Last updated: 2023-10-26

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Knit directory: 20211209_JingxinRNAseq/analysis/

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Ignored files:
    Ignored:    .DS_Store
    Ignored:    .Rhistory
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    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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Unstaged changes:
    Modified:   code/scripts/GenometracksByGenotype

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File Version Author Date Message
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

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