Overview

This repository contains code to generate figures for the paper by M. Baretti et al. "Entinostat in combination with nivolumab in metastatic pancreatic ductal adenocarcinoma: a phase 2 clinical trial" published in Nature Communications: https://www.nature.com/articles/s41467-024-52528-7.

Input data

Most of the input data are available in the input_data folder. Restrictions apply to the availability of patient data and so the table_patients.csv file is not publicly available. However, the patient data files which included limited deidentified clinical data associated with the manuscript will be available upon reasonable request to the corresponding authors and is accessible through dbGaP (accession number phs003615): https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs003615.v1.p1.

Rmarkdown

Rmarkdown files are stored in the Rmd folder. The main script is runRmd.r which installs all required packages and renders Rmd files to generate output tables in the output_data folder and html/docs reports in Rmd.

Output data

The output_data folder contains html/docs reports rendered from Rmarkdown files, as well as output tables with the analysis results.

System requirements

The code can be run on any computer with installed the R programming environment. Depending on your system, installation of all required packages can take up to an hour.

How to run

Open the R environment and run the following line:

source('runRmd.r') The code was tested on Windows 10 Pro with 32.0 GB RAM and a 2.81 GHz processor. If all required packages are installed, the runtime of the script is about 10 minutes. The script was tested in R version 4.3.2 and the following packages: ```

R version 4.3.2 (2023-10-31 ucrt)

Platform: x86_64-w64-mingw32/x64 (64-bit)

Running under: Windows 10 x64 (build 19045)

Matrix products: default

locale:

[1] LCCOLLATE=EnglishUnited States.utf8

[2] LCCTYPE=EnglishUnited States.utf8

[3] LCMONETARY=EnglishUnited States.utf8

[4] LC_NUMERIC=C

[5] LCTIME=EnglishUnited States.utf8

time zone: America/New_York

tzcode source: internal

attached base packages:

[1] grid stats4 stats graphics grDevices utils datasets

[8] methods base

other attached packages:

[1] pheatmap1.0.12 scales1.3.0

[3] Matrix1.6-3 data.table1.14.8

[5] BiocManager1.30.22 survival3.5-7

[7] binom1.1-1.1 flextable0.9.4

[9] survminer0.4.9 msigdbr7.5.1

[11] fgsea1.26.0 EnhancedVolcano1.18.0

[13] ComplexHeatmap2.16.0 DESeq21.40.2

[15] SummarizedExperiment1.30.2 Biobase2.60.0

[17] MatrixGenerics1.12.3 matrixStats1.1.0

[19] GenomicRanges1.52.1 GenomeInfoDb1.36.4

[21] IRanges2.34.1 S4Vectors0.38.2

[23] BiocGenerics0.46.0 kableExtra1.3.4

[25] pals1.8 gridExtra2.3

[27] DT0.30 ggrepel0.9.4

[29] ggpubr0.6.0 ggplot23.4.4

[31] dplyr1.1.2 knitr1.45

loaded via a namespace (and not attached):

[1] splines4.3.2 later1.3.1 bitops_1.0-7

[4] tibble3.2.1 lifecycle1.0.4 rstatix_0.7.2

[7] mixsqp0.3-54 doParallel1.0.17 lattice_0.21-9

[10] crosstalk1.2.1 backports1.4.1 magrittr_2.0.3

[13] sass0.4.8 rmarkdown2.25 jquerylib_0.1.4

[16] yaml2.3.7 httpuv1.6.12 zip_2.3.0

[19] askpass1.2.0 cowplot1.1.2 mapproj_1.2.11

[22] RColorBrewer1.1-3 maps3.4.1.1 abind_1.4-5

[25] zlibbioc1.46.0 rvest1.0.3 purrr_1.0.2

[28] RCurl1.98-1.13 gdtools0.3.4 circlize_0.4.15

[31] GenomeInfoDbData1.2.10 KMsurv0.1-5 irlba_2.3.5.1

[34] crul1.4.0 svglite2.1.2 commonmark_1.9.0

[37] codetools0.2-19 DelayedArray0.26.7 ggtext_0.1.2

[40] xml21.3.5 tidyselect1.2.0 shape_1.4.6

[43] httpcode0.3.0 farver2.1.1 webshot_0.5.5

[46] jsonlite1.8.7 GetoptLong1.0.5 ellipsis_0.3.2

[49] iterators1.0.14 systemfonts1.0.5 foreach_1.5.2

[52] tools4.3.2 ragg1.2.6 snow_0.4-4

[55] Rcpp1.0.11 glue1.6.2 xfun_0.39

[58] withr2.5.2 fastmap1.1.1 fansi_1.0.4

[61] openssl2.1.1 digest0.6.33 truncnorm_1.0-9

[64] R62.5.1 mime0.12 textshaping_0.3.7

[67] colorspace2.1-0 dichromat2.0-0.1 markdown_1.12

[70] utf81.2.3 tidyr1.3.0 generics_0.1.3

[73] fontLiberation0.1.0 httr1.4.7 htmlwidgets_1.6.4

[76] S4Arrays1.0.6 pkgconfig2.0.3 gtable_0.3.4

[79] XVector0.40.0 survMisc0.5.6 htmltools_0.5.7

[82] fontBitstreamVera0.1.1 carData3.0-5 clue_0.3-65

[85] png0.1-8 ashr2.2-63 km.ci_0.5-6

[88] rstudioapi0.15.0 reshape21.4.4 rjson_0.2.21

[91] uuid1.1-1 curl5.1.0 zoo_1.8-12

[94] cachem1.0.8 GlobalOptions0.1.2 stringr_1.5.1

[97] parallel4.3.2 pillar1.9.0 vctrs_0.6.3

[100] promises1.2.1 car3.1-2 xtable_1.8-4

[103] cluster2.1.4 evaluate0.23 invgamma_1.1

[106] cli3.6.1 locfit1.5-9.8 compiler_4.3.2

[109] rlang1.1.1 crayon1.5.2 SQUAREM_2021.1

[112] ggsignif0.6.4 labeling0.4.3 plyr_1.8.9

[115] stringi1.8.1 viridisLite0.4.2 BiocParallel_1.34.2

[118] babelgene22.9 munsell0.5.0 fontquiver_0.2.1

[121] gfonts0.2.0 shiny1.8.0 highr_0.10

[124] gridtext0.1.5 broom1.0.5 bslib_0.6.1

[127] fastmatch1.1-4 officer0.6.3

````