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@CompEpigen Computational Cancer Biology and Epigenomics

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    53 repositories

    • methylbert

      Public
      A Transformer-based model for read-level DNA methylation pattern identification and tumour deconvolution
      methylationlanguage-modelbertdeconvolutiontumour
      Jupyter Notebook
      •
      MIT License
      •3•21•2•0•Updated Dec 10, 2024Dec 10, 2024

    • wf_WGS

      Public
      Nextflow workflow to process WGS data
      Python
      •0•4•0•0•Updated Nov 27, 2024Nov 27, 2024

    • pyjacker

      Public
      Enhancer hijacking detection using WGS + RNA-seq
      Python
      •
      MIT License
      •1•2•0•0•Updated Nov 27, 2024Nov 27, 2024

    • figeno

      Public
      Tool for plotting sequencing data along genomic coordinates.
      Python
      •
      GNU General Public License v3.0
      •8•253•3•0•Updated Nov 20, 2024Nov 20, 2024

    • wgbs_atlas_simulation

      Public
      Read-level methylome simulation for WGBS normal cell atlas data (https://doi.org/10.1038/s41586-022-05580-6)
      Python
      •
      MIT License
      •0•0•0•0•Updated Nov 1, 2024Nov 1, 2024

    • methylseq_simulation

      Public
      Read-level methylome simulator
      Python
      •
      MIT License
      •0•4•0•0•Updated Nov 1, 2024Nov 1, 2024

    • epiCHAOS

      Public
      R
      •
      Other
      •0•3•1•0•Updated Oct 17, 2024Oct 17, 2024

    • epiCHAOS-manuscript

      Public
      R
      •0•1•0•0•Updated Oct 2, 2024Oct 2, 2024

    • cutandrun_SRSF2_Wagner2023

      Public
      Python
      •0•2•0•0•Updated Sep 26, 2024Sep 26, 2024

    • CompEpigen.github.io

      Public
      CompEpigen IO
      CSS
      •0•0•0•0•Updated Sep 16, 2024Sep 16, 2024

    • PipelineOlympics

      Public
      R
      •0•0•0•0•Updated Aug 21, 2024Aug 21, 2024

    • digital_sorter

      Public
      R
      •
      MIT License
      •0•0•9•0•Updated Aug 21, 2024Aug 21, 2024

    • scformatter

      Public
      Interoperability between Seurat, SingleCellExperiment, and Scanpy anndata
      Python
      •0•0•6•0•Updated Aug 21, 2024Aug 21, 2024

    • methrix

      Public
      An R 📦 for fast and flexible DNA methylation analysis
      bioinformaticsdna-methylationbedgraph
      R
      •
      Other
      •12•30•0•1•Updated Jul 24, 2024Jul 24, 2024

    • quothic

      Public
      This package provides tools to calculate transcription heterogeneity indices like Silhouette score, Shannon entropy, Simpson's index (TBA), and the Gini index (TBA) for single-cell RNA-seq data using Seurat objects.
      R
      •0•1•1•0•Updated Jul 19, 2024Jul 19, 2024

    • MeDeCom

      Public
      Decomposition of heterogeneous DNA methylomes
      HTML
      •16•22•9•0•Updated Jul 10, 2024Jul 10, 2024

    • FactorViz

      Public
      Visualisation server for methylome decomposition experiments
      R
      •
      GNU General Public License v3.0
      •1•2•3•2•Updated Jul 10, 2024Jul 10, 2024

    • DecompPipeline

      Public
      Large automated pipeline for running the MeDeCom
      HTML
      •
      GNU General Public License v3.0
      •6•4•0•0•Updated Oct 27, 2023Oct 27, 2023

    • SeqDeconv_Pipeline

      Public
      Sequencing-based deconvolution pipeline examples
      MIT License
      •0•2•0•0•Updated Aug 30, 2023Aug 30, 2023

    • CancerEpigenomicsTutorial

      Public
      Yearly tutorial for the Cancer Biology M.Sc. students
      R
      •1•0•0•0•Updated May 8, 2023May 8, 2023

    • pyMeDeCom

      Public
      Python
      •0•0•0•0•Updated Mar 17, 2023Mar 17, 2023

    • WGS_pipeline

      Public
      Python
      •0•1•0•0•Updated Feb 27, 2023Feb 27, 2023

    • BS_Benchmarking_CWL

      Public
      Common Workflow Language
      •
      MIT License
      •0•0•0•0•Updated Jul 5, 2022Jul 5, 2022

    • hapcounter

      Public
      Minimal tool to count genotypic frequencies at two loci covered by same read fragments
      Rust
      •0•0•0•0•Updated Jun 9, 2022Jun 9, 2022

    • scMethrix

      Public
      An R 📦 for fast and flexible scDNA methylation analysis
      R
      •
      Other
      •2•2•1•0•Updated Apr 18, 2022Apr 18, 2022

    • BasicR

      Public
      HTML
      •
      Other
      •2•3•0•0•Updated Mar 28, 2022Mar 28, 2022

    • dxm

      Public
      Deconvolution of Methylation Sequencing Data
      Python
      •
      GNU General Public License v3.0
      •2•0•0•0•Updated Mar 3, 2022Mar 3, 2022

    • bed-beta

      Public
      More extensive tools for bayesian epiallele detection (beta version)
      R
      •
      MIT License
      •2•0•0•0•Updated Feb 28, 2022Feb 28, 2022

    • MethylPurify

      Public
      Upgrade version of MethylPurify
      Python
      •
      MIT License
      •0•0•0•0•Updated Feb 14, 2022Feb 14, 2022

    • prism

      Public
      Methylation Pattern-based, Reference-free Inference of Subclonal Makeup
      Python
      •1•0•0•0•Updated Feb 9, 2022Feb 9, 2022