation Sequencing Data
Language:Python1 0
CompEpigen/epiCHAOS
Language:R1 0
CompEpigen/hapcounter
Minimal tool to count genotypic frequencies at two loci covered by same read fragments
Language:Rust3 0
CompEpigen/methrixEasysetup
Language:R3 0
CompEpigen/MethylPurify
Upgrade version of MethylPurify
Language:Python3 0
CompEpigen/prism
Methylation Pattern-based, Reference-free Inference of Subclonal Makeup
Language:Python1 0
CompEpigen/pyMeDeCom
Language:Python1 0