--- id: "claim:normalization-for-sampled-count-data-2026-06-10-biorxiv-v3:de72c6017e7acae1e8bd" kind: "claim" title: "How to jointly achieve variance stabilization and depth normalization remains debated." description: "" url: "https://sina.bio/claim/how-to-jointly-achieve-variance-stabilization-and-depth-normalization-r-4646f09a" --- # How to jointly achieve variance stabilization and depth normalization remains debated. ## Content How to jointly achieve variance stabilization and depth normalization remains debated. ## Metadata ```json { "claim_position": 9, "source_publication_id": "version:normalization-for-sampled-count-data--2026-06-10-biorxiv-v3", "source_work_id": "work:normalization-for-sampled-count-data" } ``` ## Connections (9) ### Comparison of transformations for single-cell RNA-seq data - ID: `version:citing:2023-comparison-of-transformations-for-single-cell-rna-seq-data` - Kind: `publication` - Direction: `outgoing` - URL: This publication is cited in support of this claim. > While variance stabilization > has been studied for over 90 years (Bartlett, 1936), the ques- > tion of how to achieve both variance stabilization and depth > normalization for single-cell RNA-seq is a matter of ongoing > debate (Booeshaghi and Pachter, 2021; Lun et al., 2016; Lun, > 2018; Ahlmann-Eltze and Huber, 2023; Cuevas-Diaz Duran > et al., 2024; Lu et al., 2025; Huang et al., 2025). Source: 2026-06-10-biorxiv-v3.pdf — ### Compositional data modeling of high-dimensional single cell RNA-seq (CoDA-hd): its advantages over commonly used normalization approaches - ID: `publication:doi:10.1186/s12967-025-07157-z` - Kind: `publication` - Direction: `outgoing` - URL: This publication is cited in support of this claim. > While variance stabilization > has been studied for over 90 years (Bartlett, 1936), the ques- > tion of how to achieve both variance stabilization and depth > normalization for single-cell RNA-seq is a matter of ongoing > debate (Booeshaghi and Pachter, 2021; Lun et al., 2016; Lun, > 2018; Ahlmann-Eltze and Huber, 2023; Cuevas-Diaz Duran > et al., 2024; Lu et al., 2025; Huang et al., 2025). Source: 2026-06-10-biorxiv-v3.pdf — ### Data normalization for addressing the challenges in the analysis of single-cell transcriptomic datasets - ID: `publication:doi:10.1186/s12864-024-10364-5` - Kind: `publication` - Direction: `outgoing` - URL: This publication is cited in support of this claim. > While variance stabilization > has been studied for over 90 years (Bartlett, 1936), the ques- > tion of how to achieve both variance stabilization and depth > normalization for single-cell RNA-seq is a matter of ongoing > debate (Booeshaghi and Pachter, 2021; Lun et al., 2016; Lun, > 2018; Ahlmann-Eltze and Huber, 2023; Cuevas-Diaz Duran > et al., 2024; Lu et al., 2025; Huang et al., 2025). Source: 2026-06-10-biorxiv-v3.pdf — ### Depth normalization for single-cell genomics count data - ID: `version:normalization-for-sampled-count-data--2026-06-10-biorxiv-v3` - Kind: `publication` - Direction: `incoming` - URL: This publication contains this grounded claim. > the ques- tion of how to achieve both variance stabilization and depth normalization for single-cell RNA-seq is a matter of ongoing debate Source: 2026-06-10-biorxiv-v3.pdf — ### Normalization of single-cell RNA-seq counts by log (x+ 1) or log (1+ x) - ID: `version:normalization-of-single-cell-rna-seq-counts-by-log-x-1-or-log-1-x--2021-03-02-bioinformatics` - Kind: `publication` - Direction: `outgoing` - URL: This publication is cited in support of this claim. > While variance stabilization > has been studied for over 90 years (Bartlett, 1936), the ques- > tion of how to achieve both variance stabilization and depth > normalization for single-cell RNA-seq is a matter of ongoing > debate (Booeshaghi and Pachter, 2021; Lun et al., 2016; Lun, > 2018; Ahlmann-Eltze and Huber, 2023; Cuevas-Diaz Duran > et al., 2024; Lu et al., 2025; Huang et al., 2025). Source: 2026-06-10-biorxiv-v3.pdf — ### Overcoming systematic errors caused by log-transformation of normalized single-cell RNA sequencing data - ID: `publication:doi:10.1101/404962` - Kind: `publication` - Direction: `outgoing` - URL: This publication is cited in support of this claim. > While variance stabilization > has been studied for over 90 years (Bartlett, 1936), the ques- > tion of how to achieve both variance stabilization and depth > normalization for single-cell RNA-seq is a matter of ongoing > debate (Booeshaghi and Pachter, 2021; Lun et al., 2016; Lun, > 2018; Ahlmann-Eltze and Huber, 2023; Cuevas-Diaz Duran > et al., 2024; Lu et al., 2025; Huang et al., 2025). Source: 2026-06-10-biorxiv-v3.pdf — ### Pooling across cells to normalize single-cell RNA sequencing data with many zero counts - ID: `publication:doi:10.1186/s13059-016-0947-7` - Kind: `publication` - Direction: `outgoing` - URL: This publication is cited in support of this claim. > While variance stabilization > has been studied for over 90 years (Bartlett, 1936), the ques- > tion of how to achieve both variance stabilization and depth > normalization for single-cell RNA-seq is a matter of ongoing > debate (Booeshaghi and Pachter, 2021; Lun et al., 2016; Lun, > 2018; Ahlmann-Eltze and Huber, 2023; Cuevas-Diaz Duran > et al., 2024; Lu et al., 2025; Huang et al., 2025). Source: 2026-06-10-biorxiv-v3.pdf — ### The Square Root Transformation in Analysis of Variance - ID: `publication:doi:10.2307/2983678` - Kind: `publication` - Direction: `outgoing` - URL: This publication is cited in support of this claim. > While variance stabilization > has been studied for over 90 years (Bartlett, 1936), the ques- > tion of how to achieve both variance stabilization and depth > normalization for single-cell RNA-seq is a matter of ongoing > debate (Booeshaghi and Pachter, 2021; Lun et al., 2016; Lun, > 2018; Ahlmann-Eltze and Huber, 2023; Cuevas-Diaz Duran > et al., 2024; Lu et al., 2025; Huang et al., 2025). Source: 2026-06-10-biorxiv-v3.pdf — ### Transcriptome size matters for single-cell RNA-seq normalization and bulk deconvolution - ID: `version:citing:2025-transcriptome-size-matters-for-single-cell-rna-seq-normalization-and-bulk-deconvolution` - Kind: `publication` - Direction: `outgoing` - URL: This publication is cited in support of this claim. > While variance stabilization > has been studied for over 90 years (Bartlett, 1936), the ques- > tion of how to achieve both variance stabilization and depth > normalization for single-cell RNA-seq is a matter of ongoing > debate (Booeshaghi and Pachter, 2021; Lun et al., 2016; Lun, > 2018; Ahlmann-Eltze and Huber, 2023; Cuevas-Diaz Duran > et al., 2024; Lu et al., 2025; Huang et al., 2025). Source: 2026-06-10-biorxiv-v3.pdf —