10x Genomics
Single Cell Immune Profiling
Cell Ranger, printed on 09/07/2024
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