# diffloop: Identifying differential DNA loops from chromatin topology data

#### Caleb Lareau & Martin Aryee

#### 2017-10-30

    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 3.4.2 Patched (2017-10-07 r73498)
    ## 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_1.18.0              SummarizedExperiment_1.8.0
    ##  [3] DelayedArray_0.4.0         matrixStats_0.52.2
    ##  [5] Biobase_2.38.0             ggrepel_0.7.0
    ##  [7] GenomicRanges_1.30.0       GenomeInfoDb_1.14.0
    ##  [9] IRanges_2.12.0             S4Vectors_0.16.0
    ## [11] BiocGenerics_0.24.0        ggplot2_2.2.1
    ## [13] diffloopdata_1.5.0         diffloop_1.6.0
    ##
    ## 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] rprojroot_1.2            tools_3.4.2
    ##  [7] backports_1.1.1          R6_2.2.2
    ##  [9] rpart_4.1-11             Hmisc_4.0-3
    ## [11] DBI_0.7                  lazyeval_0.2.1
    ## [13] colorspace_1.3-2         nnet_7.3-12
    ## [15] gridExtra_2.3            prettyunits_1.0.2
    ## [17] bit_1.1-12               compiler_3.4.2
    ## [19] htmlTable_1.9            rtracklayer_1.38.0
    ## [21] scales_0.5.0             checkmate_1.8.5
    ## [23] readr_1.1.1              genefilter_1.60.0
    ## [25] pbapply_1.3-3            stringr_1.2.0
    ## [27] digest_0.6.12            Rsamtools_1.30.0
    ## [29] foreign_0.8-69           rmarkdown_1.6
    ## [31] XVector_0.18.0           base64enc_0.1-3
    ## [33] pkgconfig_2.0.1          htmltools_0.3.6
    ## [35] limma_3.34.0             htmlwidgets_0.9
    ## [37] rlang_0.1.2              RSQLite_2.0
    ## [39] bindr_0.1                zoo_1.8-0
    ## [41] BiocParallel_1.12.0      acepack_1.4.1
    ## [43] dplyr_0.7.4              RCurl_1.95-4.8
    ## [45] magrittr_1.5             Sushi_1.16.0
    ## [47] GenomeInfoDbData_0.99.1  Formula_1.2-2
    ## [49] Matrix_1.2-11            Rcpp_0.12.13
    ## [51] munsell_0.4.3            stringi_1.1.5
    ## [53] yaml_2.1.14              edgeR_3.20.0
    ## [55] zlibbioc_1.24.0          plyr_1.8.4
    ## [57] grid_3.4.2               blob_1.1.0
    ## [59] lattice_0.20-35          Biostrings_2.46.0
    ## [61] splines_3.4.2            annotate_1.56.0
    ## [63] hms_0.3                  locfit_1.5-9.1
    ## [65] knitr_1.17               geneplotter_1.56.0
    ## [67] reshape2_1.4.2           codetools_0.2-15
    ## [69] biomaRt_2.34.0           XML_3.98-1.9
    ## [71] glue_1.2.0               evaluate_0.10.1
    ## [73] latticeExtra_0.6-28      data.table_1.10.4-3
    ## [75] foreach_1.4.3            gtable_0.2.0
    ## [77] assertthat_0.2.0         xtable_1.8-2
    ## [79] survival_2.41-3          tibble_1.3.4
    ## [81] iterators_1.0.8          GenomicAlignments_1.14.0
    ## [83] AnnotationDbi_1.40.0     memoise_1.1.0
    ## [85] bindrcpp_0.2             cluster_2.0.6
    ## [87] 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).