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MyImmune Docs

Overview

MyImmune is a platform for immune repertoire analysis. It provides a web application where users submit bioinformatics jobs, and an backend that executes those jobs. There is an Python SDK which allows users to interact with the platform programmatically.

How it works

Section titled “How it works”
  1. Submit a job via the web app — choose a pipeline, upload files, configure parameters.
  2. Wait for execution — the system processes your job asynchronously.
  3. View results in the web app — job status, logs, and downloadable output files.

Available pipelines

Section titled “Available pipelines”

FASTQ Pipeline

Pipeline to convert FASTQ files to AIRR (Adaptive Immune Receptor Repertoire) formatted TSV files

SRA Data Pipeline

Pipeline to download data from SRA (Sequence Read Archive) and convert to AIRR (Adaptive Immune Receptor Repertoire) formatted TSV files

Adaptive Biotech Pipeline

Pipeline to convert data from Adaptive Biotechnologies’ ImmuneSEQ platform to AIRR (Adaptive Immune Receptor Repertoire) formatted TSV files

Pseudo-Sequence Alignment

Aligns paratope amino acid sequences using the IMGT numbering scheme to produce standardized pseudo-sequences for downstream analysis

TCR to Amino Acid

Assembles full germline amino acid sequences from V/J gene calls and CDR3 sequences

Clustering Pipeline

Pipeline for clustering BCR / TCR paratope sequences

Stratification Pipeline

Pipeline for running patient stratification models to classify responders from non-responders to a treatment

Sequence Search

Pipeline for bulk BCR/TCR sequence search across multiple databases with numerous comparison metrics

Epitope Prediction

Pipeline for bulk Epitope prediction from BCR sequences (paired and unpaired)

Experimental

Section titled “Experimental”

Early access features under active development. Behavior may change without notice.

Single Sequence Search

Search a single amino acid sequence against reference databases with interactive scoring and visualization.

Single Epitope Prediction

Predict epitope clusters for a single antibody by heavy and light chain sequences.

Next steps

Section titled “Next steps”