# diffloop: Identifying differential DNA loops from chromatin topology data

#### Caleb Lareau & Martin Aryee

#### 2019-10-29

    library(diffloop)
    library(diffloopdata)
    library(ggplot2)
    library(GenomicRanges)
    library(ggrepel)
    library(DESeq2)

## About

Due to the maintainer’s inability to figure out data package resubmission to Bioc, a compiled vignette is hosted here.

## Notes on Data

All data used in these analyses were processed from GEO and are contained in the `diffloopdata` package. Please feel free to contact Caleb (the maintainer) with any questions concerning the data or this workflow. The diffloopdata package is available here

## Session info

    sessionInfo()

    ## R version 3.6.1 (2019-07-05)
    ## Platform: x86_64-w64-mingw32/x64 (64-bit)
    ## Running under: Windows Server 2012 R2 x64 (build 9600)
    ##
    ## Matrix products: default
    ##
    ## locale:
    ## [1] LC_COLLATE=C
    ## [2] LC_CTYPE=English_United States.1252
    ## [3] LC_MONETARY=English_United States.1252
    ## [4] LC_NUMERIC=C
    ## [5] LC_TIME=English_United States.1252
    ##
    ## attached base packages:
    ## [1] parallel  stats4    stats     graphics  grDevices utils     datasets
    ## [8] methods   base
    ##
    ## other attached packages:
    ##  [1] DESeq2_1.26.0               SummarizedExperiment_1.16.0
    ##  [3] DelayedArray_0.12.0         BiocParallel_1.20.0
    ##  [5] matrixStats_0.55.0          Biobase_2.46.0
    ##  [7] ggrepel_0.8.1               GenomicRanges_1.38.0
    ##  [9] GenomeInfoDb_1.22.0         IRanges_2.20.0
    ## [11] S4Vectors_0.24.0            BiocGenerics_0.32.0
    ## [13] ggplot2_3.2.1               diffloopdata_1.13.0
    ## [15] diffloop_1.14.0
    ##
    ## loaded via a namespace (and not attached):
    ##  [1] bitops_1.0-6             bit64_0.9-7
    ##  [3] RColorBrewer_1.1-2       progress_1.2.2
    ##  [5] httr_1.4.1               tools_3.6.1
    ##  [7] backports_1.1.5          R6_2.4.0
    ##  [9] rpart_4.1-15             Hmisc_4.2-0
    ## [11] DBI_1.0.0                lazyeval_0.2.2
    ## [13] colorspace_1.4-1         nnet_7.3-12
    ## [15] withr_2.1.2              gridExtra_2.3
    ## [17] tidyselect_0.2.5         prettyunits_1.0.2
    ## [19] bit_1.1-14               curl_4.2
    ## [21] compiler_3.6.1           htmlTable_1.13.2
    ## [23] rtracklayer_1.46.0       checkmate_1.9.4
    ## [25] scales_1.0.0             genefilter_1.68.0
    ## [27] readr_1.3.1              pbapply_1.4-2
    ## [29] askpass_1.1              rappdirs_0.3.1
    ## [31] stringr_1.4.0            digest_0.6.22
    ## [33] Rsamtools_2.2.0          foreign_0.8-72
    ## [35] rmarkdown_1.16           XVector_0.26.0
    ## [37] base64enc_0.1-3          pkgconfig_2.0.3
    ## [39] htmltools_0.4.0          dbplyr_1.4.2
    ## [41] limma_3.42.0             htmlwidgets_1.5.1
    ## [43] rlang_0.4.1              rstudioapi_0.10
    ## [45] RSQLite_2.1.2            zoo_1.8-6
    ## [47] acepack_1.4.1            dplyr_0.8.3
    ## [49] RCurl_1.95-4.12          magrittr_1.5
    ## [51] Sushi_1.24.0             GenomeInfoDbData_1.2.2
    ## [53] Formula_1.2-3            Matrix_1.2-17
    ## [55] Rcpp_1.0.2               munsell_0.5.0
    ## [57] stringi_1.4.3            yaml_2.2.0
    ## [59] edgeR_3.28.0             zlibbioc_1.32.0
    ## [61] plyr_1.8.4               BiocFileCache_1.10.0
    ## [63] grid_3.6.1               blob_1.2.0
    ## [65] crayon_1.3.4             lattice_0.20-38
    ## [67] Biostrings_2.54.0        splines_3.6.1
    ## [69] annotate_1.64.0          hms_0.5.1
    ## [71] locfit_1.5-9.1           zeallot_0.1.0
    ## [73] knitr_1.25               pillar_1.4.2
    ## [75] geneplotter_1.64.0       reshape2_1.4.3
    ## [77] codetools_0.2-16         biomaRt_2.42.0
    ## [79] XML_3.98-1.20            glue_1.3.1
    ## [81] evaluate_0.14            latticeExtra_0.6-28
    ## [83] data.table_1.12.6        vctrs_0.2.0
    ## [85] foreach_1.4.7            gtable_0.3.0
    ## [87] openssl_1.4.1            purrr_0.3.3
    ## [89] assertthat_0.2.1         xfun_0.10
    ## [91] xtable_1.8-4             survival_2.44-1.1
    ## [93] tibble_2.1.3             iterators_1.0.12
    ## [95] GenomicAlignments_1.22.0 AnnotationDbi_1.48.0
    ## [97] memoise_1.1.0            cluster_2.1.0
    ## [99] statmod_1.4.32

## Citations

\(^1\)Hnisz, Denes, et al. “Activation of proto-oncogenes by disruption of chromosome neighborhoods.” Science (2016).
\(^2\)Ji, Xiong, et al. “3D Chromosome Regulatory Landscape of Human Pluripotent Cells.” Cell stem cell (2015).
\(^3\)Phanstiel, D, et al. “Mango: A bias correcting ChIA-PET analysis pipeline.” Bioinformatics (2015).
\(^4\)Robinson, M, et al. “edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.” Bioinformatics (2010).
\(^5\)Law, C, et al. “Voom: precision weights unlock linear model analysis tools for RNA-seq read counts.” Genome Biology (2014).