# diffloop: Identifying differential DNA loops from chromatin topology data

#### Caleb Lareau & Martin Aryee

#### 2021-10-26

    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 4.1.1 (2021-08-10)
    ## Platform: x86_64-w64-mingw32/x64 (64-bit)
    ## Running under: Windows Server x64 (build 17763)
    ##
    ## 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] stats4    stats     graphics  grDevices utils     datasets  methods
    ## [8] base
    ##
    ## other attached packages:
    ##  [1] DESeq2_1.34.0               SummarizedExperiment_1.24.0
    ##  [3] Biobase_2.54.0              MatrixGenerics_1.6.0
    ##  [5] matrixStats_0.61.0          ggrepel_0.9.1
    ##  [7] GenomicRanges_1.46.0        GenomeInfoDb_1.30.0
    ##  [9] IRanges_2.28.0              S4Vectors_0.32.0
    ## [11] BiocGenerics_0.40.0         ggplot2_3.3.5
    ## [13] diffloopdata_1.21.0         diffloop_1.22.0
    ##
    ## 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_4.1.1              bslib_0.3.1              utf8_1.2.2
    ##  [10] R6_2.5.1                 DBI_1.1.1                colorspace_2.0-2
    ##  [13] withr_2.4.2              tidyselect_1.1.1         prettyunits_1.1.1
    ##  [16] bit_4.0.4                curl_4.3.2               compiler_4.1.1
    ##  [19] xml2_1.3.2               DelayedArray_0.20.0      rtracklayer_1.54.0
    ##  [22] sass_0.4.0               scales_1.1.1             genefilter_1.76.0
    ##  [25] readr_2.0.2              pbapply_1.5-0            rappdirs_0.3.3
    ##  [28] Rsamtools_2.10.0         stringr_1.4.0            digest_0.6.28
    ##  [31] rmarkdown_2.11           XVector_0.34.0           pkgconfig_2.0.3
    ##  [34] htmltools_0.5.2          dbplyr_2.1.1             fastmap_1.1.0
    ##  [37] limma_3.50.0             rlang_0.4.12             RSQLite_2.2.8
    ##  [40] jquerylib_0.1.4          BiocIO_1.4.0             generics_0.1.1
    ##  [43] zoo_1.8-9                jsonlite_1.7.2           BiocParallel_1.28.0
    ##  [46] dplyr_1.0.7              RCurl_1.98-1.5           magrittr_2.0.1
    ##  [49] Sushi_1.32.0             GenomeInfoDbData_1.2.7   Matrix_1.3-4
    ##  [52] Rcpp_1.0.7               munsell_0.5.0            fansi_0.5.0
    ##  [55] lifecycle_1.0.1          stringi_1.7.5            yaml_2.2.1
    ##  [58] edgeR_3.36.0             zlibbioc_1.40.0          plyr_1.8.6
    ##  [61] BiocFileCache_2.2.0      grid_4.1.1               blob_1.2.2
    ##  [64] parallel_4.1.1           crayon_1.4.1             lattice_0.20-45
    ##  [67] splines_4.1.1            Biostrings_2.62.0        annotate_1.72.0
    ##  [70] hms_1.1.1                KEGGREST_1.34.0          locfit_1.5-9.4
    ##  [73] knitr_1.36               pillar_1.6.4             rjson_0.2.20
    ##  [76] geneplotter_1.72.0       reshape2_1.4.4           codetools_0.2-18
    ##  [79] biomaRt_2.50.0           XML_3.99-0.8             glue_1.4.2
    ##  [82] evaluate_0.14            data.table_1.14.2        png_0.1-7
    ##  [85] vctrs_0.3.8              tzdb_0.1.2               foreach_1.5.1
    ##  [88] gtable_0.3.0             purrr_0.3.4              assertthat_0.2.1
    ##  [91] cachem_1.0.6             xfun_0.27                xtable_1.8-4
    ##  [94] restfulr_0.0.13          survival_3.2-13          tibble_3.1.5
    ##  [97] iterators_1.0.13         GenomicAlignments_1.30.0 AnnotationDbi_1.56.0
    ## [100] 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).