# diffloop: Identifying differential DNA loops from chromatin topology data

#### Caleb Lareau & Martin Aryee

#### 2017-04-24

    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 3.4.0 (2017-04-21)
    ## 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_1.16.0              SummarizedExperiment_1.6.0
    ##  [3] DelayedArray_0.2.0         matrixStats_0.52.2
    ##  [5] Biobase_2.36.0             ggrepel_0.6.5
    ##  [7] GenomicRanges_1.28.0       GenomeInfoDb_1.12.0
    ##  [9] IRanges_2.10.0             S4Vectors_0.14.0
    ## [11] BiocGenerics_0.22.0        ggplot2_2.2.1
    ## [13] diffloopdata_1.3.0         diffloop_1.4.0
    ##
    ## loaded via a namespace (and not attached):
    ##  [1] edgeR_3.18.0             splines_3.4.0
    ##  [3] foreach_1.4.3            Formula_1.2-1
    ##  [5] assertthat_0.2.0         statmod_1.4.29
    ##  [7] latticeExtra_0.6-28      GenomeInfoDbData_0.99.0
    ##  [9] Rsamtools_1.28.0         yaml_2.1.14
    ## [11] RSQLite_1.1-2            backports_1.0.5
    ## [13] lattice_0.20-35          limma_3.32.0
    ## [15] digest_0.6.12            checkmate_1.8.2
    ## [17] RColorBrewer_1.1-2       XVector_0.16.0
    ## [19] colorspace_1.3-2         htmltools_0.3.5
    ## [21] Matrix_1.2-9             plyr_1.8.4
    ## [23] XML_3.98-1.6             biomaRt_2.32.0
    ## [25] genefilter_1.58.0        zlibbioc_1.22.0
    ## [27] xtable_1.8-2             scales_0.4.1
    ## [29] BiocParallel_1.10.0      annotate_1.54.0
    ## [31] htmlTable_1.9            tibble_1.3.0
    ## [33] pbapply_1.3-2            nnet_7.3-12
    ## [35] lazyeval_0.2.0           survival_2.41-3
    ## [37] magrittr_1.5             memoise_1.1.0
    ## [39] evaluate_0.10            foreign_0.8-67
    ## [41] tools_3.4.0              data.table_1.10.4
    ## [43] hms_0.3                  stringr_1.2.0
    ## [45] munsell_0.4.3            locfit_1.5-9.1
    ## [47] cluster_2.0.6            AnnotationDbi_1.38.0
    ## [49] Biostrings_2.44.0        compiler_3.4.0
    ## [51] grid_3.4.0               RCurl_1.95-4.8
    ## [53] iterators_1.0.8          htmlwidgets_0.8
    ## [55] bitops_1.0-6             base64enc_0.1-3
    ## [57] rmarkdown_1.4            gtable_0.2.0
    ## [59] codetools_0.2-15         DBI_0.6-1
    ## [61] reshape2_1.4.2           R6_2.2.0
    ## [63] gridExtra_2.2.1          GenomicAlignments_1.12.0
    ## [65] zoo_1.8-0                knitr_1.15.1
    ## [67] dplyr_0.5.0              rtracklayer_1.36.0
    ## [69] Sushi_1.14.0             Hmisc_4.0-2
    ## [71] rprojroot_1.2            readr_1.1.0
    ## [73] stringi_1.1.5            Rcpp_0.12.10
    ## [75] geneplotter_1.54.0       rpart_4.1-11
    ## [77] acepack_1.4.1

## 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).