
clusterProfiler v4.18.4 Learn more at https://yulab-smu.top/contribution-knowledge-mining/

Please cite:

S Xu, E Hu, Y Cai, Z Xie, X Luo, L Zhan, W Tang, Q Wang, B Liu, R Wang,
W Xie, T Wu, L Xie, G Yu. Using clusterProfiler to characterize
multiomics data. Nature Protocols. 2024, 19(11):3292-3320

Attaching package: 'clusterProfiler'

The following object is masked from 'package:stats':

    filter

Warning message:
package 'clusterProfiler' was built under R version 4.5.3 

=== p.adjust threshold: 0.02 ===
  Ligand_ID Receptor_ID TF_ID               Pathway Ligand_Symbol
1 100506658   100506658  2626 hsa04530_3,hsa04530_5          OCLN
2 100506658   100506658  8531            hsa04530_2          OCLN
3     10344        1230  2309            hsa04062_5         CCL26
4     10344        1230  3551            hsa04062_5         CCL26
  Receptor_Symbol TF_Symbol
1            OCLN     GATA4
2            OCLN      YBX3
3            CCR1     FOXO3
4            CCR1     IKBKB
[1] "step1: compute means of gene"
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 [21] "21"   "22"   "23"   "24"   "25"   "26"   "27"   "28"   "29"   "30"  
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 [81] "356"  "357"  "358"  "359"  "360"  "361"  "362"  "363"  "364"  "365" 
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[101] "376"  "377"  "378"  "379"  "380"  "381"  "382"  "383"  "384"  "385" 
[111] "386"  "387"  "388"  "389"  "390"  "391"  "392"  "393"  "394"  "395" 
[121] "396"  "397"  "398"  "399"  "400"  "401"  "402"  "403"  "404"  "405" 
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[141] "416"  "417"  "418"  "419"  "420"  "421"  "422"  "423"  "424"  "425" 
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[161] "436"  "437"  "438"  "439"  "440"  "441"  "442"  "443"  "444"  "445" 
[171] "446"  "447"  "448"  "449"  "450"  "451"  "452"  "453"  "454"  "455" 
[181] "456"  "457"  "458"  "459"  "460"  "461"  "462"  "463"  "464"  "465" 
[191] "466"  "467"  "468"  "469"  "472"  "473"  "474"  "475"  "477"  "480" 
[201] "481"  "482"  "483"  "485"  "487"  "488"  "489"  "490"  "491"  "492" 
[211] "494"  "495"  "496"  "497"  "498"  "499"  "500"  "501"  "502"  "503" 
[221] "504"  "505"  "506"  "507"  "508"  "509"  "510"  "512"  "513"  "514" 
[231] "515"  "516"  "517"  "518"  "519"  "520"  "521"  "522"  "523"  "524" 
[241] "525"  "526"  "527"  "528"  "529"  "530"  "531"  "532"  "533"  "534" 
[251] "535"  "536"  "537"  "538"  "539"  "540"  "541"  "542"  "543"  "544" 
[261] "545"  "546"  "547"  "548"  "549"  "550"  "551"  "552"  "553"  "554" 
[271] "555"  "556"  "557"  "558"  "559"  "560"  "562"  "563"  "564"  "565" 
[281] "566"  "567"  "568"  "569"  "570"  "571"  "572"  "573"  "575"  "576" 
[291] "577"  "578"  "579"  "580"  "581"  "582"  "583"  "584"  "585"  "586" 
[301] "587"  "588"  "589"  "590"  "591"  "592"  "593"  "594"  "595"  "596" 
[311] "598"  "599"  "600"  "601"  "602"  "603"  "604"  "605"  "606"  "607" 
[321] "608"  "609"  "612"  "613"  "615"  "619"  "621"  "622"  "623"  "624" 
[331] "625"  "626"  "627"  "628"  "633"  "634"  "635"  "636"  "638"  "639" 
[341] "640"  "641"  "642"  "643"  "644"  "646"  "647"  "649"  "650"  "651" 
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[1] "step2: filter tf-gene with correlation, then score regulons"
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