# diffloop: Identifying differential DNA loops from chromatin topology data

#### Caleb Lareau & Martin Aryee

#### 2019-05-03

    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 3.6.0 (2019-04-26)
    ## 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_1.24.0               SummarizedExperiment_1.14.0
    ##  [3] DelayedArray_0.10.0         BiocParallel_1.18.0
    ##  [5] matrixStats_0.54.0          Biobase_2.44.0
    ##  [7] ggrepel_0.8.0               GenomicRanges_1.36.0
    ##  [9] GenomeInfoDb_1.20.0         IRanges_2.18.0
    ## [11] S4Vectors_0.22.0            BiocGenerics_0.30.0
    ## [13] ggplot2_3.1.1               diffloopdata_1.11.0
    ## [15] diffloop_1.12.0
    ##
    ## 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_1.4.0               backports_1.1.4
    ##  [7] tools_3.6.0              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               compiler_3.6.0
    ## [21] htmlTable_1.13.1         rtracklayer_1.44.0
    ## [23] checkmate_1.9.1          scales_1.0.0
    ## [25] genefilter_1.66.0        readr_1.3.1
    ## [27] pbapply_1.4-0            stringr_1.4.0
    ## [29] digest_0.6.18            Rsamtools_2.0.0
    ## [31] foreign_0.8-71           rmarkdown_1.12
    ## [33] XVector_0.24.0           base64enc_0.1-3
    ## [35] pkgconfig_2.0.2          htmltools_0.3.6
    ## [37] limma_3.40.0             htmlwidgets_1.3
    ## [39] rlang_0.3.4              rstudioapi_0.10
    ## [41] RSQLite_2.1.1            zoo_1.8-5
    ## [43] acepack_1.4.1            dplyr_0.8.0.1
    ## [45] RCurl_1.95-4.12          magrittr_1.5
    ## [47] Sushi_1.22.0             GenomeInfoDbData_1.2.1
    ## [49] Formula_1.2-3            Matrix_1.2-17
    ## [51] Rcpp_1.0.1               munsell_0.5.0
    ## [53] stringi_1.4.3            yaml_2.2.0
    ## [55] edgeR_3.26.0             zlibbioc_1.30.0
    ## [57] plyr_1.8.4               grid_3.6.0
    ## [59] blob_1.1.1               crayon_1.3.4
    ## [61] lattice_0.20-38          Biostrings_2.52.0
    ## [63] splines_3.6.0            annotate_1.62.0
    ## [65] hms_0.4.2                locfit_1.5-9.1
    ## [67] knitr_1.22               pillar_1.3.1
    ## [69] geneplotter_1.62.0       reshape2_1.4.3
    ## [71] codetools_0.2-16         biomaRt_2.40.0
    ## [73] XML_3.98-1.19            glue_1.3.1
    ## [75] evaluate_0.13            latticeExtra_0.6-28
    ## [77] data.table_1.12.2        foreach_1.4.4
    ## [79] gtable_0.3.0             purrr_0.3.2
    ## [81] assertthat_0.2.1         xfun_0.6
    ## [83] xtable_1.8-4             survival_2.44-1.1
    ## [85] tibble_2.1.1             iterators_1.0.10
    ## [87] GenomicAlignments_1.20.0 AnnotationDbi_1.46.0
    ## [89] memoise_1.1.0            cluster_2.0.9
    ## [91] 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).