Home

Last updated: 2021-01-14

Checks: 1 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.

Repository version: f14dd60

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:    output/figures/r_objects/BRAF/enrichment/

Untracked files:
    Untracked:  figure/
    Untracked:  output/figures/paper_fig/figure_meth_genes.pdf
    Untracked:  output/figures/paper_fig/figure_meth_genes.svg
    Untracked:  output/figures/r_objects/Methylation/de_genes/EGFR.rds
    Untracked:  output/figures/r_objects/Methylation/de_genes/EGR1.rds
    Untracked:  output/figures/r_objects/Methylation/de_genes/NFATC1.rds
    Untracked:  output/figures/r_objects/Methylation/de_genes/SOX11.rds
    Untracked:  output/figures/r_objects/SF3B1/de_genes/AHSP.rds
    Untracked:  output/figures/r_objects/SF3B1/de_genes/ARHGEF16.rds
    Untracked:  output/figures/r_objects/SF3B1/de_genes/C6orf223.rds
    Untracked:  output/figures/r_objects/SF3B1/de_genes/CAMK4.rds
    Untracked:  output/figures/r_objects/SF3B1/de_genes/CAMSAP2.rds
    Untracked:  output/figures/r_objects/SF3B1/de_genes/CDH1.rds
    Untracked:  output/figures/r_objects/SF3B1/de_genes/CKM.rds
    Untracked:  output/figures/r_objects/SF3B1/de_genes/CPT1C.rds
    Untracked:  output/figures/r_objects/SF3B1/de_genes/E2F4.rds
    Untracked:  output/figures/r_objects/SF3B1/de_genes/ELOVL7.rds
    Untracked:  output/figures/r_objects/SF3B1/de_genes/EPDR1.rds
    Untracked:  output/figures/r_objects/SF3B1/de_genes/FAM184A.rds
    Untracked:  output/figures/r_objects/SF3B1/de_genes/FOSL1.rds
    Untracked:  output/figures/r_objects/SF3B1/de_genes/HAVCR1.rds
    Untracked:  output/figures/r_objects/SF3B1/de_genes/HPCAL4.rds
    Untracked:  output/figures/r_objects/SF3B1/de_genes/IFI44L.rds
    Untracked:  output/figures/r_objects/SF3B1/de_genes/IGKV1-17.rds
    Untracked:  output/figures/r_objects/SF3B1/de_genes/IGKV1-33.rds
    Untracked:  output/figures/r_objects/SF3B1/de_genes/IL22RA1.rds
    Untracked:  output/figures/r_objects/SF3B1/de_genes/KIF27.rds
    Untracked:  output/figures/r_objects/SF3B1/de_genes/KIF7.rds
    Untracked:  output/figures/r_objects/SF3B1/de_genes/KIFC1.rds
    Untracked:  output/figures/r_objects/SF3B1/de_genes/LINC02102.rds
    Untracked:  output/figures/r_objects/SF3B1/de_genes/LINC02298.rds
    Untracked:  output/figures/r_objects/SF3B1/de_genes/LMOD1.rds
    Untracked:  output/figures/r_objects/SF3B1/de_genes/LOXL2.rds
    Untracked:  output/figures/r_objects/SF3B1/de_genes/MX1.rds
    Untracked:  output/figures/r_objects/SF3B1/de_genes/NEDD4.rds
    Untracked:  output/figures/r_objects/SF3B1/de_genes/NRIR.rds
    Untracked:  output/figures/r_objects/SF3B1/de_genes/PALD1.rds
    Untracked:  output/figures/r_objects/SF3B1/de_genes/PLXNB1.rds
    Untracked:  output/figures/r_objects/SF3B1/de_genes/RAI1.rds
    Untracked:  output/figures/r_objects/SF3B1/de_genes/RIBC2.rds
    Untracked:  output/figures/r_objects/SF3B1/de_genes/RLN3.rds
    Untracked:  output/figures/r_objects/SF3B1/de_genes/RNF112.rds
    Untracked:  output/figures/r_objects/SF3B1/de_genes/S100A2.rds
    Untracked:  output/figures/r_objects/SF3B1/de_genes/SLC4A1AP.rds
    Untracked:  output/figures/r_objects/SF3B1/de_genes/SOX8.rds
    Untracked:  output/figures/r_objects/SF3B1/de_genes/TFCP2L1.rds
    Untracked:  output/figures/r_objects/SF3B1/de_genes/TGM1.rds
    Untracked:  output/figures/r_objects/SF3B1/de_genes/TNXB.rds
    Untracked:  output/figures/r_objects/SF3B1/de_genes/TPM3P7.rds
    Untracked:  output/figures/r_objects/SF3B1/de_genes/USP18.rds
    Untracked:  output/figures/r_objects/SF3B1/enrich_dot2.rds
    Untracked:  output/figures/r_objects/SF3B1/enrich_dot_hm.rds
    Untracked:  output/figures/r_objects/SF3B1/enrich_net_hm.rds
    Untracked:  output/figures/r_objects/SF3B1/enrich_net_kegg.rds
    Untracked:  output/figures/r_objects/TP53/de_genes/ATP9A.rds
    Untracked:  output/figures/r_objects/TP53/de_genes/CRYBB1.rds
    Untracked:  output/figures/r_objects/TP53/de_genes/DPF3.rds
    Untracked:  output/figures/r_objects/TP53/de_genes/ENPP3.rds
    Untracked:  output/figures/r_objects/TP53/de_genes/EPS8L1.rds
    Untracked:  output/figures/r_objects/TP53/de_genes/FDXR.rds
    Untracked:  output/figures/r_objects/TP53/de_genes/GRIN2D.rds
    Untracked:  output/figures/r_objects/TP53/de_genes/GYPB.rds
    Untracked:  output/figures/r_objects/TP53/de_genes/HCAR1.rds
    Untracked:  output/figures/r_objects/TP53/de_genes/HEMGN.rds
    Untracked:  output/figures/r_objects/TP53/de_genes/IFIT1B.rds
    Untracked:  output/figures/r_objects/TP53/de_genes/IGHGP.rds
    Untracked:  output/figures/r_objects/TP53/de_genes/IGHV1-2.rds
    Untracked:  output/figures/r_objects/TP53/de_genes/IGHV3-53.rds
    Untracked:  output/figures/r_objects/TP53/de_genes/IGKV2-28.rds
    Untracked:  output/figures/r_objects/TP53/de_genes/IGLV1-51.rds
    Untracked:  output/figures/r_objects/TP53/de_genes/IQSEC3.rds
    Untracked:  output/figures/r_objects/TP53/de_genes/KIF7.rds
    Untracked:  output/figures/r_objects/TP53/de_genes/NOTCH4.rds
    Untracked:  output/figures/r_objects/TP53/de_genes/OTUD4P1.rds
    Untracked:  output/figures/r_objects/TP53/de_genes/PTPRB.rds
    Untracked:  output/figures/r_objects/TP53/de_genes/SH3RF1.rds
    Untracked:  output/figures/r_objects/TP53/de_genes/SLC22A14.rds
    Untracked:  output/figures/r_objects/TP53/de_genes/TEX14.rds
    Untracked:  output/figures/r_objects/TP53/de_genes/TFCP2L1.rds
    Untracked:  output/figures/r_objects/TP53/de_genes/TNS1.rds
    Untracked:  output/figures/r_objects/TP53/de_genes/WNT7B.rds
    Untracked:  output/figures/r_objects/TP53/enrich_dot2.rds
    Untracked:  output/figures/r_objects/TP53/enrich_dot_hm.rds
    Untracked:  output/figures/r_objects/TP53/enrich_net_hm.rds
    Untracked:  output/figures/r_objects/TP53/enrich_net_kegg.rds

Unstaged changes:
    Modified:   analysis/SF3B1.Rmd
    Modified:   analysis/TP53.Rmd
    Modified:   analysis/de_analysis.Rmd
    Modified:   analysis/index.Rmd
    Modified:   analysis/methylation_groups.Rmd
    Deleted:    docs/figure/epistatisis_drug.Rmd/drugEpistasis-1.pdf
    Modified:   output/enrichment/SF3B1_gsea.rds
    Modified:   output/figures/paper_fig/figure1.pdf
    Modified:   output/figures/paper_fig/figure1.svg
    Modified:   output/figures/paper_fig/figure_SF3B1.pdf
    Modified:   output/figures/paper_fig/figure_SF3B1.svg
    Modified:   output/figures/paper_fig/figure_TP53.pdf
    Modified:   output/figures/paper_fig/figure_TP53.svg
    Modified:   output/figures/paper_fig/figure_tri12.pdf
    Modified:   output/figures/paper_fig/figure_tri12.svg
    Modified:   output/figures/paper_fig/generate_figures.Rmd
    Modified:   output/figures/r_objects/Methylation/de_genes/ADAMTS7.rds
    Modified:   output/figures/r_objects/Methylation/de_genes/AGPAT4.rds
    Modified:   output/figures/r_objects/Methylation/de_genes/CDHR1.rds
    Modified:   output/figures/r_objects/Methylation/de_genes/DGKH.rds
    Modified:   output/figures/r_objects/Methylation/de_genes/DNAH14.rds
    Modified:   output/figures/r_objects/Methylation/de_genes/DPY19L2.rds
    Modified:   output/figures/r_objects/Methylation/de_genes/FAM174B.rds
    Modified:   output/figures/r_objects/Methylation/de_genes/FRMD4B.rds
    Modified:   output/figures/r_objects/Methylation/de_genes/GFI1.rds
    Modified:   output/figures/r_objects/Methylation/de_genes/IGLC6.rds
    Modified:   output/figures/r_objects/Methylation/de_genes/IGLV3-9.rds
    Modified:   output/figures/r_objects/Methylation/de_genes/LDOC1.rds
    Modified:   output/figures/r_objects/Methylation/de_genes/MSI2.rds
    Modified:   output/figures/r_objects/Methylation/de_genes/NETO1.rds
    Modified:   output/figures/r_objects/Methylation/de_genes/NUGGC.rds
    Modified:   output/figures/r_objects/Methylation/de_genes/PLD1.rds
    Modified:   output/figures/r_objects/Methylation/de_genes/PLEKHG4B.rds
    Modified:   output/figures/r_objects/Methylation/de_genes/PRR18.rds
    Modified:   output/figures/r_objects/Methylation/de_genes/PTPRB.rds
    Modified:   output/figures/r_objects/Methylation/de_genes/SCAMP5.rds
    Modified:   output/figures/r_objects/Methylation/de_genes/SEPT10.rds
    Modified:   output/figures/r_objects/Methylation/de_genes/SLC16A9.rds
    Modified:   output/figures/r_objects/Methylation/de_genes/SOWAHC.rds
    Modified:   output/figures/r_objects/Methylation/de_genes/TFEC.rds
    Modified:   output/figures/r_objects/Methylation/de_genes/TP63.rds
    Modified:   output/figures/r_objects/Methylation/de_genes/TRPM4.rds
    Modified:   output/figures/r_objects/Methylation/de_genes/VSIG10.rds
    Modified:   output/figures/r_objects/Methylation/de_genes/WSB2.rds
    Modified:   output/figures/r_objects/Methylation/de_genes/ZDHHC11.rds
    Modified:   output/figures/r_objects/Methylation/de_genes/ZNF667.rds
    Modified:   output/figures/r_objects/Methylation/methylation_heatmap.rds
    Modified:   output/figures/r_objects/Methylation/methylation_pca150_genes.rds
    Modified:   output/figures/r_objects/SF3B1/SF3B1_enrichment_dn.rds
    Modified:   output/figures/r_objects/SF3B1/SF3B1_enrichment_up.rds
    Modified:   output/figures/r_objects/SF3B1/SF3B1_heatmap.rds
    Modified:   output/figures/r_objects/SF3B1/de_genes/ADAM11.rds
    Modified:   output/figures/r_objects/SF3B1/de_genes/BNIP3P41.rds
    Modified:   output/figures/r_objects/SF3B1/de_genes/CRYBA4.rds
    Modified:   output/figures/r_objects/SF3B1/de_genes/CRYBB1.rds
    Modified:   output/figures/r_objects/SF3B1/de_genes/FBLN2.rds
    Modified:   output/figures/r_objects/SF3B1/de_genes/FBN1.rds
    Modified:   output/figures/r_objects/SF3B1/de_genes/FOXRED1.rds
    Modified:   output/figures/r_objects/SF3B1/de_genes/FSTL3.rds
    Modified:   output/figures/r_objects/SF3B1/de_genes/GYPB.rds
    Modified:   output/figures/r_objects/SF3B1/de_genes/HBG2.rds
    Modified:   output/figures/r_objects/SF3B1/de_genes/IFI27.rds
    Modified:   output/figures/r_objects/SF3B1/de_genes/IGHV3-21.rds
    Modified:   output/figures/r_objects/SF3B1/de_genes/LRRC75A-AS1.rds
    Modified:   output/figures/r_objects/SF3B1/de_genes/MICF.rds
    Modified:   output/figures/r_objects/SF3B1/de_genes/NLRP2B.rds
    Modified:   output/figures/r_objects/SF3B1/de_genes/P2RX6.rds
    Modified:   output/figures/r_objects/SF3B1/de_genes/PIPOX.rds
    Modified:   output/figures/r_objects/SF3B1/de_genes/PLEKHG4B.rds
    Modified:   output/figures/r_objects/SF3B1/de_genes/PRSS50.rds
    Modified:   output/figures/r_objects/SF3B1/de_genes/PSD2.rds
    Modified:   output/figures/r_objects/SF3B1/de_genes/RASSF6.rds
    Modified:   output/figures/r_objects/SF3B1/de_genes/SHB.rds
    Modified:   output/figures/r_objects/SF3B1/de_genes/SLC22A14.rds
    Modified:   output/figures/r_objects/SF3B1/de_genes/SRRM5.rds
    Modified:   output/figures/r_objects/SF3B1/de_genes/TAS1R1.rds
    Modified:   output/figures/r_objects/SF3B1/de_genes/UQCC1.rds
    Modified:   output/figures/r_objects/SF3B1/de_genes/WIF1.rds
    Modified:   output/figures/r_objects/TP53/TP53_heatmap.rds
    Modified:   output/figures/r_objects/TP53/de_genes/ASPM.rds
    Modified:   output/figures/r_objects/TP53/de_genes/CDK12.rds
    Modified:   output/figures/r_objects/TP53/de_genes/CMYA5.rds
    Modified:   output/figures/r_objects/TP53/de_genes/CTDNEP1.rds
    Modified:   output/figures/r_objects/TP53/de_genes/DRG2.rds
    Modified:   output/figures/r_objects/TP53/de_genes/ELOVL7.rds
    Modified:   output/figures/r_objects/TP53/de_genes/FLII.rds
    Modified:   output/figures/r_objects/TP53/de_genes/FXR2.rds
    Modified:   output/figures/r_objects/TP53/de_genes/GPAT3.rds
    Modified:   output/figures/r_objects/TP53/de_genes/HYPK.rds
    Modified:   output/figures/r_objects/TP53/de_genes/LINC01315.rds
    Modified:   output/figures/r_objects/TP53/de_genes/LINC02354.rds
    Modified:   output/figures/r_objects/TP53/de_genes/LMOD1.rds
    Modified:   output/figures/r_objects/TP53/de_genes/LRRC63.rds
    Modified:   output/figures/r_objects/TP53/de_genes/MAP2K4.rds
    Modified:   output/figures/r_objects/TP53/de_genes/MDM2.rds
    Modified:   output/figures/r_objects/TP53/de_genes/MED11.rds
    Modified:   output/figures/r_objects/TP53/de_genes/MIR641.rds
    Modified:   output/figures/r_objects/TP53/de_genes/MPDU1.rds
    Modified:   output/figures/r_objects/TP53/de_genes/PAX9.rds
    Modified:   output/figures/r_objects/TP53/de_genes/PGBD2.rds
    Modified:   output/figures/r_objects/TP53/de_genes/PIK3IP1-AS1.rds
    Modified:   output/figures/r_objects/TP53/de_genes/PMEPA1.rds
    Modified:   output/figures/r_objects/TP53/de_genes/PTK7.rds
    Modified:   output/figures/r_objects/TP53/de_genes/RNF167.rds
    Modified:   output/figures/r_objects/TP53/de_genes/RUNDC3A.rds
    Modified:   output/figures/r_objects/TP53/de_genes/SCML1.rds
    Modified:   output/figures/r_objects/TP53/de_genes/SGF29.rds
    Modified:   output/figures/r_objects/TP53/de_genes/SHISA7.rds
    Modified:   output/figures/r_objects/TP53/de_genes/SPAG7.rds
    Modified:   output/figures/r_objects/TP53/de_genes/TNFSF12.rds
    Modified:   output/figures/r_objects/TP53/de_genes/TOP3A.rds
    Modified:   output/figures/r_objects/TP53/de_genes/TPX2.rds
    Modified:   output/figures/r_objects/TP53/de_genes/ZFAND2B.rds
    Modified:   output/figures/r_objects/ighv/ighv_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	8fef211	aluetge	2020-12-23	update index
Rmd	e171169	aluetge	2020-12-23	remove old files and directories
html	026e8e9	aluetge	2019-11-18	Build site.
html	672654d	aluetge	2019-11-13	Build site.
Rmd	7913207	aluetge	2019-11-13	wflow_publish(c(“analysis/methylation_IP_vs_all.Rmd”, “analysis/methylation_HP_vs_IP.Rmd”, “analysis/index.Rmd”))
html	cc24f92	aluetge	2019-07-28	Build site.
Rmd	b20d1a9	aluetge	2019-06-27	add variants
html	3514378	aluetge	2019-05-17	Build site.
Rmd	5de142b	aluetge	2019-05-17	Add more variants
html	8632648	aluetge	2019-05-17	Build site.
Rmd	9b1cab8	aluetge	2019-05-17	change index
html	7b048d9	aluetge	2019-05-17	Build site.
Rmd	51fa522	aluetge	2019-05-17	Publish analysis structure
html	fb20e9f	aluetge	2019-05-11	Build site.
Rmd	c2f16a2	aluetge	2019-05-11	Start workflowr project.

Home

Transcriptome CLL analysis

General Analysis

Variants

Epistasis