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MINTsC learns multi-way chromatin interactions from single cell high throughput chromatin conformation data.

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Paper

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The authors' code

R · 188 lines · 5.3 KB · no license

  1. options(scipen = 100, digits = 4)
  4. pacman::p_load(purrr, furrr, parallel, data.table, dplyr,stringr,gtools,igraph)
  7. find_cliques=function(binsize=500000,
  8. data_dir='/storage10/kwangmoon/MINTsC/data/Ramani2017/',
  9. output_dir='/storage10/kwangmoon/MINTsC/results/Ramani2017/',
  10. corenum_celltype=1,
  11. corenum_cells=20,
  12. chrnum=23,
  13. sizefile='hg19.chrom.sizes',
  14. ncellsthreshold_c0=1,ncellsthreshold_c1=0,Smax=6,
  15. chrlist=NULL){
  18. if(is.null(chrlist)){chrlist=c(paste0("chr",c(1:(chrnum-1),"X")))}
  21. setwd(data_dir)
  22. cell_type=qs::qread("cell_type.qs")
  23. ctlists=unique(cell_type[,2])
  25. future::plan(multicore, workers = corenum_celltype)
  28. future_map(ctlists,function(ct){
  32. hic_df_ct=lapply(1:chrnum,function(x)qs::qread(paste0(chrlist[x],'/hic_df_',chrlist[x],'_',ct,'.qs'))[,c('cell','chr','binA','binB')] )
  33. hic_df_ct=do.call('rbind',hic_df_ct)
  34. hic_df_ct=split(hic_df_ct,by='cell')
  36. future::plan(multicore, workers = corenum_cells)
  37. system(paste0('mkdir ',output_dir,"/","'",ct,"'"))
  38. future_map(hic_df_ct,function(tmp){
  40. if(!paste0("cell_clique_",tmp$cell[1],'.qs')%in%list.files(paste0(output_dir,"/",ct))){
  43. nodes<-c(paste0(tmp$chr,"_",tmp$binA),paste0(tmp$chr,"_",tmp$binB)) %>% unique
  44. vertices=data.frame(nodes)
  46. edges <-tmp[,.('from'=paste0(chr,"_",binA),'to'=paste0(chr,"_",binB))]
  48. g <- igraph::graph_from_data_frame(edges, directed=FALSE, vertices=nodes)
  49. three_clique<-igraph::cliques(g,min=3,max=Smax)
  51. tmpres=unlist(lapply(three_clique,function(x)paste(mixedsort(names(x)),collapse="-")))
  53. qs::qsave(tmpres, paste0(output_dir,"/",ct,"/cell_clique_",tmp$cell[1],'.qs'))
  57. }
  60. })
  62. #If you do setwd within lapply, it will globally setwd as well. be careful.
  63. cliques_loop=lapply(list.files(paste0(output_dir,"/",ct)),function(x){qs::qread(paste0(output_dir,"/",ct,"/",x))})
  65. rm(hic_df_ct)
  66. gc()
  69. qs::qsave(cliques_loop,paste0(output_dir,"/cliques_loop_3tomax_",ct,".qs"))
  70. print(paste0(ct," done"))
  76. }
  77. )
  81. cat('Clique finding for each cell coimplete...')
  82. cat("\n")
  85. cliques_loop_ct=list()
  86. for(ct in ctlists){
  88. cliques_loop_ct[[ct]]=qs::qread(paste0(output_dir,"/cliques_loop_3tomax_",ct,".qs"))
  90. }
  91. qs::qsave(cliques_loop_ct,paste0(output_dir,"/cliques_loop_3tomax.qs"))
  96. cat('Saving cliques')
  97. cat("\n")
  104. Q=unlist(cliques_loop_ct)
  105. qs::qsave(Q,paste0(output_dir,"/Q_notunique.qs"))
  106. tableQ=Q %>% table
  109. print('Sorting cluques and generating pairwise interactions within each clique...')
  110. cat("\n")
  113. Q_unique=names(tableQ)
  114. cliquesize<-sapply(strsplit(Q_unique, "-"), length)
  115. chrlabel=word(Q_unique,1,sep="_")
  116. Smax=max(cliquesize)
  120. options(future.globals.maxSize= Inf)
  121. future::plan(multicore, workers = length(3:Smax))
  124. Qdat=data.table(Q_unique,chrlabel,cliquesize,ncell=as.numeric(tableQ ))
  125. rm(Q_unique)
  126. rm(chrlabel)
  127. rm(tableQ)
  128. rm(cliquesize)
  129. gc()
  130. qs::qsave(Qdat,
  131. paste0(output_dir,'/Q_summary.qs'))
  135. qs::qsave(lapply(chrlist,function(x){Qdat[cliquesize==3&chrlabel==x&ncell>ncellsthreshold_c0]$Q_unique}),
  136. paste0(output_dir,'/Q3_filtered_list.qs'))
  140. future_map(4:Smax,function(S){
  144. qs::qsave(lapply(chrlist,function(x){Qdat[cliquesize==S&chrlabel==x&ncell>ncellsthreshold_c1]$Q_unique}),
  145. paste0(output_dir,'/Q',S,'_filtered_list.qs'))
  147. }
  149. )
  151. # Q3=unique(Q[Q%in%Q_unique[cliquesize==3&tableQ>ncellsthreshold]])
  152. # chrlabel_3=word(Q3,1,sep="_")
  153. # qs::qsave(lapply(chrlist,function(x){Q3[chrlabel_3==x]}),
  154. # paste0(output_dir,'/Q3_filtered_list.qs'))
  159. rm(Qdat)
  160. gc()
  164. # for(S in 3:Smax){
  165. future_map(3:Smax,function(S){
  166. tmp_list=list()
  167. for(chr in 1:chrnum){
  169. tmp=lapply(qs::qread(paste0(output_dir,'/Q',S,'_filtered_list.qs'))[[chr]] ,function(x)strsplit(x, "-"))
  170. tmp_list[[chr]]=lapply(tmp,function(x)apply(combn(x[[1]],2),2,function(x)paste(x,collapse = "-")))
  172. }
  173. qs::qsave(tmp_list,paste0(output_dir,'/pairwise_',S,'_filtered_list.qs'))
  174. }
  175. # }
  179. )
  188. }

find_cliques.R at commit e121729, no license · at the source

Overview

Authors: Kwangmoon Park1, Tianchuan Gao2, Jingwen Yan2, Sündüz Keleş1,3
ORCID iDs: Kwangmoon Park, Sündüz Keleş
  1. Department of Statistics, University of Wisconsin - Madison,Madison, WI USA
  2. Department of Biomedical Engineering and Informatics, Indiana University Indianapolis,Indianapolis, IN USA
  3. Department of Biostatistics and Medical Informatics, University of Wisconsin - Madison,Madison, WI USA
Institutions: University of Wisconsin–Madison (United States); Indiana University Indianapolis (United States)
Journal: Nature communications, volume 17, issue 1, article 7077
Dates: received 31 July 2024; accepted 14 May 2026; published online 2 June 2026
Type: Research article · Language: English
License: CC BY-NC-ND
Identifiers: DOI 10.1038/s41467-026-73773-y · PMID 42230572 · PMCID PMC13392375 · OpenAlex W4394759233
Open access: gold, a free copy (OpenAlex)
Preprint: doi:10.1101/2024.04.08.588641
Status: code verified
Categories: human (organism)
Methods: Statistics, Preprocessing, fMRI & imaging
Keywords: Chromatin structure, Chromosomes, Genome, Genome informatics
MeSH: Chromatin*, Single-Cell Analysis*, Genomics, Humans, Software (* major topic)
Topic: Epigenetics and DNA Methylation (Molecular Biology, Biochemistry, Genetics and Molecular Biology), according to OpenAlex
Funding: NIH (HG003747, HG012881); Chan Zuckerberg Initiative (CZI) single-cell data insights grant
Citations: cited by 1 paper (Europe PMC); 46 references in the paper

Abstract

The abstract is not reproduced here: the paper's license (CC BY-NC-ND) does not allow it. Read it in the paper, at the publisher or on Europe PMC.

Repositories

Its files are read in the Code ↔ Paper reader above.

keleslab/MINTsC

License: none: the authors keep all their rights
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Commit: e121729fd15493fcb637e0373cfd318248bd3e1d, 15 November 2025
Languages: R (3), Jupyter (1)
Size: 102 files, 4 scripts
Software Heritage: not archived
Found in: “Code availability”
Holds: README, 1 notebook
Not found: license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: tidyverse (3 files), data.table (2 files), ggpubr (1 file), igraph (1 file)
Availability: 1 check, the latest on 27 September 2026: the link answers
  • 27 September 2026: the link answers
5 files
At the source: github.com/keleslab/MINTsC

Zenodo 19502488

License: CC-BY-4.0
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Size: 1 file
Software Heritage: not checked
Found in: “Code availability”
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Availability: 1 check, the latest on 27 September 2026: the link answers (HTTP 200)
  • 27 September 2026: the link answers (HTTP 200)
At the source:

Zenodo 19502489

License: CC-BY-4.0
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Size: 1 file
Software Heritage: not checked
Found in: the references
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Availability: 1 check, the latest on 27 September 2026: the link answers (HTTP 200)
  • 27 September 2026: the link answers (HTTP 200)
At the source:

Code availability statement

The paper has a code availability statement. Its license (CC BY-NC-ND) does not allow reproducing it here; in short, from what the harvester recognized in it:

Read it in the paper: doi.org/10.1038/s41467-026-73773-y.

Tracing map

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Data

Datasets cited

Data availability statement

The paper has a data availability statement. Its license (CC BY-NC-ND) does not allow reproducing it here; in short, from what the harvester recognized in it:

Read it in the paper: doi.org/10.1038/s41467-026-73773-y.

Versions

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Version 1, 27 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 4 authors, 4 keywords, 5 MeSH terms, 2 funders, 45 references.

Cite

This paper

Park, K., Gao, T., Yan, J., & Keleş, S. (2026). MINTsC learns multi-way chromatin interactions from single cell high throughput chromatin conformation data. Nature communications, 17(1), 7077. https://doi.org/10.1038/s41467-026-73773-y

BibTeX

@article{park2026mintsc,
author = {Park, Kwangmoon and Gao, Tianchuan and Yan, Jingwen and Keleş, Sündüz},
title = {{MINTsC learns multi-way chromatin interactions from single cell high throughput chromatin conformation data}},
journal = {Nature communications},
year = {2026},
month = jun,
volume = {17},
number = {1},
pages = {7077},
publisher = {Nature Publishing Group},
issn = {2041-1723},
doi = {10.1038/s41467-026-73773-y},
url = {https://doi.org/10.1038/s41467-026-73773-y},
pmid = {42230572},
pmcid = {PMC13392375}
}

RIS

TY - JOUR
AU - Park, Kwangmoon
AU - Gao, Tianchuan
AU - Yan, Jingwen
AU - Keleş, Sündüz
TI - MINTsC learns multi-way chromatin interactions from single cell high throughput chromatin conformation data
T2 - Nature communications
J2 - Nat Commun
PY - 2026
DA - 2026/06/02
VL - 17
IS - 1
SP - 7077
SN - 2041-1723
PB - Nature Publishing Group
DO - 10.1038/s41467-026-73773-y
UR - https://doi.org/10.1038/s41467-026-73773-y
LA - en
ER -

CSL-JSON

{
"id": "10.1038/s41467-026-73773-y",
"type": "article-journal",
"title": "MINTsC learns multi-way chromatin interactions from single cell high throughput chromatin conformation data",
"container-title": "Nature communications",
"author": [
{
"family": "Park",
"given": "Kwangmoon"
},
{
"family": "Gao",
"given": "Tianchuan"
},
{
"family": "Yan",
"given": "Jingwen"
},
{
"family": "Keleş",
"given": "Sündüz"
}
],
"container-title-short": "Nat Commun",
"volume": "17",
"issue": "1",
"page": "7077",
"DOI": "10.1038/s41467-026-73773-y",
"PMID": "42230572",
"PMCID": "PMC13392375",
"ISSN": "2041-1723",
"publisher": "Nature Publishing Group",
"URL": "https://doi.org/10.1038/s41467-026-73773-y",
"language": "en",
"issued": {
"date-parts": [
[
2026,
6,
2
]
]
}
}

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