isoespy 1.1.0

This package visualizes isoform structures, expression levels and functional features.

Isoespy

Isoespy is a visualization and functional annotation tool for transcript isoforms identified from long-read transcriptome data. It assists in the interpretation of isoform-level transcriptomic models, which are identified and quantified from RNA-seq data, by supporting differential expression analysis, novel isoform ORF prediction, and integration of external functional predictions. The tool provides intuitive visualizations of gene expression states, based on these processed data.

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🔧 Features

• Differential expression visualization between two sample groups (e.g., tumor vs. normal)
• Visualization of:
  • CDS (coding sequence) predictions
  • Pfam domains
  • Signal peptides
  • NMD-susceptible isoforms
• Visualizations are based on transcript-level GTF files

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📦 Installation

Isoespy can be installed via PyPI:

pip install isoespy

or

python -m pip install isoespy

Requires Python 3.8+

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🚀 Commands Overview

Isoespy provides six CLI commands:

1. isoespy-orfpred

Predicts ORFs for unannotated transcripts using CPAT and TransDecoder.

isoespy-orfpred --workdir <dir> --hexamer <Path to hexamer table> --model <Path to model> \
                --fasta <nt fasta> --cpatoutprefix <prefix> --transdecoder_path <Path to TransDecoder> \
                --gtf <GTF file> --meta <metadata>

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2. isoespy-makefa

Extracts transcript nucleotide or amino acid sequences from GTF and genome reference.

isoespy-makefa --gtf <GTF file> --genome <genome reference> --meta <metadata> \
               --feature <exon/CDS> --type <nucleotide/amino_acid>

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3. isoespy-edger

Performs DE analysis using edgeR with a prepared R script and sample metadata.

isoespy-edger --r_script <R script> --meta_data <metadata> --count_data <expression count> \
              --output_de <DE output> --output_cpm <CPM output>

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4. isoespy-makegtf

Merges external annotation TSV into a GTF file for visualization.

isoespy-makegtf --gtfprep_file <input TSV> --gtf_file <original GTF> --meta_file <metadata> \
                --output <output GTF> --frame_file <frame info file from makefa>

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5. isoespy-de

Visualizes DE results for a gene with intron compression and outlier control.

isoespy-de --gene_name <gene> --gtf_data <GTF> --expression_data <expression> \
           --det_data <DE result> --meta_data <metadata> --compress_introns <int size> \
           --show_outliers <True/False>

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6. isoespy-ff

Visualizes functional annotations (domains, signals, etc.) for isoforms.

isoespy-ff --gene_name <gene> --gtf_data <GTF> --meta_data <metadata> \
           --compress_introns <int size> --annotation <annotation TSV>

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📁 Requirements

Files

• Reference genome FASTA and index
• CPAT pretrained hexamer and model files

External Tools

• CPAT
• TransDecoder

Python Libraries

• pysam
• matplotlib
• pandas
• seaborn
• numpy

R Libraries

• edgeR

Users are responsible for preparing the required files and ensuring edgeR is installed in their R environment.

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🪪 License

MIT License

Developed by Ko Ikemoto