EUbar

EUbar predicts the effect of noncoding single nucleotide variants on transcription factor binding affinity using accessible chromatin regions as sequence probes and matched ChIP-seq signal as a measure of binding intensity. It also supports whole-region scanning for mutational effect landscapes and affinity-based motif discovery.

Installation

pip install eubar

# or

git clone https://github.com/SvenBaileyLab/EUbar
cd EUbar
pip install .

Signal extraction also requires the external bedtools executable. For YAML jobs, install the optional dependency with pip install 'eubar[yaml]'.

Confirm the install:

eubar --help

Workflow overview

For contiguous sequence analyses:

1. Build an array file — index all k-mers in your accessible regions
2. Compute probe intensities — summarise ChIP-seq signal across those regions
3. Run analysis — predict SNV effects, scan a region, or discover motifs

Masked SNV and motif analyses use probe intensities and genome sequence directly, without an array file. Calibration compares probe caps or candidate masks before you choose settings for an analysis.

Commands

Command-specific help is available with eubar <command> --help.

Quick start

# 1. Build array
eubar array \
  --bed regions.bed --genome hg38.fa \
  --kmer-size 8 --output regions_8mer.txt

# 2. Compute intensities
eubar intensities \
  --bed regions.bed --signal tf_chipseq.bw \
  --genome-fasta hg38.fa --output probe_intensities.tsv

# 3. Predict SNV effect
eubar snv \
  --intensities probe_intensities.tsv --array regions_8mer.txt \
  --genome hg38.fa --snv-list "chr5:1295113:C>T" \
  --best-pval --holm --diagnostics

Tutorials

Step-by-step tutorials using real ENCODE data (MCF7 DNase-seq + GABPA ChIP-seq):

• Data preparation — download data, build array, compute intensities
• SNV analysis — predict allelic effects on TF binding
• Scan analysis — scan a genomic region for binding effects
• Motif discovery — contiguous and masked motifs
• Masks and calibration — spacing, probe limits and recommendation tables
• YAML jobs — reusable tasks and pipelines

Citation

If you use EUbar in your research, please cite:

[manuscript citation — to be added on publication]

License

GNU General Public License v3.0.

Python API and tests

See the Python task API for calling tasks directly and the test suite for regression checks.