# diffloop: Identifying differential DNA loops from chromatin topology data

#### Caleb Lareau & Martin Aryee

#### 2021-05-19

    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 4.1.0 (2021-05-18)
    ## Platform: x86_64-pc-linux-gnu (64-bit)
    ## Running under: Ubuntu 20.04.2 LTS
    ##
    ## Matrix products: default
    ## BLAS:   /home/biocbuild/bbs-3.13-bioc/R/lib/libRblas.so
    ## LAPACK: /home/biocbuild/bbs-3.13-bioc/R/lib/libRlapack.so
    ##
    ## locale:
    ##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
    ##  [3] LC_TIME=en_GB              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_1.32.0               SummarizedExperiment_1.22.0
    ##  [3] Biobase_2.52.0              MatrixGenerics_1.4.0
    ##  [5] matrixStats_0.58.0          ggrepel_0.9.1
    ##  [7] GenomicRanges_1.44.0        GenomeInfoDb_1.28.0
    ##  [9] IRanges_2.26.0              S4Vectors_0.30.0
    ## [11] BiocGenerics_0.38.0         ggplot2_3.3.3
    ## [13] diffloopdata_1.19.0         diffloop_1.20.0
    ##
    ## loaded via a namespace (and not attached):
    ##  [1] bitops_1.0-7             bit64_4.0.5              RColorBrewer_1.1-2
    ##  [4] filelock_1.0.2           progress_1.2.2           httr_1.4.2
    ##  [7] tools_4.1.0              bslib_0.2.5.1            utf8_1.2.1
    ## [10] R6_2.5.0                 DBI_1.1.1                colorspace_2.0-1
    ## [13] withr_2.4.2              tidyselect_1.1.1         prettyunits_1.1.1
    ## [16] bit_4.0.4                curl_4.3.1               compiler_4.1.0
    ## [19] DelayedArray_0.18.0      rtracklayer_1.52.0       sass_0.4.0
    ## [22] scales_1.1.1             genefilter_1.74.0        readr_1.4.0
    ## [25] pbapply_1.4-3            rappdirs_0.3.3           stringr_1.4.0
    ## [28] digest_0.6.27            Rsamtools_2.8.0          rmarkdown_2.8
    ## [31] XVector_0.32.0           pkgconfig_2.0.3          htmltools_0.5.1.1
    ## [34] dbplyr_2.1.1             fastmap_1.1.0            limma_3.48.0
    ## [37] rlang_0.4.11             RSQLite_2.2.7            jquerylib_0.1.4
    ## [40] BiocIO_1.2.0             generics_0.1.0           zoo_1.8-9
    ## [43] jsonlite_1.7.2           BiocParallel_1.26.0      dplyr_1.0.6
    ## [46] RCurl_1.98-1.3           magrittr_2.0.1           Sushi_1.30.0
    ## [49] GenomeInfoDbData_1.2.6   Matrix_1.3-3             Rcpp_1.0.6
    ## [52] munsell_0.5.0            fansi_0.4.2              lifecycle_1.0.0
    ## [55] stringi_1.6.2            yaml_2.2.1               edgeR_3.34.0
    ## [58] zlibbioc_1.38.0          plyr_1.8.6               BiocFileCache_2.0.0
    ## [61] grid_4.1.0               blob_1.2.1               crayon_1.4.1
    ## [64] lattice_0.20-44          splines_4.1.0            Biostrings_2.60.0
    ## [67] annotate_1.70.0          hms_1.1.0                KEGGREST_1.32.0
    ## [70] locfit_1.5-9.4           knitr_1.33               pillar_1.6.1
    ## [73] rjson_0.2.20             geneplotter_1.70.0       reshape2_1.4.4
    ## [76] codetools_0.2-18         biomaRt_2.48.0           XML_3.99-0.6
    ## [79] glue_1.4.2               evaluate_0.14            data.table_1.14.0
    ## [82] png_0.1-7                vctrs_0.3.8              foreach_1.5.1
    ## [85] gtable_0.3.0             purrr_0.3.4              assertthat_0.2.1
    ## [88] cachem_1.0.5             xfun_0.23                xtable_1.8-4
    ## [91] restfulr_0.0.13          survival_3.2-11          tibble_3.1.2
    ## [94] iterators_1.0.13         GenomicAlignments_1.28.0 AnnotationDbi_1.54.0
    ## [97] memoise_2.0.0            statmod_1.4.36           ellipsis_0.3.2

## 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).