# diffloop: Identifying differential DNA loops from chromatin topology data

#### Caleb Lareau & Martin Aryee

#### 2018-10-30

    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 3.5.1 Patched (2018-07-12 r74967)
    ## Platform: x86_64-apple-darwin15.6.0 (64-bit)
    ## Running under: OS X El Capitan 10.11.6
    ##
    ## Matrix products: default
    ## BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
    ## LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
    ##
    ## locale:
    ## [1] C/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
    ##
    ## attached base packages:
    ## [1] parallel  stats4    stats     graphics  grDevices utils     datasets
    ## [8] methods   base
    ##
    ## other attached packages:
    ##  [1] DESeq2_1.22.0               SummarizedExperiment_1.12.0
    ##  [3] DelayedArray_0.8.0          BiocParallel_1.16.0
    ##  [5] matrixStats_0.54.0          Biobase_2.42.0
    ##  [7] ggrepel_0.8.0               GenomicRanges_1.34.0
    ##  [9] GenomeInfoDb_1.18.0         IRanges_2.16.0
    ## [11] S4Vectors_0.20.0            BiocGenerics_0.28.0
    ## [13] ggplot2_3.1.0               diffloopdata_1.9.0
    ## [15] diffloop_1.10.0
    ##
    ## loaded via a namespace (and not attached):
    ##  [1] bitops_1.0-6             bit64_0.9-7
    ##  [3] RColorBrewer_1.1-2       progress_1.2.0
    ##  [5] httr_1.3.1               rprojroot_1.3-2
    ##  [7] tools_3.5.1              backports_1.1.2
    ##  [9] R6_2.3.0                 rpart_4.1-13
    ## [11] Hmisc_4.1-1              DBI_1.0.0
    ## [13] lazyeval_0.2.1           colorspace_1.3-2
    ## [15] nnet_7.3-12              withr_2.1.2
    ## [17] gridExtra_2.3            tidyselect_0.2.5
    ## [19] prettyunits_1.0.2        bit_1.1-14
    ## [21] compiler_3.5.1           htmlTable_1.12
    ## [23] rtracklayer_1.42.0       checkmate_1.8.5
    ## [25] scales_1.0.0             genefilter_1.64.0
    ## [27] readr_1.1.1              pbapply_1.3-4
    ## [29] stringr_1.3.1            digest_0.6.18
    ## [31] Rsamtools_1.34.0         foreign_0.8-71
    ## [33] rmarkdown_1.10           XVector_0.22.0
    ## [35] base64enc_0.1-3          pkgconfig_2.0.2
    ## [37] htmltools_0.3.6          limma_3.38.0
    ## [39] htmlwidgets_1.3          rlang_0.3.0.1
    ## [41] rstudioapi_0.8           RSQLite_2.1.1
    ## [43] bindr_0.1.1              zoo_1.8-4
    ## [45] acepack_1.4.1            dplyr_0.7.7
    ## [47] RCurl_1.95-4.11          magrittr_1.5
    ## [49] Sushi_1.20.0             GenomeInfoDbData_1.2.0
    ## [51] Formula_1.2-3            Matrix_1.2-14
    ## [53] Rcpp_0.12.19             munsell_0.5.0
    ## [55] stringi_1.2.4            yaml_2.2.0
    ## [57] edgeR_3.24.0             zlibbioc_1.28.0
    ## [59] plyr_1.8.4               grid_3.5.1
    ## [61] blob_1.1.1               crayon_1.3.4
    ## [63] lattice_0.20-35          Biostrings_2.50.0
    ## [65] splines_3.5.1            annotate_1.60.0
    ## [67] hms_0.4.2                locfit_1.5-9.1
    ## [69] knitr_1.20               pillar_1.3.0
    ## [71] geneplotter_1.60.0       reshape2_1.4.3
    ## [73] codetools_0.2-15         biomaRt_2.38.0
    ## [75] XML_3.98-1.16            glue_1.3.0
    ## [77] evaluate_0.12            latticeExtra_0.6-28
    ## [79] data.table_1.11.8        foreach_1.4.4
    ## [81] gtable_0.2.0             purrr_0.2.5
    ## [83] assertthat_0.2.0         xtable_1.8-3
    ## [85] survival_2.43-1          tibble_1.4.2
    ## [87] iterators_1.0.10         GenomicAlignments_1.18.0
    ## [89] AnnotationDbi_1.44.0     memoise_1.1.0
    ## [91] cluster_2.0.7-1          bindrcpp_0.2.2
    ## [93] statmod_1.4.30

## 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).