# diffloop: Identifying differential DNA loops from chromatin topology data

#### Caleb Lareau & Martin Aryee

#### 2020-04-27

    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 (2020-04-24)
    ## Platform: x86_64-pc-linux-gnu (64-bit)
    ## Running under: Ubuntu 18.04.4 LTS
    ##
    ## Matrix products: default
    ## BLAS:   /home/biocbuild/bbs-3.11-bioc/R/lib/libRblas.so
    ## LAPACK: /home/biocbuild/bbs-3.11-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_1.28.0               SummarizedExperiment_1.18.0
    ##  [3] DelayedArray_0.14.0         matrixStats_0.56.0
    ##  [5] Biobase_2.48.0              ggrepel_0.8.2
    ##  [7] GenomicRanges_1.40.0        GenomeInfoDb_1.24.0
    ##  [9] IRanges_2.22.0              S4Vectors_0.26.0
    ## [11] BiocGenerics_0.34.0         ggplot2_3.3.0
    ## [13] diffloopdata_1.15.0         diffloop_1.16.0
    ##
    ## 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_2.2.0              tidyselect_1.0.0         prettyunits_1.1.1
    ## [13] bit_1.1-15.2             curl_4.3                 compiler_4.0.0
    ## [16] rtracklayer_1.48.0       scales_1.1.0             readr_1.3.1
    ## [19] genefilter_1.70.0        pbapply_1.4-2            askpass_1.1
    ## [22] rappdirs_0.3.1           stringr_1.4.0            digest_0.6.25
    ## [25] Rsamtools_2.4.0          rmarkdown_2.1            XVector_0.28.0
    ## [28] pkgconfig_2.0.3          htmltools_0.4.0          dbplyr_1.4.3
    ## [31] limma_3.44.0             rlang_0.4.5              RSQLite_2.2.0
    ## [34] zoo_1.8-7                BiocParallel_1.22.0      dplyr_0.8.5
    ## [37] RCurl_1.98-1.2           magrittr_1.5             Sushi_1.26.0
    ## [40] GenomeInfoDbData_1.2.3   Matrix_1.2-18            Rcpp_1.0.4.6
    ## [43] munsell_0.5.0            lifecycle_0.2.0          stringi_1.4.6
    ## [46] yaml_2.2.1               edgeR_3.30.0             zlibbioc_1.34.0
    ## [49] plyr_1.8.6               BiocFileCache_1.12.0     grid_4.0.0
    ## [52] blob_1.2.1               crayon_1.3.4             lattice_0.20-41
    ## [55] splines_4.0.0            Biostrings_2.56.0        annotate_1.66.0
    ## [58] hms_0.5.3                locfit_1.5-9.4           knitr_1.28
    ## [61] pillar_1.4.3             geneplotter_1.66.0       reshape2_1.4.4
    ## [64] codetools_0.2-16         biomaRt_2.44.0           XML_3.99-0.3
    ## [67] glue_1.4.0               evaluate_0.14            data.table_1.12.8
    ## [70] vctrs_0.2.4              foreach_1.5.0            gtable_0.3.0
    ## [73] openssl_1.4.1            purrr_0.3.4              assertthat_0.2.1
    ## [76] xfun_0.13                xtable_1.8-4             survival_3.1-12
    ## [79] tibble_3.0.1             iterators_1.0.12         GenomicAlignments_1.24.0
    ## [82] AnnotationDbi_1.50.0     memoise_1.1.0            statmod_1.4.34
    ## [85] 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).