Author: Caleb Lareau & Martin Aryee
Date: 2022-04-26

# diffloop: Identifying differential DNA loops from chromatin topology data

#### Caleb Lareau & Martin Aryee

#### 2022-04-26

    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 4.2.0 RC (2022-04-19 r82224)
    ## Platform: x86_64-pc-linux-gnu (64-bit)
    ## Running under: Ubuntu 20.04.4 LTS
    ##
    ## Matrix products: default
    ## BLAS:   /home/biocbuild/bbs-3.15-bioc/R/lib/libRblas.so
    ## LAPACK: /home/biocbuild/bbs-3.15-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] stats4    stats     graphics  grDevices utils     datasets  methods
    ## [8] base
    ##
    ## other attached packages:
    ##  [1] DESeq2_1.36.0               SummarizedExperiment_1.26.0
    ##  [3] Biobase_2.56.0              MatrixGenerics_1.8.0
    ##  [5] matrixStats_0.62.0          ggrepel_0.9.1
    ##  [7] GenomicRanges_1.48.0        GenomeInfoDb_1.32.0
    ##  [9] IRanges_2.30.0              S4Vectors_0.34.0
    ## [11] BiocGenerics_0.42.0         ggplot2_3.3.5
    ## [13] diffloopdata_1.23.0         diffloop_1.24.0
    ##
    ## loaded via a namespace (and not attached):
    ##   [1] bitops_1.0-7             bit64_4.0.5              RColorBrewer_1.1-3
    ##   [4] filelock_1.0.2           progress_1.2.2           httr_1.4.2
    ##   [7] tools_4.2.0              bslib_0.3.1              utf8_1.2.2
    ##  [10] R6_2.5.1                 DBI_1.1.2                colorspace_2.0-3
    ##  [13] withr_2.5.0              tidyselect_1.1.2         prettyunits_1.1.1
    ##  [16] bit_4.0.4                curl_4.3.2               compiler_4.2.0
    ##  [19] cli_3.3.0                xml2_1.3.3               DelayedArray_0.22.0
    ##  [22] rtracklayer_1.56.0       sass_0.4.1               scales_1.2.0
    ##  [25] genefilter_1.78.0        readr_2.1.2              pbapply_1.5-0
    ##  [28] rappdirs_0.3.3           Rsamtools_2.12.0         stringr_1.4.0
    ##  [31] digest_0.6.29            rmarkdown_2.14           XVector_0.36.0
    ##  [34] pkgconfig_2.0.3          htmltools_0.5.2          dbplyr_2.1.1
    ##  [37] fastmap_1.1.0            limma_3.52.0             rlang_1.0.2
    ##  [40] RSQLite_2.2.12           BiocIO_1.6.0             jquerylib_0.1.4
    ##  [43] generics_0.1.2           zoo_1.8-10               jsonlite_1.8.0
    ##  [46] BiocParallel_1.30.0      dplyr_1.0.8              RCurl_1.98-1.6
    ##  [49] magrittr_2.0.3           Sushi_1.34.0             GenomeInfoDbData_1.2.8
    ##  [52] Matrix_1.4-1             Rcpp_1.0.8.3             munsell_0.5.0
    ##  [55] fansi_1.0.3              lifecycle_1.0.1          stringi_1.7.6
    ##  [58] yaml_2.3.5               edgeR_3.38.0             zlibbioc_1.42.0
    ##  [61] plyr_1.8.7               BiocFileCache_2.4.0      grid_4.2.0
    ##  [64] blob_1.2.3               parallel_4.2.0           crayon_1.5.1
    ##  [67] lattice_0.20-45          splines_4.2.0            Biostrings_2.64.0
    ##  [70] annotate_1.74.0          hms_1.1.1                KEGGREST_1.36.0
    ##  [73] locfit_1.5-9.5           knitr_1.38               pillar_1.7.0
    ##  [76] rjson_0.2.21             geneplotter_1.74.0       reshape2_1.4.4
    ##  [79] codetools_0.2-18         biomaRt_2.52.0           XML_3.99-0.9
    ##  [82] glue_1.6.2               evaluate_0.15            data.table_1.14.2
    ##  [85] png_0.1-7                vctrs_0.4.1              tzdb_0.3.0
    ##  [88] foreach_1.5.2            gtable_0.3.0             purrr_0.3.4
    ##  [91] assertthat_0.2.1         cachem_1.0.6             xfun_0.30
    ##  [94] xtable_1.8-4             restfulr_0.0.13          survival_3.3-1
    ##  [97] tibble_3.1.6             iterators_1.0.14         GenomicAlignments_1.32.0
    ## [100] AnnotationDbi_1.58.0     memoise_2.0.1            statmod_1.4.36
    ## [103] 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).