# diffloop: Identifying differential DNA loops from chromatin topology data

#### Caleb Lareau & Martin Aryee

#### 2018-04-30

    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 3.5.0 (2018-04-23)
    ## Platform: x86_64-pc-linux-gnu (64-bit)
    ## Running under: Ubuntu 16.04.4 LTS
    ##
    ## Matrix products: default
    ## BLAS: /home/biocbuild/bbs-3.7-bioc/R/lib/libRblas.so
    ## LAPACK: /home/biocbuild/bbs-3.7-bioc/R/lib/libRlapack.so
    ##
    ## locale:
    ##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
    ##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=C
    ##  [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
    ##
    ## attached base packages:
    ## [1] parallel  stats4    stats     graphics  grDevices utils     datasets
    ## [8] methods   base
    ##
    ## other attached packages:
    ##  [1] DESeq2_1.20.0               SummarizedExperiment_1.10.0
    ##  [3] DelayedArray_0.6.0          BiocParallel_1.14.0
    ##  [5] matrixStats_0.53.1          Biobase_2.40.0
    ##  [7] ggrepel_0.7.0               GenomicRanges_1.32.0
    ##  [9] GenomeInfoDb_1.16.0         IRanges_2.14.0
    ## [11] S4Vectors_0.18.0            BiocGenerics_0.26.0
    ## [13] ggplot2_2.2.1               diffloopdata_1.7.0
    ## [15] diffloop_1.8.0
    ##
    ## loaded via a namespace (and not attached):
    ##  [1] bitops_1.0-6             bit64_0.9-7
    ##  [3] RColorBrewer_1.1-2       progress_1.1.2
    ##  [5] httr_1.3.1               rprojroot_1.3-2
    ##  [7] tools_3.5.0              backports_1.1.2
    ##  [9] R6_2.2.2                 rpart_4.1-13
    ## [11] Hmisc_4.1-1              DBI_0.8
    ## [13] lazyeval_0.2.1           colorspace_1.3-2
    ## [15] nnet_7.3-12              gridExtra_2.3
    ## [17] prettyunits_1.0.2        bit_1.1-12
    ## [19] compiler_3.5.0           htmlTable_1.11.2
    ## [21] rtracklayer_1.40.0       scales_0.5.0
    ## [23] checkmate_1.8.5          genefilter_1.62.0
    ## [25] readr_1.1.1              pbapply_1.3-4
    ## [27] stringr_1.3.0            digest_0.6.15
    ## [29] Rsamtools_1.32.0         foreign_0.8-70
    ## [31] rmarkdown_1.9            XVector_0.20.0
    ## [33] base64enc_0.1-3          pkgconfig_2.0.1
    ## [35] htmltools_0.3.6          limma_3.36.0
    ## [37] htmlwidgets_1.2          rlang_0.2.0
    ## [39] rstudioapi_0.7           RSQLite_2.1.0
    ## [41] bindr_0.1.1              zoo_1.8-1
    ## [43] acepack_1.4.1            dplyr_0.7.4
    ## [45] RCurl_1.95-4.10          magrittr_1.5
    ## [47] Sushi_1.18.0             GenomeInfoDbData_1.1.0
    ## [49] Formula_1.2-2            Matrix_1.2-14
    ## [51] Rcpp_0.12.16             munsell_0.4.3
    ## [53] stringi_1.1.7            yaml_2.1.18
    ## [55] edgeR_3.22.0             zlibbioc_1.26.0
    ## [57] plyr_1.8.4               grid_3.5.0
    ## [59] blob_1.1.1               lattice_0.20-35
    ## [61] Biostrings_2.48.0        splines_3.5.0
    ## [63] annotate_1.58.0          hms_0.4.2
    ## [65] locfit_1.5-9.1           knitr_1.20
    ## [67] pillar_1.2.2             geneplotter_1.58.0
    ## [69] reshape2_1.4.3           codetools_0.2-15
    ## [71] biomaRt_2.36.0           XML_3.98-1.11
    ## [73] glue_1.2.0               evaluate_0.10.1
    ## [75] latticeExtra_0.6-28      data.table_1.10.4-3
    ## [77] foreach_1.4.4            gtable_0.2.0
    ## [79] assertthat_0.2.0         xtable_1.8-2
    ## [81] survival_2.42-3          tibble_1.4.2
    ## [83] iterators_1.0.9          GenomicAlignments_1.16.0
    ## [85] AnnotationDbi_1.42.0     memoise_1.1.0
    ## [87] bindrcpp_0.2.2           cluster_2.0.7-1
    ## [89] 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).