ClonoLoom

Genes and junctions

The Genes and Junctions parts of the Repertoire view show what each sample's clonotypes are made of, each share of the clonotypes (each counted once) or of the abundance, with its 95% interval, for each sample or each condition.

Genes

The Genes part: a heatmap of each sample's TRBV gene usage by clonotypes, and one gene's share across the samples with 95% intervalsThe Genes part: a heatmap of each sample's TRBV gene usage by clonotypes, and one gene's share across the samples with 95% intervals
Each sample's V genes by clonotypes, and one gene across the samples.

Open Repertoire › Genes and choose Count genes and junctions; one result serves both parts and is kept with the project.

A clonotype's genes are its rearrangements', in proportion to their counts. A call between several genes gives each an equal part, and what was not called is said, never dropped.

Junctions

The Junctions part: each sample's junction lengths, their mean with its interval, and the amino acids of the junctionsThe Junctions part: each sample's junction lengths, their mean with its interval, and the amino acids of the junctions
The simulated samples' spectratypes, mean lengths and amino acids.

Clonotypes or abundance, samples or conditions

Clonotypes counts each clonotype once: what the repertoire is made of. Abundance weights each by its cells or molecules: what the sample is mostly made of, dominated by its largest clones. Intervals come from 200 bootstrap replicates of each sample's clonotypes. Conditions summarizes each condition (from the samples' annotation or metadata) by the mean of its samples, each counted once, with their range.

Using the result

The heatmaps and plots save as figures, Export writes every share as CSV, and the methods paragraph says what was counted and how. Scripts use gene_usage (Remote control).