vignettes/cell_type_specific_epigenomics.Rmd
cell_type_specific_epigenomics.Rmdechoannot includes data generated by “Nott2019”:
Nott A, Holtman IR, Coufal NG, … Glass CK. Brain cell type-specific enhancer-promoter interactome maps and disease-risk association. Science. 2019 Nov 29;366(6469):1134-1139. doi: 10.1126/science.aay0793. Epub 2019 Nov 14. PMID: 31727856; PMCID: PMC7028213.
superenhancers <- echoannot::get_NOTT2019_superenhancer_interactome()
enhancers_promoters <- echoannot::NOTT2019_get_promoter_interactome_data()
peaks <- echoannot::NOTT2019_get_epigenomic_peaks() echoannot also includes data generated by “Corces2019”:
Corces, M.R., Shcherbina, A., Kundu, S. et al. Single-cell epigenomic analyses implicate candidate causal variants at inherited risk loci for Alzheimer’s and Parkinson’s diseases. Nat Genet 52, 1158–1168 (2020). https://doi.org/10.1038/s41588-020-00721-x
bulkATACseq_peaks <- echoannot::get_CORCES2020_bulkATACseq_peaks()
cicero_coaccessibility <- echoannot::get_CORCES2020_cicero_coaccessibility()
hichip_fithichip_loop_calls <- echoannot::get_CORCES2020_hichip_fithichip_loop_calls()
scATACseq_celltype_peaks <- echoannot::get_CORCES2020_scATACseq_celltype_peaks()
scATACseq_peaks <- echoannot::get_CORCES2020_scATACseq_peaks()
peak_dat <- echoannot::granges_overlap(
dat1 = dat,
chrom_col.1 = "CHR",
start_col.1 = "POS",
dat2 = scATACseq_celltype_peaks,
chrom_col.2 = "hg38_Chromosome",
start_col.2 = "hg38_Start",
end_col.2 = "hg38_Stop")
ggbio::autoplot(peak_dat,
ggplot2::aes(y=ExcitatoryNeurons, color=Effect))
utils::sessionInfo()## R Under development (unstable) (2026-03-12 r89607)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.4 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so; LAPACK version 3.12.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## time zone: UTC
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] echoannot_1.0.1 BiocStyle_2.39.0
##
## loaded via a namespace (and not attached):
## [1] aws.s3_0.3.22 BiocIO_1.21.0
## [3] bitops_1.0-9 filelock_1.0.3
## [5] tibble_3.3.1 R.oo_1.27.1
## [7] cellranger_1.1.0 basilisk.utils_1.23.1
## [9] graph_1.89.1 XML_3.99-0.22
## [11] rpart_4.1.24 lifecycle_1.0.5
## [13] OrganismDbi_1.53.2 ensembldb_2.35.0
## [15] lattice_0.22-9 MASS_7.3-65
## [17] backports_1.5.0 magrittr_2.0.4
## [19] openxlsx_4.2.8.1 Hmisc_5.2-5
## [21] sass_0.4.10 rmarkdown_2.30
## [23] jquerylib_0.1.4 yaml_2.3.12
## [25] otel_0.2.0 zip_2.3.3
## [27] reticulate_1.45.0 ggbio_1.59.0
## [29] gld_2.6.8 DBI_1.3.0
## [31] RColorBrewer_1.1-3 abind_1.4-8
## [33] expm_1.0-0 GenomicRanges_1.63.1
## [35] purrr_1.2.1 R.utils_2.13.0
## [37] AnnotationFilter_1.35.0 biovizBase_1.59.0
## [39] BiocGenerics_0.57.0 RCurl_1.98-1.17
## [41] nnet_7.3-20 VariantAnnotation_1.57.1
## [43] IRanges_2.45.0 S4Vectors_0.49.0
## [45] pkgdown_2.2.0 echodata_1.0.0
## [47] piggyback_0.1.5 codetools_0.2-20
## [49] DelayedArray_0.37.0 DT_0.34.0
## [51] xml2_1.5.2 tidyselect_1.2.1
## [53] UCSC.utils_1.7.1 farver_2.1.2
## [55] matrixStats_1.5.0 stats4_4.6.0
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## [67] DescTools_0.99.60 Rcpp_1.1.1
## [69] glue_1.8.0 gridExtra_2.3
## [71] SparseArray_1.11.11 xfun_0.56
## [73] MatrixGenerics_1.23.0 GenomeInfoDb_1.47.2
## [75] dplyr_1.2.0 withr_3.0.2
## [77] BiocManager_1.30.27 fastmap_1.2.0
## [79] basilisk_1.23.0 boot_1.3-32
## [81] digest_0.6.39 R6_2.6.1
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## [91] data.table_1.18.2.1 rtracklayer_1.71.3
## [93] class_7.3-23 httr_1.4.8
## [95] htmlwidgets_1.6.4 S4Arrays_1.11.1
## [97] pkgconfig_2.0.3 gtable_0.3.6
## [99] Exact_3.3 blob_1.3.0
## [101] S7_0.2.1 XVector_0.51.0
## [103] echoconda_1.0.0 htmltools_0.5.9
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## [109] Biobase_2.71.0 lmom_3.2
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## [113] rstudioapi_0.18.0 tzdb_0.5.0
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## [121] stringr_1.6.0 rootSolve_1.8.2.4
## [123] parallel_4.6.0 foreign_0.8-91
## [125] AnnotationDbi_1.73.0 restfulr_0.0.16
## [127] desc_1.4.3 pillar_1.11.1
## [129] grid_4.6.0 vctrs_0.7.1
## [131] cluster_2.1.8.2 htmlTable_2.4.3
## [133] evaluate_1.0.5 readr_2.2.0
## [135] GenomicFeatures_1.63.1 mvtnorm_1.3-5
## [137] cli_3.6.5 compiler_4.6.0
## [139] Rsamtools_2.27.1 rlang_1.1.7
## [141] crayon_1.5.3 aws.signature_0.6.0
## [143] plyr_1.8.9 forcats_1.0.1
## [145] fs_1.6.7 stringi_1.8.7
## [147] BiocParallel_1.45.0 Biostrings_2.79.5
## [149] lazyeval_0.2.2 Matrix_1.7-4
## [151] downloadR_1.0.0 dir.expiry_1.19.0
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## [163] bit_4.6.0 readxl_1.4.5