Last updated: 2021-03-22

Checks: 6 1

Knit directory: transcriptome_cll/

This reproducible R Markdown analysis was created with workflowr (version 1.4.0). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

R Markdown file: uncommitted changes

The R Markdown file has unstaged changes. To know which version of the R Markdown file created these results, you’ll want to first commit it to the Git repo. If you’re still working on the analysis, you can ignore this warning. When you’re finished, you can run wflow_publish to commit the R Markdown file and build the HTML.

Environment: empty

Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.

Seed: set.seed(20190511)

The command set.seed(20190511) was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.

Session information: recorded

Great job! Recording the operating system, R version, and package versions is critical for reproducibility.

Cache: none

Nice! There were no cached chunks for this analysis, so you can be confident that you successfully produced the results during this run.

File paths: relative

Great job! Using relative paths to the files within your workflowr project makes it easier to run your code on other machines.

Repository version: 50a8daa

Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility. The version displayed above was the version of the Git repository at the time these results were generated.

Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:


Ignored files:
    Ignored:    .Rhistory
    Ignored:    .Rproj.user/
    Ignored:    analysis/figure/
    Ignored:    output/figures/r_objects/BRAF/enrichment/

Untracked files:
    Untracked:  docs/figure/Del13q14.Rmd/
    Untracked:  docs/figure/Del17p13.Rmd/
    Untracked:  docs/figure/Del8p12.Rmd/
    Untracked:  docs/figure/Gain8q24.Rmd/
    Untracked:  docs/figure/Med12.Rmd/
    Untracked:  docs/figure/Notch1.Rmd/
    Untracked:  docs/figure/TP53.Rmd/
    Untracked:  docs/figure/del11q22.Rmd/
    Untracked:  output/enrichment/NOTCH1_gsea.rds
    Untracked:  output/enrichment/del13q14_gsea.rds
    Untracked:  output/enrichment/del17p13_gsea.rds
    Untracked:  output/enrichment/gain8q24_gsea.rds
    Untracked:  output/figures/r_objects/Notch1/Notch1_enrichment_dn.rds
    Untracked:  output/figures/r_objects/Notch1/Notch1_enrichment_up.rds
    Untracked:  output/figures/r_objects/Notch1/de_genes/AAAS.rds
    Untracked:  output/figures/r_objects/Notch1/de_genes/ARHGEF37.rds
    Untracked:  output/figures/r_objects/Notch1/de_genes/ASH2LP1.rds
    Untracked:  output/figures/r_objects/Notch1/de_genes/CCDC114.rds
    Untracked:  output/figures/r_objects/Notch1/de_genes/CD1A.rds
    Untracked:  output/figures/r_objects/Notch1/de_genes/CELSR2.rds
    Untracked:  output/figures/r_objects/Notch1/de_genes/CNFN.rds
    Untracked:  output/figures/r_objects/Notch1/de_genes/CR1.rds
    Untracked:  output/figures/r_objects/Notch1/de_genes/DNAH2.rds
    Untracked:  output/figures/r_objects/Notch1/de_genes/FOXP2.rds
    Untracked:  output/figures/r_objects/Notch1/de_genes/IGHV1-3.rds
    Untracked:  output/figures/r_objects/Notch1/de_genes/IGLV1-47.rds
    Untracked:  output/figures/r_objects/Notch1/de_genes/IGLV2-23.rds
    Untracked:  output/figures/r_objects/Notch1/de_genes/IGLV3-10.rds
    Untracked:  output/figures/r_objects/Notch1/de_genes/IGLV4-69.rds
    Untracked:  output/figures/r_objects/Notch1/de_genes/IGLV5-37.rds
    Untracked:  output/figures/r_objects/Notch1/de_genes/MOB3B.rds
    Untracked:  output/figures/r_objects/Notch1/de_genes/OCA2.rds
    Untracked:  output/figures/r_objects/Notch1/de_genes/POU6F2.rds
    Untracked:  output/figures/r_objects/Notch1/de_genes/SERPINE2.rds
    Untracked:  output/figures/r_objects/Notch1/de_genes/SPAG17.rds
    Untracked:  output/figures/r_objects/Notch1/de_genes/SPTBN5.rds
    Untracked:  output/figures/r_objects/Notch1/de_genes/TMPRSS4.rds
    Untracked:  output/figures/r_objects/atm/de_genes/CYP51A1-AS1.rds
    Untracked:  output/figures/r_objects/atm/de_genes/IGHV1-18.rds
    Untracked:  output/figures/r_objects/atm/de_genes/IGLV3-27.rds
    Untracked:  output/figures/r_objects/atm/de_genes/NCAPGP1.rds
    Untracked:  output/figures/r_objects/atm/de_genes/PPM1E.rds
    Untracked:  output/figures/r_objects/atm/de_genes/PRSS21.rds
    Untracked:  output/figures/r_objects/atm/de_genes/PTPRQ.rds
    Untracked:  output/figures/r_objects/atm/de_genes/SNTB1.rds
    Untracked:  output/figures/r_objects/atm/de_genes/TM6SF1.rds
    Untracked:  output/figures/r_objects/del11q22/de_genes/CLDN3.rds
    Untracked:  output/figures/r_objects/del11q22/de_genes/IGHE.rds
    Untracked:  output/figures/r_objects/del11q22/de_genes/TFCP2L1.rds
    Untracked:  output/figures/r_objects/del13q14/de_genes/ARNTL2.rds
    Untracked:  output/figures/r_objects/del13q14/de_genes/CCDC151.rds
    Untracked:  output/figures/r_objects/del13q14/de_genes/CSGALNACT1.rds
    Untracked:  output/figures/r_objects/del13q14/de_genes/FBLN2.rds
    Untracked:  output/figures/r_objects/del13q14/de_genes/FRMD5.rds
    Untracked:  output/figures/r_objects/del13q14/de_genes/IGHV1-2.rds
    Untracked:  output/figures/r_objects/del13q14/de_genes/IGHV3-33.rds
    Untracked:  output/figures/r_objects/del13q14/de_genes/IGKV1-39.rds
    Untracked:  output/figures/r_objects/del13q14/de_genes/IGKV1-5.rds
    Untracked:  output/figures/r_objects/del13q14/de_genes/IGKV1-8.rds
    Untracked:  output/figures/r_objects/del13q14/de_genes/IGKV1D-39.rds
    Untracked:  output/figures/r_objects/del13q14/de_genes/INHBA.rds
    Untracked:  output/figures/r_objects/del13q14/de_genes/LAMP3.rds
    Untracked:  output/figures/r_objects/del13q14/de_genes/RAI14.rds
    Untracked:  output/figures/r_objects/del13q14/de_genes/RASSF8.rds
    Untracked:  output/figures/r_objects/del13q14/de_genes/RNF157.rds
    Untracked:  output/figures/r_objects/del13q14/de_genes/SEPT10.rds
    Untracked:  output/figures/r_objects/del13q14/de_genes/SLC19A1.rds
    Untracked:  output/figures/r_objects/del13q14/del13q14_enrichment_dn.rds
    Untracked:  output/figures/r_objects/del13q14/del13q14_enrichment_up.rds
    Untracked:  output/figures/r_objects/del17p13/de_genes/ARNTL2.rds
    Untracked:  output/figures/r_objects/del17p13/de_genes/CDH2.rds
    Untracked:  output/figures/r_objects/del17p13/de_genes/CEP55.rds
    Untracked:  output/figures/r_objects/del17p13/de_genes/COL6A1.rds
    Untracked:  output/figures/r_objects/del17p13/de_genes/FLT4.rds
    Untracked:  output/figures/r_objects/del17p13/de_genes/IGHV3-11.rds
    Untracked:  output/figures/r_objects/del17p13/de_genes/IGKV1-16.rds
    Untracked:  output/figures/r_objects/del17p13/de_genes/KIF7.rds
    Untracked:  output/figures/r_objects/del17p13/de_genes/MDM2.rds
    Untracked:  output/figures/r_objects/del17p13/de_genes/MEIS1.rds
    Untracked:  output/figures/r_objects/del17p13/de_genes/MIR4538.rds
    Untracked:  output/figures/r_objects/del17p13/de_genes/MRAP2.rds
    Untracked:  output/figures/r_objects/del17p13/de_genes/MYL12BP2.rds
    Untracked:  output/figures/r_objects/del17p13/de_genes/NPTX1.rds
    Untracked:  output/figures/r_objects/del17p13/de_genes/NRP2.rds
    Untracked:  output/figures/r_objects/del17p13/de_genes/PPM1H.rds
    Untracked:  output/figures/r_objects/del17p13/de_genes/RNF157.rds
    Untracked:  output/figures/r_objects/del17p13/de_genes/SLFNL1.rds
    Untracked:  output/figures/r_objects/del17p13/de_genes/SRP72P2.rds
    Untracked:  output/figures/r_objects/del17p13/de_genes/TFCP2L1.rds
    Untracked:  output/figures/r_objects/del17p13/de_genes/WDR87.rds
    Untracked:  output/figures/r_objects/del17p13/del17p13_enrichment_dn.rds
    Untracked:  output/figures/r_objects/del17p13/del17p13_enrichment_up.rds
    Untracked:  output/figures/r_objects/del8p12/de_genes/IGHJ2P.rds
    Untracked:  output/figures/r_objects/del8p12/de_genes/OVCH1-AS1.rds
    Untracked:  output/figures/r_objects/del8p12/de_genes/PLCB1.rds
    Untracked:  output/figures/r_objects/del8p12/de_genes/TM6SF1.rds
    Untracked:  output/figures/r_objects/epistasis/de_genes/CD38.rds
    Untracked:  output/figures/r_objects/gain8q24/de_genes/C1orf127.rds
    Untracked:  output/figures/r_objects/gain8q24/de_genes/CBS.rds
    Untracked:  output/figures/r_objects/gain8q24/de_genes/FAM160B2.rds
    Untracked:  output/figures/r_objects/gain8q24/de_genes/FAM85B.rds
    Untracked:  output/figures/r_objects/gain8q24/de_genes/IGLV1-51.rds
    Untracked:  output/figures/r_objects/gain8q24/de_genes/MTERF3.rds
    Untracked:  output/figures/r_objects/gain8q24/de_genes/RPL23AP53.rds
    Untracked:  output/figures/r_objects/gain8q24/de_genes/TM6SF1.rds
    Untracked:  output/figures/r_objects/gain8q24/de_genes/TMEM242.rds
    Untracked:  output/figures/r_objects/gain8q24/de_genes/ZNF662.rds
    Untracked:  output/figures/r_objects/gain8q24/gain8q24_enrichment_dn.rds
    Untracked:  output/figures/r_objects/gain8q24/gain8q24_enrichment_up.rds
    Untracked:  output/figures/r_objects/med12/de_genes/C10orf105.rds
    Untracked:  output/figures/r_objects/med12/de_genes/COL1A1.rds
    Untracked:  output/figures/r_objects/med12/de_genes/DUSP2.rds
    Untracked:  output/figures/r_objects/med12/de_genes/ENTPD4.rds
    Untracked:  output/figures/r_objects/med12/de_genes/ERRFI1.rds
    Untracked:  output/figures/r_objects/med12/de_genes/HSPA1A.rds
    Untracked:  output/figures/r_objects/med12/de_genes/HSPA1B.rds
    Untracked:  output/figures/r_objects/med12/de_genes/HSPA6.rds
    Untracked:  output/figures/r_objects/med12/de_genes/IGHJ2P.rds
    Untracked:  output/figures/r_objects/med12/de_genes/IGHV1-45.rds
    Untracked:  output/figures/r_objects/med12/de_genes/IGKV2-28.rds
    Untracked:  output/figures/r_objects/med12/de_genes/IGLV6-57.rds
    Untracked:  output/figures/r_objects/med12/de_genes/LTBP1.rds
    Untracked:  output/figures/r_objects/med12/de_genes/MTUS1.rds
    Untracked:  output/figures/r_objects/med12/de_genes/RASSF1.rds
    Untracked:  output/figures/r_objects/med12/de_genes/SNCAIP.rds
    Untracked:  output/figures/r_objects/med12/de_genes/TMPRSS11E.rds
    Untracked:  output/figures/r_objects/med12/de_genes/TRIM16L.rds

Unstaged changes:
    Modified:   analysis/ATM.Rmd
    Modified:   analysis/Del8p12.Rmd
    Modified:   analysis/Med12.Rmd
    Modified:   output/enrichment/del11q22.3_gsea.rds
    Modified:   output/figures/paper_fig/figure_epi.pdf
    Modified:   output/figures/paper_fig/figure_epi.svg
    Modified:   output/figures/paper_fig/generate_figures.Rmd
    Modified:   output/figures/r_objects/Notch1/de_genes/CLN8.rds
    Modified:   output/figures/r_objects/Notch1/de_genes/COL5A2.rds
    Modified:   output/figures/r_objects/Notch1/de_genes/GJB7.rds
    Modified:   output/figures/r_objects/Notch1/de_genes/IGLC6.rds
    Modified:   output/figures/r_objects/Notch1/de_genes/IGLV7-46.rds
    Modified:   output/figures/r_objects/Notch1/de_genes/KLK4.rds
    Modified:   output/figures/r_objects/Notch1/de_genes/MSI2.rds
    Modified:   output/figures/r_objects/Notch1/de_genes/NOTCH4.rds
    Modified:   output/figures/r_objects/Notch1/de_genes/SEPT3.rds
    Modified:   output/figures/r_objects/Notch1/de_genes/SPACA9.rds
    Modified:   output/figures/r_objects/Notch1/notch1_heatmap.rds
    Modified:   output/figures/r_objects/TP53/enrich_dot2.rds
    Modified:   output/figures/r_objects/TP53/enrich_net_hm.rds
    Modified:   output/figures/r_objects/TP53/enrich_net_kegg.rds
    Modified:   output/figures/r_objects/atm/atm_heatmap.rds
    Modified:   output/figures/r_objects/atm/de_genes/AHRR.rds
    Modified:   output/figures/r_objects/atm/de_genes/MECOM.rds
    Modified:   output/figures/r_objects/atm/de_genes/P4HA2.rds
    Modified:   output/figures/r_objects/atm/de_genes/PLCB1.rds
    Modified:   output/figures/r_objects/atm/de_genes/RBFOX2.rds
    Modified:   output/figures/r_objects/atm/de_genes/RNASE1.rds
    Modified:   output/figures/r_objects/atm/de_genes/SAXO2.rds
    Modified:   output/figures/r_objects/atm/de_genes/TMC5.rds
    Modified:   output/figures/r_objects/atm/de_genes/WNK2.rds
    Modified:   output/figures/r_objects/del11q22/de_genes/ACAT1.rds
    Modified:   output/figures/r_objects/del11q22/de_genes/AIRE.rds
    Modified:   output/figures/r_objects/del11q22/de_genes/ALG9.rds
    Modified:   output/figures/r_objects/del11q22/de_genes/ALKBH8.rds
    Modified:   output/figures/r_objects/del11q22/de_genes/ATM.rds
    Modified:   output/figures/r_objects/del11q22/de_genes/C11orf57.rds
    Modified:   output/figures/r_objects/del11q22/de_genes/CUL5.rds
    Modified:   output/figures/r_objects/del11q22/de_genes/CWF19L2.rds
    Modified:   output/figures/r_objects/del11q22/de_genes/DDX10.rds
    Modified:   output/figures/r_objects/del11q22/de_genes/DPY19L2.rds
    Modified:   output/figures/r_objects/del11q22/de_genes/IGHV3-11.rds
    Modified:   output/figures/r_objects/del11q22/de_genes/IGHV4-34.rds
    Modified:   output/figures/r_objects/del11q22/de_genes/IGHV4-39.rds
    Modified:   output/figures/r_objects/del11q22/de_genes/KBTBD3.rds
    Modified:   output/figures/r_objects/del11q22/de_genes/NPAT.rds
    Modified:   output/figures/r_objects/del11q22/de_genes/NT5E.rds
    Modified:   output/figures/r_objects/del11q22/de_genes/PPP2R1B.rds
    Modified:   output/figures/r_objects/del11q22/de_genes/RBM7.rds
    Modified:   output/figures/r_objects/del11q22/de_genes/REXO2.rds
    Modified:   output/figures/r_objects/del11q22/de_genes/SIK2.rds
    Modified:   output/figures/r_objects/del11q22/de_genes/TEAD1.rds
    Modified:   output/figures/r_objects/del11q22/de_genes/TMPRSS5.rds
    Modified:   output/figures/r_objects/del11q22/de_genes/TTC12.rds
    Modified:   output/figures/r_objects/del11q22/de_genes/USP28.rds
    Modified:   output/figures/r_objects/del11q22/de_genes/ZW10.rds
    Modified:   output/figures/r_objects/del11q22/del11q22_enrichment_dn.rds
    Modified:   output/figures/r_objects/del11q22/del11q22_enrichment_up.rds
    Modified:   output/figures/r_objects/del11q22/del11q22_heatmap.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/ANK3.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/AXL.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/C10orf10.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/C1orf127.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/C9orf139.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/CD1A.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/CDCP1.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/CELSR2.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/CLEC4A.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/CNFN.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/CTAGE9.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/ENPP3.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/F12.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/IGHV1-24.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/IGHV3-23.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/IGHV3-49.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/IGKV2-24.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/IGKV4-1.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/IGLV1-40.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/IGLV3-10.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/ILDR2.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/ISL2.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/ITM2B.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/KCNRG.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/KIAA1549.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/KIF7.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/LARGE1.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/LINC00470.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/LINC00861.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/LINC02363.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/MAF.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/MIOX.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/MOGAT2.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/MTCO3P40.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/MTUS1.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/MYLK.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/NT5E.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/PALD1.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/PERP.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/PI16.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/PLEKHG7.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/RAMP1.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/RGL3.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/SCIN.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/SDC3.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/SERPINE2.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/SLC1A6.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/SMAD3.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/SNTB1.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/SOAT2.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/TFCP2L1.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/TM6SF1.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/TMPRSS4.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/TSPAN13.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/UACA.rds
    Modified:   output/figures/r_objects/del13q14/de_genes/UBE2F.rds
    Modified:   output/figures/r_objects/del13q14/del13q14_heatmap.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/ACAP1.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/ANKRD36BP2.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/BTBD18.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/CA1.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/CDHR1.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/CPT1C.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/CTC1.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/CTNS.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/DPH1.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/DRC3.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/DSE.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/DVL2.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/FOXA3.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/FXR2.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/GK3P.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/GLOD4.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/GPS2.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/IGKV2-24.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/IGKV2D-28.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/IGLV9-49.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/KIAA0753.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/MAP2K4.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/MELK.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/MPDU1.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/MT-RNR1.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/MTMR11.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/MYH3.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/NEURL4.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/NLRP1.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/RABEP1.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/RNF167.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/SENP3.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/SMG6.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/SOX15.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/TNK1.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/TRPC5.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/UPK1A.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/VPS53.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/WRAP53.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/ZBTB4.rds
    Modified:   output/figures/r_objects/del17p13/de_genes/ZZEF1.rds
    Modified:   output/figures/r_objects/del17p13/del17p13_heatmap.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/ADGRG7.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/ALG1L13P.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/C8orf58.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/DDX43.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/ELP3.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/EPHX2.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/ERICH1.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/FAM160B2.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/FBXO25.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/GTF2E2.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/HMBOX1.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/IGKV1-5.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/IGKV3-20.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/INTS10.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/INTS9.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/KIF13B.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/LGSN.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/LINC01016.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/MAPRE3.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/MCPH1.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/MEF2B.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/MTCO3P12.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/NEIL2.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/OVCH1.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/PNOC.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/PPP3CC.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/PRDM16.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/PSPHP1.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/PTCH1.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/PTK2B.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/PTP4A3.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/PTPRQ.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/R3HCC1.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/REEP4.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/SCUBE2.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/SLC44A5.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/SLC6A9.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/SNTB1.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/TRPM2-AS.rds
    Modified:   output/figures/r_objects/del8p12/de_genes/XPO7.rds
    Modified:   output/figures/r_objects/del8p12/del8p12_heatmap.rds
    Modified:   output/figures/r_objects/epistasis/de_genes/ABLIM2.rds
    Modified:   output/figures/r_objects/epistasis/de_genes/BCL2A1.rds
    Modified:   output/figures/r_objects/epistasis/de_genes/CAMK2N1.rds
    Modified:   output/figures/r_objects/epistasis/de_genes/CHAD.rds
    Modified:   output/figures/r_objects/epistasis/de_genes/CRIM1.rds
    Modified:   output/figures/r_objects/epistasis/de_genes/E2F2.rds
    Modified:   output/figures/r_objects/epistasis/de_genes/EBF1.rds
    Modified:   output/figures/r_objects/epistasis/de_genes/EBF4.rds
    Modified:   output/figures/r_objects/epistasis/de_genes/EML6.rds
    Modified:   output/figures/r_objects/epistasis/de_genes/ENPP3.rds
    Modified:   output/figures/r_objects/epistasis/de_genes/EPHB1.rds
    Modified:   output/figures/r_objects/epistasis/de_genes/EPHB6.rds
    Modified:   output/figures/r_objects/epistasis/de_genes/FAM212A.rds
    Modified:   output/figures/r_objects/epistasis/de_genes/FGD6.rds
    Modified:   output/figures/r_objects/epistasis/de_genes/FGF2.rds
    Modified:   output/figures/r_objects/epistasis/de_genes/GEN1.rds
    Modified:   output/figures/r_objects/epistasis/de_genes/GP5.rds
    Modified:   output/figures/r_objects/epistasis/de_genes/JAG1.rds
    Modified:   output/figures/r_objects/epistasis/de_genes/LEF1.rds
    Modified:   output/figures/r_objects/epistasis/de_genes/PPP1R14A.rds
    Modified:   output/figures/r_objects/epistasis/de_genes/RAI14.rds
    Modified:   output/figures/r_objects/epistasis/de_genes/SLC4A8.rds
    Modified:   output/figures/r_objects/epistasis/de_genes/SYBU.rds
    Modified:   output/figures/r_objects/epistasis/de_genes/TCTN1.rds
    Modified:   output/figures/r_objects/epistasis/de_genes/TIMELESS.rds
    Modified:   output/figures/r_objects/epistasis/de_genes/TMPRSS11E.rds
    Modified:   output/figures/r_objects/epistasis/enrich_dot2.rds
    Modified:   output/figures/r_objects/epistasis/enrich_dot_buffering.rds
    Modified:   output/figures/r_objects/epistasis/enrich_dot_hm.rds
    Modified:   output/figures/r_objects/epistasis/enrich_dot_inversion.rds
    Modified:   output/figures/r_objects/epistasis/enrich_dot_supression.rds
    Modified:   output/figures/r_objects/epistasis/enrich_dot_synergy.rds
    Modified:   output/figures/r_objects/epistasis/enrich_net_kegg.rds
    Modified:   output/figures/r_objects/epistasis/epistasis_heatmap.rds
    Modified:   output/figures/r_objects/epistasis/epistasis_scheme.rds
    Modified:   output/figures/r_objects/epistasis/epistasis_scheme_lolli.rds
    Modified:   output/figures/r_objects/gain8q24/de_genes/ADAMDEC1.rds
    Modified:   output/figures/r_objects/gain8q24/de_genes/ALG1L13P.rds
    Modified:   output/figures/r_objects/gain8q24/de_genes/C8orf33.rds
    Modified:   output/figures/r_objects/gain8q24/de_genes/C8orf76.rds
    Modified:   output/figures/r_objects/gain8q24/de_genes/CPQ.rds
    Modified:   output/figures/r_objects/gain8q24/de_genes/CTHRC1.rds
    Modified:   output/figures/r_objects/gain8q24/de_genes/CYHR1.rds
    Modified:   output/figures/r_objects/gain8q24/de_genes/E2F5.rds
    Modified:   output/figures/r_objects/gain8q24/de_genes/EBAG9.rds
    Modified:   output/figures/r_objects/gain8q24/de_genes/FAM49B.rds
    Modified:   output/figures/r_objects/gain8q24/de_genes/FAM86B3P.rds
    Modified:   output/figures/r_objects/gain8q24/de_genes/IGKV3-20.rds
    Modified:   output/figures/r_objects/gain8q24/de_genes/INTS9.rds
    Modified:   output/figures/r_objects/gain8q24/de_genes/MTBP.rds
    Modified:   output/figures/r_objects/gain8q24/de_genes/PABPC1.rds
    Modified:   output/figures/r_objects/gain8q24/de_genes/PHF20L1.rds
    Modified:   output/figures/r_objects/gain8q24/de_genes/PLCD3.rds
    Modified:   output/figures/r_objects/gain8q24/de_genes/POLR2K.rds
    Modified:   output/figures/r_objects/gain8q24/de_genes/POTEM.rds
    Modified:   output/figures/r_objects/gain8q24/de_genes/PTPRQ.rds
    Modified:   output/figures/r_objects/gain8q24/de_genes/RAD21.rds
    Modified:   output/figures/r_objects/gain8q24/de_genes/RRM2B.rds
    Modified:   output/figures/r_objects/gain8q24/de_genes/SLC44A5.rds
    Modified:   output/figures/r_objects/gain8q24/de_genes/SNTB1.rds
    Modified:   output/figures/r_objects/gain8q24/de_genes/TATDN1.rds
    Modified:   output/figures/r_objects/gain8q24/de_genes/TMEM55A.rds
    Modified:   output/figures/r_objects/gain8q24/de_genes/TSTA3.rds
    Modified:   output/figures/r_objects/gain8q24/de_genes/UST.rds
    Modified:   output/figures/r_objects/gain8q24/de_genes/UTP23.rds
    Modified:   output/figures/r_objects/gain8q24/de_genes/ZNF16.rds
    Modified:   output/figures/r_objects/gain8q24/de_genes/ZNF251.rds
    Modified:   output/figures/r_objects/gain8q24/de_genes/ZNF462.rds
    Modified:   output/figures/r_objects/gain8q24/de_genes/ZNF7.rds
    Modified:   output/figures/r_objects/gain8q24/de_genes/ZNF706.rds
    Modified:   output/figures/r_objects/gain8q24/de_genes/ZNF707.rds
    Modified:   output/figures/r_objects/gain8q24/gain8q24_heatmap.rds
    Modified:   output/figures/r_objects/med12/de_genes/ADGRG7.rds
    Modified:   output/figures/r_objects/med12/de_genes/CDH20.rds
    Modified:   output/figures/r_objects/med12/de_genes/CLCNKA.rds
    Modified:   output/figures/r_objects/med12/de_genes/CSPG5.rds
    Modified:   output/figures/r_objects/med12/de_genes/DCHS1.rds
    Modified:   output/figures/r_objects/med12/de_genes/DDX43.rds
    Modified:   output/figures/r_objects/med12/de_genes/FCRL4.rds
    Modified:   output/figures/r_objects/med12/de_genes/FXYD6.rds
    Modified:   output/figures/r_objects/med12/de_genes/IGLV1-40.rds
    Modified:   output/figures/r_objects/med12/de_genes/IL15.rds
    Modified:   output/figures/r_objects/med12/de_genes/MTA1.rds
    Modified:   output/figures/r_objects/med12/de_genes/MYO5C.rds
    Modified:   output/figures/r_objects/med12/de_genes/NRCAM.rds
    Modified:   output/figures/r_objects/med12/de_genes/TCTN1.rds
    Modified:   output/figures/r_objects/med12/med12_heatmap.rds

Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

These are the previous versions of the R Markdown and HTML files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view them.

File	Version	Author	Date	Message
html	6b377e8	aluetge	2019-11-19	Build site.
Rmd	a5e23fd	aluetge	2019-11-19	wflow_publish(c(“analysis/ATM.Rmd”, “analysis/Del13q14.Rmd”,
html	2a4a1c9	aluetge	2019-11-17	Build site.
html	0b836e2	aluetge	2019-11-13	Build site.
Rmd	8f9f56f	aluetge	2019-11-13	wflow_publish(c(“analysis/ATM.Rmd”, “analysis/Del13q14.Rmd”))
html	cc24f92	aluetge	2019-07-28	Build site.

ATM signature

Differentially expressed genes

1. Differential expression analysis

load packages

library(DESeq2)
library(tidyverse)
library(ggsci)
library(matrixStats)
library(piano)
library(reshape2)
library(genefilter)
library(Biobase)
library(ComplexHeatmap)
library(ggplot2)
library(gtable)
library(grid)
library(circlize)
library(gridExtra)
library(ggpubr)
library(RColorBrewer)
library(here)

load data

data_dir <- here("data")
output_dir <- here("output")
figure_dir <- here("output/figures")

#dds data set. gene expression data + patmetadata
load(paste0(data_dir, "/ddsrnaCLL_150218.RData"))

variant <- "ATM"
#filter for patients without NA in variant
ddsCLL <- ddsCLL[, !is.na(colData(ddsCLL)[,variant])]

#differentially expressed genes between ATM groups (see differential expression.html)
diff_all <- read.csv(file=paste0(output_dir, "/diff_genes/", variant, "_diffGenes.csv"))


rownames(diff_all) <- diff_all$X
diff_all <- diff_all[which(diff_all$padj < 0.01 ),-1]
diff <- diff_all[which(abs(diff_all$stat) > 4.5) ,]



mutStatus <- data.frame(colData(ddsCLL)) %>% arrange(ATM)
colnames(ddsCLL) <-colData(ddsCLL)$PatID
ddsCLL <- ddsCLL[, mutStatus$PatID]

#expression data
ddsCLL <- estimateSizeFactors(ddsCLL)
RNAnorm <- varianceStabilizingTransformation(ddsCLL, blind = T)

Expression matrix

#filter for sign. genes in variant
exprMat <- assay(RNAnorm)
exprVariant <- exprMat[rownames(diff),]
colnames(exprVariant) <- colData(ddsCLL)$PatID
exprVariant.new <- log2(exprVariant)
exprVariant.new <- t(scale(t(exprVariant.new)))
exprVariant.new[exprVariant.new > 4] <- 4
exprVariant.new[exprVariant.new < -4] <- -4
rownames(exprVariant.new) <- rowData(RNAnorm[rownames(diff),])$symbol

Expression signature

#colors
colors = colorRamp2(c(-4,-2,0,2,4), c("#2166ac","#4393c3", "#f7f7f7", "#d6604d","#b2182b"))
annocol <- get_palette("jco", 10)
annocolor <- list(ATM = c("1" = annocol[8], "0" = annocol[9]))
rowcolors <-colorRampPalette(brewer.pal(5, "Set1"))(5)
rowcolors[6] <- "white"


feature <- as.data.frame(colData(ddsCLL)[,c(variant)])
colnames(feature) <- c(variant)  

ha_col <- HeatmapAnnotation(df = feature, col = annocolor, annotation_height = unit(c(rep(1.9, 1)), "cm"), 
                            simple_anno_size = unit(1, "cm"),
                            annotation_name_gp = gpar(fontsize = 22, fontface = "bold"),
                            annotation_legend_param = list(title_gp = gpar(fontsize = 23), 
                                                           labels_gp = gpar(fontsize = 18),  
                                                           grid_height = unit(1.2, "cm"), 
                                                           grid_width = unit(1.2, "cm")))


h1 <- Heatmap(exprVariant.new ,                                                     
              km = 2,
              gap = unit(0.5, "cm"),
              cluster_columns = F,
              clustering_distance_rows = "pearson",
              clustering_method_rows = "ward.D2",
              column_title = paste0("Gene signature: ", variant),                      
              col = colors,
              column_title_gp = gpar(fontsize = 25, fontface = "bold"), 
              heatmap_legend_param = list(title = "expr", 
                                          title_gp = gpar(fontsize = 23), 
                                          grid_height = unit(1.5, "cm"), 
                                          grid_width = unit(1.2, "cm"), 
                                          gap = unit(2, "cm"), 
                                          labels_gp = gpar(fontsize = 18)), 
              column_dend_height = unit(1, "cm"),
              show_row_dend = FALSE, 
              show_column_names = FALSE , 
              show_row_names = TRUE, 
              row_names_gp = gpar(fontsize = 12),
              top_annotation = ha_col)


#svg(filename=paste0(figure_dir, "/", variant, "_gene_expr.svg"), width=30, height=45)
#pdf(file=paste0(figure_dir, "/", variant, "_gene_expr.pdf"), width=22, height=25)

draw(h1 )

Version	Author	Date
2a4a1c9	aluetge	2019-11-17
0b836e2	aluetge	2019-11-13
cc24f92	aluetge	2019-07-28

#dev.off()

saveRDS(h1, file = paste0(output_dir, "/figures/r_objects/atm/atm_heatmap.rds"))

Sample and gene specific expression - top genes

#function to create stripchart plots for specific genes
gene_count <- function(gene_nam){
  geneEnsID <- rownames(ddsCLL)[which(rowData(ddsCLL)$symbol %in% gene_nam)]
  geneNum <- exprMat[geneEnsID,]
  mutPat <- as.data.frame(colData(ddsCLL)[, c(variant)])
  colnames(mutPat) <- c("genotype")
  geneDat <- cbind(mutPat, geneNum)
  colnames(geneDat) <- c("genotype", "counts")
  
  p <- ggstripchart(geneDat, x = "genotype", y = "counts",
          color = "genotype",
          size = 3,
          palette = "jco",
          add = "mean_sd",
          add.params = list(size = 1.2),
          title = paste(gene_nam),
          font.x = 20, font.y = 20, font.legend = 20, 
          ylab = "normalized counts") + font("xy.text", size = 20) + font("title", size = 20, face = "bold")
  saveRDS(p, file = paste0(output_dir, "/figures/r_objects/atm/de_genes/", gene_nam, ".rds"))
  p
}

diff <- diff_all[which(diff_all$stat > 4),]
geneList <- as.character(diff$Symbol)
geneList <- geneList[-which(geneList %in% "")]


lapply(geneList, gene_count)

[[1]]

Version	Author	Date
6b377e8	aluetge	2019-11-19
2a4a1c9	aluetge	2019-11-17
cc24f92	aluetge	2019-07-28


[[2]]

Version	Author	Date
6b377e8	aluetge	2019-11-19
2a4a1c9	aluetge	2019-11-17
cc24f92	aluetge	2019-07-28


[[3]]

Version	Author	Date
6b377e8	aluetge	2019-11-19
2a4a1c9	aluetge	2019-11-17
cc24f92	aluetge	2019-07-28


[[4]]

Version	Author	Date
6b377e8	aluetge	2019-11-19
cc24f92	aluetge	2019-07-28


[[5]]

Version	Author	Date
6b377e8	aluetge	2019-11-19
2a4a1c9	aluetge	2019-11-17
cc24f92	aluetge	2019-07-28


[[6]]

Version	Author	Date
6b377e8	aluetge	2019-11-19
2a4a1c9	aluetge	2019-11-17
cc24f92	aluetge	2019-07-28


[[7]]

Version	Author	Date
6b377e8	aluetge	2019-11-19
2a4a1c9	aluetge	2019-11-17
cc24f92	aluetge	2019-07-28


[[8]]

Version	Author	Date
6b377e8	aluetge	2019-11-19
2a4a1c9	aluetge	2019-11-17
cc24f92	aluetge	2019-07-28


[[9]]

Version	Author	Date
6b377e8	aluetge	2019-11-19
2a4a1c9	aluetge	2019-11-17
cc24f92	aluetge	2019-07-28


[[10]]

Version	Author	Date
6b377e8	aluetge	2019-11-19
2a4a1c9	aluetge	2019-11-17
cc24f92	aluetge	2019-07-28


[[11]]

Version	Author	Date
6b377e8	aluetge	2019-11-19
2a4a1c9	aluetge	2019-11-17
cc24f92	aluetge	2019-07-28


[[12]]

Version	Author	Date
6b377e8	aluetge	2019-11-19
2a4a1c9	aluetge	2019-11-17
cc24f92	aluetge	2019-07-28


[[13]]

Version	Author	Date
6b377e8	aluetge	2019-11-19
2a4a1c9	aluetge	2019-11-17
cc24f92	aluetge	2019-07-28


[[14]]

Version	Author	Date
cc24f92	aluetge	2019-07-28


[[15]]

Version	Author	Date
cc24f92	aluetge	2019-07-28


[[16]]

Version	Author	Date
cc24f92	aluetge	2019-07-28


[[17]]

Version	Author	Date
cc24f92	aluetge	2019-07-28


[[18]]

Version	Author	Date
cc24f92	aluetge	2019-07-28

Gene set enrichment analysis

Gene sets

#load gene set collection
#Hallmark
gsc <- loadGSC("/home/almut/Dokumente/masterarbeit/data/h.all.v6.0.symbols.gmt", type="gmt")
#Kegg
gsc_Kegg <- loadGSC("/home/almut/Dokumente/masterarbeit/data/c2.cp.kegg.v6.0.symbols.gmt", type="gmt")


#get all de outputs
load(paste0(output_dir,"/desRes_15112019.RData"))
difftab <- function(condition){
  dataTab <- data.frame(res_list[[condition]])
  dataTab$ID <- rownames(dataTab)
  #filter using pvalues
  dataTab <- dataTab %>%
    arrange(padj) %>%
    mutate(Symbol = rowData(ddsCLL[ID,])$symbol)# %>%
    #filter(abs(log2FoldChange) > 2)
  dataTab <- dataTab[!duplicated(dataTab$Symbol),]
  dataTab <- dataTab[!is.na(dataTab$Symbol),]
  rownames(dataTab) <- dataTab$ID
   dataTab
}

diff_res <- difftab(variant)

Run piano

sessionInfo()

R version 3.6.3 (2020-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.7 LTS

Matrix products: default
BLAS:   /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0

locale:
 [1] LC_CTYPE=de_DE.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=de_DE.UTF-8        LC_COLLATE=de_DE.UTF-8    
 [5] LC_MONETARY=de_DE.UTF-8    LC_MESSAGES=de_DE.UTF-8   
 [7] LC_PAPER=de_DE.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
 [1] grid      parallel  stats4    stats     graphics  grDevices utils    
 [8] datasets  methods   base     

other attached packages:
 [1] here_0.1                    RColorBrewer_1.1-2         
 [3] ggpubr_0.2                  magrittr_1.5               
 [5] gridExtra_2.3               circlize_0.4.6             
 [7] gtable_0.3.0                ComplexHeatmap_2.0.0       
 [9] genefilter_1.66.0           reshape2_1.4.3             
[11] piano_2.0.2                 ggsci_2.9                  
[13] forcats_0.4.0               stringr_1.4.0              
[15] dplyr_0.8.1                 purrr_0.3.2                
[17] readr_1.3.1                 tidyr_0.8.3                
[19] tibble_2.1.3                ggplot2_3.1.1              
[21] tidyverse_1.2.1             DESeq2_1.24.0              
[23] SummarizedExperiment_1.14.0 DelayedArray_0.10.0        
[25] BiocParallel_1.18.0         matrixStats_0.54.0         
[27] Biobase_2.44.0              GenomicRanges_1.36.0       
[29] GenomeInfoDb_1.20.0         IRanges_2.18.1             
[31] S4Vectors_0.22.0            BiocGenerics_0.30.0        

loaded via a namespace (and not attached):
  [1] readxl_1.3.1           backports_1.1.4        Hmisc_4.2-0           
  [4] fastmatch_1.1-0        workflowr_1.4.0        plyr_1.8.4            
  [7] igraph_1.2.4.1         lazyeval_0.2.2         shinydashboard_0.7.1  
 [10] splines_3.6.3          digest_0.6.19          htmltools_0.3.6       
 [13] gdata_2.18.0           checkmate_1.9.3        memoise_1.1.0         
 [16] cluster_2.1.1          limma_3.40.2           annotate_1.62.0       
 [19] modelr_0.1.4           colorspace_1.4-1       blob_1.1.1            
 [22] rvest_0.3.4            haven_2.1.0            xfun_0.7              
 [25] crayon_1.3.4           RCurl_1.95-4.12        jsonlite_1.6          
 [28] survival_2.44-1.1      glue_1.3.1             zlibbioc_1.30.0       
 [31] XVector_0.24.0         GetoptLong_0.1.7       shape_1.4.4           
 [34] scales_1.0.0           DBI_1.0.0              relations_0.6-8       
 [37] Rcpp_1.0.1             xtable_1.8-4           htmlTable_1.13.1      
 [40] clue_0.3-57            foreign_0.8-76         bit_1.1-14            
 [43] Formula_1.2-3          DT_0.17                htmlwidgets_1.3       
 [46] httr_1.4.0             fgsea_1.10.0           gplots_3.0.1.1        
 [49] acepack_1.4.1          pkgconfig_2.0.2        XML_3.98-1.20         
 [52] nnet_7.3-15            locfit_1.5-9.1         labeling_0.3          
 [55] tidyselect_0.2.5       rlang_0.3.4            later_0.8.0           
 [58] AnnotationDbi_1.46.0   munsell_0.5.0          cellranger_1.1.0      
 [61] tools_3.6.3            visNetwork_2.0.7       cli_1.1.0             
 [64] generics_0.0.2         RSQLite_2.1.1          broom_0.5.2           
 [67] evaluate_0.14          yaml_2.2.0             knitr_1.23            
 [70] bit64_0.9-7            fs_1.3.1               caTools_1.17.1.2      
 [73] nlme_3.1-152           whisker_0.3-2          mime_0.7              
 [76] slam_0.1-45            xml2_1.2.0             compiler_3.6.3        
 [79] rstudioapi_0.10        png_0.1-7              marray_1.62.0         
 [82] geneplotter_1.62.0     stringi_1.4.3          lattice_0.20-38       
 [85] Matrix_1.3-2           shinyjs_1.0            pillar_1.4.1          
 [88] GlobalOptions_0.1.0    data.table_1.12.2      bitops_1.0-6          
 [91] httpuv_1.5.1           R6_2.4.0               latticeExtra_0.6-28   
 [94] promises_1.0.1         KernSmooth_2.23-15     gtools_3.8.1          
 [97] assertthat_0.2.1       rprojroot_1.3-2        rjson_0.2.20          
[100] withr_2.1.2            GenomeInfoDbData_1.2.1 hms_0.4.2             
[103] rpart_4.1-15           rmarkdown_1.13         git2r_0.25.2          
[106] sets_1.0-18            shiny_1.3.2            lubridate_1.7.4       
[109] base64enc_0.1-3

ATM

aluetge