10x Genomics
Single Cell Immune Profiling

Cell Ranger, printed on 11/21/2024

Release Notes for Loupe V(D)J Browser 2

Loupe V(D)J Browser 2.1.0

• Better support for allele-aware references
• New B cell paired and unpaired isotype summary charts
• Convert all proportions to percentage
• Clarify help clonotype list, comparison, and bug report text

Loupe V(D)J Browser 2.0.1

• Renames Multi-Sample Comparison to Comparison Mode
• Fixes Sample Overlap single-chain counting bug, simplifies similarity metric options
• Prevents click event from comparison mode selector from propagating to the chart underneath and hiding a sample
• Comparison Mode documentation update

Loupe V(D)J Browser 2.0.0

B Cell Support

The Chromium™ Single Cell V(D)J Solution now offers comprehensive, scalable profiling of both 5′ gene expression transcripts and full-length, paired T Cell Receptor and B cell immunoglobulin transcripts. Loupe V(D)J Browser has added a few additional features especially designed to help with analyzing B Cell samples.

• In chain view, indicate Isotype Switching alongside the barcode labels
• All existing features in Loupe V(D)J browser are compatible with B cells

Comparison Mode

Loupe V(D)J Browser 2 now allows you to load multiple samples into the same workspace and includes powerful plots, metrics, and statistics to compare multiple samples. You can also quickly switch between multiple samples a single workspace. New features include:

• Clonotype Comparison - Compare the relative abundance of clonotypes between two samples and find the clonotypes that have the greatest difference
• Sample Overlap - Determine sample similarity between paired clonotypes or unpaired chains
• Top Clonotype Overlap - Determine which top clonotypes are shared between multiple samples
• Clonotype Frequency - Plot and compare the clonotype abundances between two samples.
• Sample Table - Quickly compare high level metrics between multiple samples
• Gene Usage - Plot the gene usage of the V, D, J, and C genes accross multiple samples.

You can also export any of these charts to an image or the underlying data to a CSV.

Integrated V(D)J Clonotype + Gene Expression Analysis

When using the combined 5′ Gene Expression and T-Cell and B cell enrichment kits, it is now possible to measure whole transcriptome gene expression and V(D)J repertoire diversity from the same sample. To facilitate this analysis, Loupe V(D)J Browser 2.0 allows you to combine the V(D)J and gene expression data with a few clicks.

To find out more about how to conduct an integrated experiment, consult the Single Cell V(D)J + Gene Expression page. For a complete Loupe how-to including some example data, go to Integrated V(D)J and Gene Expression Analysis in Loupe V(D)J Browser.

The complete list of gene expression features in Loupe V(D)J Browser include:

• Import .cloupe gene expression files into a single .vloupe workspace
• Compare clonotypes identified in gene expression clusters within one or between two samples and find clonotypes that have the greatest difference
• Filter the clonotype list for clonotypes that only exist within one gene expression cluster
• On import, detect whether a V(D)J dataset is associated with the loaded gene expression data

Additional Features

• Summary Charts
  • Added new CDR3 bar graph
  • Added D Gene and C Gene Usage Charts
  • Export all summary charts as SVG
  • Export summary chart data as CSV
  • View help text for each chart by hovering over the question mark
• Export Clonotype List as clonotypes or single chains
• Support for soft-clipped alignments generated from Cell Ranger
• Added color legend for chain view variants
• Support native macOS window switching
• Augment all inputs by allowing the select all hotkey