Last updated: 2022-06-06
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apocrine_signature_mdamb453/
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| html | 7cfa8e7 | Steve Pederson | 2022-05-26 | Added TOMTOM |
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| Rmd | 8797971 | Steve Pederson | 2022-04-27 | Start workflowr project. |
This analysis compares the binding sites of AR, FOXA1, GATA3 and TFAP2B in MDA-MB-453 cells. All ChIP targets were obtained from separate experiments using Vehicle as the reference condition and DHT-treatment as the key response under investigation. Given the mostly cytoplasmic location of AR in Vehicle, the primary comparison will be performed using DHT-treated samples. For all targets, the cistrome is largely conserved across conditions. Analysis using the GRAVI workflow is available here (for those given access)
For each ChIP target, the GRAVI workflow generates two peak-sets:
This terminology may be used through the analysis
The particular analysis using the GRAVI workflow used reads aligned to GRCh37/hg19 and the set of genes defined in Gencode release 33. Gene definitions were imported directly from this workflow.
sessionInfo()R version 4.2.0 (2022-04-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.4 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
locale:
[1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8
[5] LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8
[7] LC_PAPER=en_AU.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] workflowr_1.7.0
loaded via a namespace (and not attached):
[1] Rcpp_1.0.8.3 bslib_0.3.1 compiler_4.2.0 pillar_1.7.0
[5] later_1.3.0 git2r_0.30.1 jquerylib_0.1.4 tools_4.2.0
[9] getPass_0.2-2 digest_0.6.29 jsonlite_1.8.0 evaluate_0.15
[13] tibble_3.1.7 lifecycle_1.0.1 pkgconfig_2.0.3 rlang_1.0.2
[17] cli_3.3.0 rstudioapi_0.13 yaml_2.3.5 xfun_0.31
[21] fastmap_1.1.0 httr_1.4.3 stringr_1.4.0 knitr_1.39
[25] sass_0.4.1 fs_1.5.2 vctrs_0.4.1 rprojroot_2.0.3
[29] glue_1.6.2 R6_2.5.1 processx_3.5.3 fansi_1.0.3
[33] rmarkdown_2.14 callr_3.7.0 magrittr_2.0.3 whisker_0.4
[37] ps_1.7.0 promises_1.2.0.1 htmltools_0.5.2 ellipsis_0.3.2
[41] httpuv_1.6.5 utf8_1.2.2 stringi_1.7.6 crayon_1.5.1