Last updated: 2023-11-08

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Knit directory: 20211209_JingxinRNAseq/analysis/

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Ignored files:
    Ignored:    .DS_Store
    Ignored:    .Rhistory
    Ignored:    .Rproj.user/
    Ignored:    analysis/.RData
    Ignored:    analysis/.Rhistory
    Ignored:    analysis/20220707_TitrationSeries_DE_testing.nb.html
    Ignored:    code/.DS_Store
    Ignored:    code/._DOCK7.pdf
    Ignored:    code/._DOCK7_DMSO1.pdf
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    Ignored:    code/1KG_HighCoverageCalls.samplelist.txt
    Ignored:    code/5ssSeqs.tab
    Ignored:    code/Alignments/
    Ignored:    code/Branaplam_Risdiplam_specific_introns.bed.gz
    Ignored:    code/Branaplam_Risdiplam_specific_introns.bed.gz.tbi
    Ignored:    code/ChemCLIP/
    Ignored:    code/ClinVar/
    Ignored:    code/DE_testing/
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Untracked files:
    Untracked:  code/scripts/DE_edgeR_ExpOf3.R
    Untracked:  data/202310_FullMetadata.tsv.gz

Unstaged changes:
    Modified:   analysis/2023-10-31_Explore3MoleculesOfInterest.Rmd
    Modified:   analysis/2023-11-02_3MoleculesOfInterestLeafcutterDs.Rmd
    Modified:   code/Snakefile
    Modified:   code/rules/ExpMoleculesOfInterest.smk
    Modified:   code/rules/ProcessTitrationSeries.smk
    Modified:   code/rules/Process_chRNA.smk
    Modified:   code/rules/RNASeqProcessing.smk
    Modified:   code/scripts/GenometracksByGenotype

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 repository in which changes were made to the R Markdown (analysis/index.Rmd) and HTML (docs/index.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.

File Version Author Date Message
html 5dce412 Benjmain Fair 2023-11-02 updated nb
html b3b009e Benjmain Fair 2023-10-26 lots of updates
html ea36e65 Benjmain Fair 2023-03-07 added igv session
html a8c9152 Benjmain Fair 2023-02-23 update site
html 272cd76 Benjmain Fair 2022-09-26 update site
html 7144e91 Benjmain Fair 2022-09-21 added chRNA notebook
html 2247610 Benjmain Fair 2022-09-19 fix index
html d9999f1 Benjmain Fair 2022-09-13 added more EC50 estimation with PSI
html b2a3c34 Benjmain Fair 2022-09-12 update site with branaplsm-specific analysis
Rmd 0d59720 Benjmain Fair 2022-09-08 update site
html 0d59720 Benjmain Fair 2022-09-08 update site
Rmd db9a4f0 Benjmain Fair 2022-08-01 big update
html db9a4f0 Benjmain Fair 2022-08-01 big update
Rmd 4a410f5 Benjmain Fair 2022-03-08 initial commit
html 4a410f5 Benjmain Fair 2022-03-08 initial commit

Welcome to my research website dealing with small molecule splicing stuff.

Full listing of all Rmarkdown notebooks by file name:

library(tidyverse)
── Attaching packages ─────────────────────────────────────── tidyverse 1.3.1 ──
✔ ggplot2 3.3.6     ✔ purrr   0.3.4
✔ tibble  3.1.7     ✔ dplyr   1.0.9
✔ tidyr   1.2.0     ✔ stringr 1.4.0
✔ readr   2.1.2     ✔ forcats 0.5.1
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()
rmds <- list.files(path = "../analysis/", pattern="^\\d+.+")
rmd_htmls <- str_replace(rmds, "Rmd$", "html")
for(i in rmd_htmls){
  cat("[", i, "](", i,")\n\n", sep="")
}

20211216_DifferentialSplicing.html

20220221_ExploreExpOf52.html

20220629_FirstGlanceTitrationSeries.html

20220707_TitrationSeries_DE_testing.html

20220707_TitrationSeries_DE_testing.nb.html

20220712_FitDoseResponseModels.html

20220726_Check_chRNATestSeq.html

20220804_MakeBigwigListTsv.html

20220809_geena.html

20220822_Check_chRNA.html

20220907_IdentifyTargetsForVerification.html

20220908_IdentifyTargetsForVerification2.html

20220913_TidyDataForJingxin.html

20220915_ExploreDoseResponseCryptic3ss.html

20220915_ExploreSpliceQOutput.html

20220916_CompareDE_LCL_Fibroblast.html

20220919_chRNA_IntronRetention.html

20220922_ExploreSubparRNAseq.html

20220923_ExploreSpecificityEstimates.html

20221108_MakeFigsFor10minPresentation.html

2023-10-26_ExploreDrmModels.html

2023-10-31_Explore3MoleculesOfInterest.html

2023-11-02_3MoleculesOfInterestLeafcutterDs.html

20230214_MakeSampesConfigFor52MoleculeExperiment.html

20230223_PlotPCA_WithStructures.html

20230306_CheckIntronsWithUniqueSpecifities.html

20230322_CandidateGUUAAG_bulges.html

20230418_ExploreIshigamiGEO.html

20230502_PCAPlotsForYang.html

20230915_TopHitsAcrossDoses.html

20230927_AGT_MechanismSearch.html

20231006_SearchForCausalJuncs.html

20231013_UnbiasedMotifSearch.html


sessionInfo()
R version 4.2.0 (2022-04-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /software/openblas-0.3.13-el7-x86_64/lib/libopenblas_haswellp-r0.3.13.so

locale:
 [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C         LC_TIME=C           
 [4] LC_COLLATE=C         LC_MONETARY=C        LC_MESSAGES=C       
 [7] LC_PAPER=C           LC_NAME=C            LC_ADDRESS=C        
[10] LC_TELEPHONE=C       LC_MEASUREMENT=C     LC_IDENTIFICATION=C 

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] forcats_0.5.1   stringr_1.4.0   dplyr_1.0.9     purrr_0.3.4    
[5] readr_2.1.2     tidyr_1.2.0     tibble_3.1.7    ggplot2_3.3.6  
[9] tidyverse_1.3.1

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.8.3     lubridate_1.8.0  assertthat_0.2.1 rprojroot_2.0.3 
 [5] digest_0.6.29    utf8_1.2.2       R6_2.5.1         cellranger_1.1.0
 [9] backports_1.4.1  reprex_2.0.1     evaluate_0.15    httr_1.4.3      
[13] pillar_1.7.0     rlang_1.0.2      readxl_1.4.0     rstudioapi_0.13 
[17] whisker_0.4      jquerylib_0.1.4  rmarkdown_2.14   munsell_0.5.0   
[21] broom_0.8.0      compiler_4.2.0   httpuv_1.6.5     modelr_0.1.8    
[25] xfun_0.30        pkgconfig_2.0.3  htmltools_0.5.2  tidyselect_1.1.2
[29] workflowr_1.7.0  fansi_1.0.3      crayon_1.5.1     tzdb_0.3.0      
[33] dbplyr_2.1.1     withr_2.5.0      later_1.3.0      grid_4.2.0      
[37] jsonlite_1.8.0   gtable_0.3.0     lifecycle_1.0.1  DBI_1.1.2       
[41] git2r_0.30.1     magrittr_2.0.3   scales_1.2.0     cli_3.3.0       
[45] stringi_1.7.6    fs_1.5.2         promises_1.2.0.1 xml2_1.3.3      
[49] bslib_0.3.1      ellipsis_0.3.2   generics_0.1.2   vctrs_0.4.1     
[53] tools_4.2.0      glue_1.6.2       hms_1.1.1        fastmap_1.1.0   
[57] yaml_2.3.5       colorspace_2.0-3 rvest_1.0.2      knitr_1.39      
[61] haven_2.5.0      sass_0.4.1