How liveanddeadcat/yuchen-s-little-spectral-flow- works
Little Spec is a collection of R workflows for spectral-flow cytometry, taking researchers from gated reference controls through signature assessment and unmixing to downstream analysis. The README documents this overall workflow and its capabilities, but no source excerpts were provided, so edges below reflect documented relationships only; implementation details and unsampled integrations are not inferred.
Main entry points: ref controls Gated controls · gating_ref_control.R Control gating · ols_unmixing_wAF_covarianceMatrxi_CosMatrix.Rmd Signature metrics · spectral_profile_comparisor.qmd Profile comparison
Components 12
Controls and setup
- Gated controls
ref controls - Control gating
gating_reference_controls_example/gating_ref_control.R
Signature assessment
- Profile comparison
spectral_profile_comparisor.qmd - Signature metrics
ols_unmixing_wAF_covarianceMatrxi_CosMatrix.Rmd
Unmixing
- OLS with AF
ols_unmixing_wAF_covarianceMatrxi_CosMatrix.Rmd - Weighted least squares
wls_unmixing.qmd - NNLS exploration
ols_unmixing_wAF_covarianceMatrxi_CosMatrix.Rmd
Data analysis
- Raw and unmixed EDA
EDA.Rmd - Residual analysis
residual_analysis.qmd - Unmixed-data gating
gating_unmixed_example.R - Downstream analysis
index.qmd
Other components
- Flow researcher
Connections 12
- Flow researcher → Control gating: gates controls
README.md - Control gating → Gated controls: exports controls
README.md - Gated controls → Profile comparison: compare signatures
README.md - Gated controls → Signature metrics: evaluate signatures
README.md - Signature metrics → OLS with AF: assess for unmixing
README.md - Flow researcher → OLS with AF: run unmixing
README.md - Flow researcher → Weighted least squares: explore weighting
README.md - Flow researcher → NNLS exploration: explore method
README.md - Flow researcher → Raw and unmixed EDA: inspect data
README.md - Flow researcher → Residual analysis: inspect residuals
README.md - Flow researcher → Unmixed-data gating: gate unmixed data
README.md - Flow researcher → Downstream analysis: analyze unmixed data
README.md