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Integration of ATAC-Seq and multi-assay ChIP-Seq data using IDEAS (Hidden Markov Model) approach.Multi-Epigenomic state annotation with CHDI NeuroLINCS Epigenomics data using the tool "IDEAS"

R 0.16% Shell 0.67% Jupyter Notebook 99.17%
atac-seq chip-seq epigenomics hidden-markov-model hmm integration multi-omics

hidden-markov-model-based-integration-of-multi-assay-epigenomics-samples's Introduction

CHDI-NeuroLINCS-Multi-Epigenomics-Annotation

Multi-Epigenomic state annotation with CHDI NeuroLINCS Epigenomics data using the tool "IDEAS"

Chronology:

  1. ./analysis/1_get_consensus_peaks/scripts/diffbind_get_consensus_peaks.R
  2. ./analysis/1_get_consensus_peaks/scripts/matrix_to_regions.sh
  3. ./analysis/2_define_input_regions/code/input_regions.ipynb
  4. ./analysis/3_define_input_bam/code/prepare_prepMat_input.ipynb
  5. ./analysis/4_prepMat/scripts/prepMat.sh
  6. ./analysis/4_prepMat/notebooks/average_replicates.ipynb
  7. ./analysis/5_IDEAS/scripts/IDEAS.sh
  8. ./analysis/5_IDEAS/scripts/IDEAS_control_only.sh

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