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RECOMBINE identifies recurrent composite markers of cell types and states.

Code ↔ Paper

17 matches between paragraphs of the paper and lines of its authors' code, computed by the harvester (lexical-v1). Click a colored paragraph or line to see its counterpart.

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  1. [1] § Results › RECOMBINE identifies composite marker sets for hierarchical cell identities ↔ R/recombine-package.R, the whole file · a weak match · score 0.81 · slab LASSO, sparse hierarchical clustering, recurrent composite, nearest neighbors, cell subpopulation, SHC SSL
  2. [2] § Methods › Applying RECOMBINE to biological data sets for in-depth case studies › Identifying markers that characterize a rare subpopulation of mouse intestine ↔ R/recombine-package.R, the whole file · a weak match · score 0.81 · intestinal organoid, rare cell subpopulations, scRNA, single cell, transformation, mouse
  3. [3] § Methods › Applying RECOMBINE to biological data sets for in-depth case studies › Selecting targeted panel from scRNA data for spatial molecular profiling of mouse visual cortex ↔ inst/scripts/recombinePipeline_MVCscRNA.R, lines 1–45 · score 0.80 · Allen Brain Atlas, mouse visual cortex, scRNA, downloaded, seq, genes
  4. [4] § Results › RECOMBINE identifies composite marker sets for hierarchical cell identities ↔ R/fl.R, lines 273–327 · score 0.75 · fused LASSO, L0 norm, sparse hierarchical clustering, SHC FL, feature selection, penalty
  5. [5] § Results › RECOBMINE optimizes marker panels for targeted spatial transcriptomics ↔ README.Rmd, lines 114–159 · score 0.74 · Rab3b, recurrent composite, Cck, Nrgn, Synpr, Gad1
  6. [6] § Results › RECOMBINE identifies composite marker sets for hierarchical cell identities ↔ README.Rmd, lines 17–30 · score 0.74 · unbiased selection, high dimensional, hierarchical cell subpopulations, slab LASSO, computational framework, sparse hierarchical clustering
  7. [7] § Methods › Applying RECOMBINE to biological data sets for in-depth case studies › Selecting discriminant markers of transcriptional variation shaped by spatial gradients in the mouse cerebellum ↔ R/fl.R, lines 366–429 · score 0.73 · gap statistic profile, maximum gap statistic, standard error, nearest neighbors, dimensionality, optimal
  8. [8] § Methods › Applying RECOMBINE to biological data sets for in-depth case studies ↔ R/ssl.R, lines 361–416 · score 0.72 · gap statistic profile, dissimilarity metric, squared distance, nearest neighbors, SHC SSL, matrix
  9. [9] § Methods › Applying RECOMBINE to biological data sets for in-depth case studies › Selecting discriminant markers of transcriptional variation shaped by spatial gradients in the mouse cerebellum ↔ R/lasso.R, lines 286–334 · score 0.71 · gap statistic profile, maximum gap statistic, standard error, nearest neighbors, seq, genes
  10. [10] § Methods › Applying RECOMBINE to biological data sets for in-depth case studies ↔ R/fl.R, lines 366–429 · score 0.71 · gap statistic profile, dissimilarity metric, squared distance, nearest neighbors, optimal, SHC
  11. [11] § Methods › Applying RECOMBINE to biological data sets for in-depth case studies › Identifying markers that discriminate heterogeneous cells of human tissues in Tabula Sapiens ↔ R/pipeline.R, lines 190–226 · score 0.65 · log normalized, neighborhood recurrence, batch, Seurat, Harmony, resolution
  12. [12] § Results › RECOMBINE is robust to hyperparameter variation and data sparsity, and outperforms other feature selection methods ↔ R/pipeline.R, lines 190–226 · score 0.64 · fRECOMBINE, nonzero weights, fixed hyperparameter, graph, HVGs, match
  13. [13] § Methods › Benchmarking of RECOMBINE and other feature selection methods using biological data sets › Data preprocessing ↔ inst/scripts/recombinePipeline_MVCscRNA.R, lines 47–95 · score 0.60 · Low quality cells, log normalized, filtered, clustering
  14. [14] § Methods › Overview of RECOMBINE ↔ R/ssl.R, lines 361–416 · score 0.60 · slab LASSO penalty, gap statistics, SHC SSL, spike, metrics, hyperparameters
  15. [15] § Methods › Applying RECOMBINE to biological data sets for in-depth case studies › Selecting targeted panel from scRNA data for spatial molecular profiling of mouse visual cortex ↔ inst/scripts/recombinePipeline_MVCscRNA.R, lines 1–45 · score 0.57 · mouse visual cortex, scRNA, downloaded, genes, clustering, cell
  16. [16] § Methods › Applying RECOMBINE to biological data sets for in-depth case studies › Selecting targeted panel from scRNA data for spatial molecular profiling of mouse visual cortex ↔ README.Rmd, lines 114–159 · score 0.54 · cell subpopulations, Gad1, Pcp4, Sst, Vip, filtered
  17. [17] § Methods › Benchmarking of RECOMBINE and other feature selection methods using biological data sets › Evaluation metrics ↔ R/lasso.R, lines 76–119 · score 0.54 · sparse hierarchical clustering, feature selection, objective, uniformly, norm, weights

Paper

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The authors' code

R · 95 lines · 2.5 KB · Apache-2.0 · 3 matches

  1. rm(list = ls())
  3. library(tidyverse)
  4. library(Seurat)
  5. library(recombine)
  8. # Here we use a scRNA-seq data of the mouse visual cortex from Allen Brain Atlas, which can be downloaded from:
  9. # http://celltypes.brain-map.org/api/v2/well_known_file_download/694413985
  11. # The following files are used after uncompressing the downloaded file:
  12. # mouse_VISp_2018-06-14_exon-matrix.csv
  13. # mouse_VISp_2018-06-14_genes-rows.csv
  14. # mouse_VISp_2018-06-14_samples-columns.csv
  17. # get expression matrix and cell annotation ------
  18. # expression
  19. tb <- read_csv("mouse_VISp_2018-06-14_exon-matrix.csv")
  20. colnames(tb)[1] <- "gene_entrez_id"
  21. tb_data <- tb
  23. # gene names
  24. tb <- read_csv("mouse_VISp_2018-06-14_genes-rows.csv")
  25. stopifnot(all.equal(tb_data$gene_entrez_id, tb$gene_entrez_id))
  26. tb_data$gene_symbol <- tb$gene_symbol
  28. tb_data <- tb_data %>%
  29. select(-gene_entrez_id) %>%
  30. select(gene_symbol, everything())
  32. # transpose
  33. mt <- as.matrix(tb_data[, -1])
  34. rownames(mt) <- tb_data$gene_symbol
  35. mt <- t(mt)
  36. tb_data <- tibble(cell = rownames(mt)) %>%
  37. bind_cols(as_tibble(mt))
  39. # anno
  40. tb <- read_csv("mouse_VISp_2018-06-14_samples-columns.csv")
  41. stopifnot(all.equal(tb_data$cell, tb$sample_name))
  42. tb <- tb %>%
  43. rename(cell = sample_name) %>%
  44. select(cell, class, subclass, cluster)
  45. tb_anno <- tb
  47. # filter low quality cells
  48. low_quality = c('No Class', 'Low Quality')
  49. tb_anno <- tb_anno %>%
  50. filter(!(class %in% low_quality) &
  51. !(subclass %in% low_quality) &
  52. !(cluster %in% low_quality))
  54. tb_data <- tb_data %>%
  55. filter(cell %in% tb_anno$cell)
  58. # generate log-normalized data --------
  59. # Initialize the Seurat object
  60. mt <- as.matrix(tb_data[, -1])
  61. rownames(mt) <- tb_data$cell
  62. mt <- t(mt)
  64. sobj <- CreateSeuratObject(counts = mt,
  65. project = "mvc",
  66. min.features = 0,
  67. min.cells = 0)
  69. # add cell annotation
  70. stopifnot(all.equal(rownames([email hidden]), tb_anno$cell))
  71. [email hidden] <- [email hidden] %>%
  72. cbind(tb_anno[, -1] %>% as.data.frame())
  74. # Normalizing the data
  75. sobj <- NormalizeData(sobj, normalization.method = "LogNormalize", scale.factor = 10000)
  78. # run RECOMBINE pipeline --------
  79. recombine.out <- recombine_pipeline(sobj, subpop_name = "subclass")
  81. # discriminant markers and weights
  82. recombine.out$df_w
  84. # recurrent composite markers of cell subpopulations
  85. recombine.out$df_rcm_subpop %>%
  86. filter(fract_signif_cells > 0.5 & avg_nhood_zscore > 2 & PR_AUC > 0.5) %>%
  87. group_by(subclass) %>%
  88. slice_max(avg_nhood_zscore, n = 3) %>%
  89. ungroup()
  91. recombine.out %>%
  92. saveRDS("recombine.out.rds")
  95. sessionInfo()

recombinePipeline_MVCscRNA.R at commit 8e88ef7, under Apache-2.0 · at the source

Overview

Authors: Xubin Li1, Justin Nguyen1, Anil Korkut1
  1. Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
Institutions: The University of Texas MD Anderson Cancer Center (United States)
Journal: Genome research, volume 36, issue 6, pages 1221-1237
Dates: received 21 April 2025; accepted 15 April 2026; published online June 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1101/gr.280817.125 · PMID 42161585 · PMCID PMC13262949 · OpenAlex W7161790956
Open access: green, a free copy (OpenAlex)
Status: code verified
Categories: human (organism), mouse (organism), zebrafish (organism)
Methods: Connectivity, Statistics, Smoothing, state filtering, decompositions, Machine learning, Preprocessing
MeSH: Algorithms*, Biomarkers*, Animals, Cerebellum, Humans, Mice, Visual Cortex, Zebrafish (* major topic)
Topic: Single-cell and spatial transcriptomics (Molecular Biology, Biochemistry, Genetics and Molecular Biology), according to OpenAlex
Funding: the Bioinformatics Shared Resource (U01CA253472); Andrew Sabin Family Foundation; MD Anderson Cancer Center; Cancer Prevention and Research Institute of Texas (RP240293); NCI NIH HHS (U01 CA253472, P30 CA016672); National Cancer Institute (P30 CA016672)
Citations: not cited yet (Europe PMC); 61 references in the paper

Abstract

Biological function is mediated by the hierarchical organization of cell types and states within tissue ecosystems. Identifying interpretable composite marker sets that both define and distinguish hierarchical cell identities is essential for decoding biological complexity yet remains a major challenge. Here, we present RECOMBINE, an algorithm that identifies recurrent composite marker sets to define hierarchical cell identities. Validation using both simulated and biological data sets demonstrates that RECOMBINE is robust to hyperparameter variation and data sparsity, and achieves higher accuracy in identifying discriminant markers compared with existing approaches. As a partition-free framework, RECOMBINE is particularly powerful for data sets characterized by continuous cell-state transitions, in which defining discrete boundaries is inappropriate. This capability is demonstrated by its application to zebrafish development, revealing gradual transcriptional transitions across embryonic stages, and to the mouse cerebellum, in which it uncovers transcriptional variation shaped by spatial gradients. When applied to single-cell data and validated with spatial transcriptomic data from the mouse visual cortex, RECOMBINE identifies key cell-type markers and generates a robust gene panel for targeted spatial profiling. It also uncovers markers of CD8+ T cell states, including GZMK+HAVCR2− effector memory cells associated with anti-PD-1 therapy response. Finally, using data from the Tabula Sapiens project, RECOMBINE identifies composite marker sets across a broad range of human tissues. Together, these results highlight RECOMBINE as a robust, data-driven framework for optimized marker selection, enabling the discovery and validation of hierarchical cell identities across diverse tissue contexts.

Reproduced under the paper's license (CC BY), from the paper cited above.

Repository

Its files are read in the Code ↔ Paper reader above, with 17 matches between paragraphs and lines of code.

korkutlab/recombine

License: Apache-2.0
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Commit: 8e88ef7252920745cdfd8f1fc42c3cc8d1ee18df, 20 April 2026
Languages: R (12), C++ (6), C/C++ (2)
Size: 82 files, 20 scripts
Software Heritage: archived
Found in: “Code availability”
Holds: README, license file, environment (DESCRIPTION), documentation, 1 notebook
Not found: CITATION.cff, tests, continuous integration
Tools: tidyverse (5 files), Seurat (3 files), Harmony (1 file)
Availability: 1 check, the latest on 27 September 2026: the link answers
  • 27 September 2026: the link answers
22 files
At the source: github.com/korkutlab/recombine

Code availability

The RECOMBINE R package and simulation data are available at GitHub (https://github.com/korkutlab/recombine) and as Supplemental Code.

Reproduced under the paper's license (CC BY), from the paper cited above.

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  • 20 scripts, each with its path and the digest of its content;
  • 17 matches between paragraphs of the paper and lines of the code (method lexical-v1);
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Version 1, 27 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 3 authors, 8 MeSH terms, 6 funders, 60 references.

Cite

This paper

Li, X., Nguyen, J., & Korkut, A. (2026). RECOMBINE identifies recurrent composite markers of cell types and states. Genome research, 36(6), 1221-1237. https://doi.org/10.1101/gr.280817.125

BibTeX

@article{li2026recombine,
author = {Li, Xubin and Nguyen, Justin and Korkut, Anil},
title = {{RECOMBINE identifies recurrent composite markers of cell types and states}},
journal = {Genome research},
year = {2026},
month = jun,
volume = {36},
number = {6},
pages = {1221--1237},
publisher = {Cold Spring Harbor Laboratory Press},
issn = {1088-9051},
doi = {10.1101/gr.280817.125},
url = {https://doi.org/10.1101/gr.280817.125},
pmid = {42161585},
pmcid = {PMC13262949}
}

RIS

TY - JOUR
AU - Li, Xubin
AU - Nguyen, Justin
AU - Korkut, Anil
TI - RECOMBINE identifies recurrent composite markers of cell types and states
T2 - Genome research
J2 - Genome Res
PY - 2026
DA - 2026/06/01
VL - 36
IS - 6
SP - 1221
EP - 1237
SN - 1088-9051
PB - Cold Spring Harbor Laboratory Press
DO - 10.1101/gr.280817.125
UR - https://doi.org/10.1101/gr.280817.125
LA - en
ER -

CSL-JSON

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