Last updated: 2021-09-23
Checks: 6 1
Knit directory: ChromatinSplicingQTLs/analysis/
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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 | 91f067a | Benjmain Fair | 2021-09-23 | added example ipynb to site |
| Rmd | 53ba92f | Benjmain Fair | 2021-06-07 | update side and check sample swapping |
| html | 53ba92f | Benjmain Fair | 2021-06-07 | update side and check sample swapping |
| Rmd | dd0eadb | Benjmain Fair | 2020-08-21 | initial commit |
| html | dd0eadb | Benjmain Fair | 2020-08-21 | initial commit |
Welcome to my research website.
This project will investigate the correlation of genetic effects on chromatin, splicing, transcription, and complex phenotypes, using naturally occuring human genetic variation.
We are still collecting data, but I have also been perusing around published data a bit.
Here are links to all of my rendered analysis Rmarkdowns (code here):
library(tidyverse)── Attaching packages ─────────────────────────────────────── tidyverse 1.2.1 ──✔ ggplot2 3.2.1 ✔ purrr 0.3.3
✔ tibble 3.0.4 ✔ dplyr 1.0.2
✔ tidyr 1.1.2 ✔ stringr 1.4.0
✔ readr 1.4.0 ✔ forcats 0.5.0── 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$", "html")
for(i in rmd_htmls){
cat("[", i, "](", i,")\n")
}20200110_PickSamplesForGrowth.html 20200210_PickSamplesToOrder.html 20210604_CheckSampleGenotypes.html
Also, a list of links to ipynb files that were incorporated into the snakemake. Since github renders ipynbs directly, this is not a relative link from the site folder, but rather links directly to the file to view on github (code here):
ipynbs <- list.files(path = "../docs/", pattern="^\\d+.+ipynb$")
for(i in ipynbs){
cat("[", i, "](","https://github.com/bfairkun/ChromatinSplicingQTLs/blob/master/docs/", i,")\n")
}20210921_CountSpliceSiteSNPsInSQTLs.py.ipynb
sessionInfo()R version 3.4.3 (2017-11-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Scientific Linux 7.4 (Nitrogen)
Matrix products: default
BLAS/LAPACK: /software/openblas-0.2.19-el7-x86_64/lib/libopenblas_haswellp-r0.2.19.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] forcats_0.5.0 stringr_1.4.0 dplyr_1.0.2 purrr_0.3.3
[5] readr_1.4.0 tidyr_1.1.2 tibble_3.0.4 ggplot2_3.2.1
[9] tidyverse_1.2.1
loaded via a namespace (and not attached):
[1] Rcpp_1.0.3 cellranger_1.1.0 compiler_3.4.3 pillar_1.4.7
[5] later_1.0.0 git2r_0.26.1 workflowr_1.5.0 tools_3.4.3
[9] digest_0.6.27 lubridate_1.7.9.2 jsonlite_1.6 evaluate_0.14
[13] lifecycle_0.2.0 gtable_0.3.0 pkgconfig_2.0.3 rlang_0.4.9
[17] cli_2.0.0 rstudioapi_0.10 yaml_2.2.0 haven_2.3.1
[21] xfun_0.20 withr_2.1.2 xml2_1.2.0 httr_1.4.2
[25] knitr_1.26 hms_0.5.3 generics_0.1.0 fs_1.3.1
[29] vctrs_0.3.6 rprojroot_1.3-2 grid_3.4.3 tidyselect_1.1.0
[33] glue_1.4.2 R6_2.4.1 fansi_0.4.0 readxl_1.3.1
[37] rmarkdown_2.6 modelr_0.1.8 magrittr_1.5 whisker_0.3-2
[41] backports_1.1.5 scales_1.1.0 promises_1.1.0 htmltools_0.4.0
[45] ellipsis_0.3.0 assertthat_0.2.1 rvest_0.3.6 colorspace_2.0-0
[49] httpuv_1.5.2 stringi_1.4.3 lazyeval_0.2.2 munsell_0.5.0
[53] broom_0.7.3 crayon_1.3.4