# diffloop: Identifying differential DNA loops from chromatin topology data

#### Caleb Lareau & Martin Aryee

#### 2020-04-07

    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 4.0.0 alpha (2020-04-05 r78150)
    ## Platform: x86_64-apple-darwin17.0 (64-bit)
    ## Running under: macOS Mojave 10.14.6
    ##
    ## Matrix products: default
    ## BLAS:   /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
    ## LAPACK: /Library/Frameworks/R.framework/Versions/4.0/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_1.27.29              SummarizedExperiment_1.17.5
    ##  [3] DelayedArray_0.13.10        matrixStats_0.56.0
    ##  [5] Biobase_2.47.3              ggrepel_0.8.2
    ##  [7] GenomicRanges_1.39.3        GenomeInfoDb_1.23.16
    ##  [9] IRanges_2.21.8              S4Vectors_0.25.15
    ## [11] BiocGenerics_0.33.3         ggplot2_3.3.0
    ## [13] diffloopdata_1.15.0         diffloop_1.15.0
    ##
    ## loaded via a namespace (and not attached):
    ##  [1] bitops_1.0-6             bit64_0.9-7              RColorBrewer_1.1-2
    ##  [4] progress_1.2.2           httr_1.4.1               tools_4.0.0
    ##  [7] R6_2.4.1                 DBI_1.1.0                colorspace_1.4-1
    ## [10] withr_2.1.2              tidyselect_1.0.0         prettyunits_1.1.1
    ## [13] bit_1.1-15.2             curl_4.3                 compiler_4.0.0
    ## [16] cli_2.0.2                rtracklayer_1.47.0       scales_1.1.0
    ## [19] genefilter_1.69.0        readr_1.3.1              pbapply_1.4-2
    ## [22] askpass_1.1              rappdirs_0.3.1           stringr_1.4.0
    ## [25] digest_0.6.25            Rsamtools_2.3.7          rmarkdown_2.1
    ## [28] XVector_0.27.2           pkgconfig_2.0.3          htmltools_0.4.0
    ## [31] dbplyr_1.4.2             limma_3.43.5             rlang_0.4.5
    ## [34] RSQLite_2.2.0            zoo_1.8-7                BiocParallel_1.21.2
    ## [37] dplyr_0.8.5              RCurl_1.98-1.1           magrittr_1.5
    ## [40] Sushi_1.25.0             GenomeInfoDbData_1.2.2   Matrix_1.2-18
    ## [43] Rcpp_1.0.4.6             munsell_0.5.0            fansi_0.4.1
    ## [46] lifecycle_0.2.0          stringi_1.4.6            yaml_2.2.1
    ## [49] edgeR_3.29.1             zlibbioc_1.33.1          plyr_1.8.6
    ## [52] BiocFileCache_1.11.4     grid_4.0.0               blob_1.2.1
    ## [55] crayon_1.3.4             lattice_0.20-41          splines_4.0.0
    ## [58] Biostrings_2.55.7        annotate_1.65.1          hms_0.5.3
    ## [61] locfit_1.5-9.4           knitr_1.28               pillar_1.4.3
    ## [64] geneplotter_1.65.0       reshape2_1.4.3           codetools_0.2-16
    ## [67] biomaRt_2.43.5           XML_3.99-0.3             glue_1.4.0
    ## [70] evaluate_0.14            data.table_1.12.8        vctrs_0.2.4
    ## [73] foreach_1.5.0            gtable_0.3.0             openssl_1.4.1
    ## [76] purrr_0.3.3              assertthat_0.2.1         xfun_0.12
    ## [79] xtable_1.8-4             survival_3.1-11          tibble_3.0.0
    ## [82] iterators_1.0.12         GenomicAlignments_1.23.2 AnnotationDbi_1.49.1
    ## [85] memoise_1.1.0            statmod_1.4.34           ellipsis_0.3.0

## 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).