Last updated: 2022-06-08
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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
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File | Version | Author | Date | Message |
---|---|---|---|---|
html | fe6333b | Benjmain Fair | 2022-05-25 | update site and molQTL coloc |
html | 0c8ee9c | Benjmain Fair | 2022-01-18 | update site |
html | 237b549 | Benjmain Fair | 2021-12-29 | rebuilt some site analyses |
html | 2f0181f | Benjmain Fair | 2021-12-15 | Added genewise hyprcoloc rules |
html | 50ad818 | Benjmain Fair | 2021-12-07 | update site |
html | a166e86 | Benjmain Fair | 2021-10-06 | added test notebook |
Rmd | 24331d7 | cfbuenabadn | 2021-09-23 | adding chRNA-seq processing smk |
html | 24331d7 | cfbuenabadn | 2021-09-23 | adding chRNA-seq processing smk |
html | ee655cc | Benjmain Fair | 2021-09-23 | fixed site links |
html | afc10fb | Benjmain Fair | 2021-09-23 | fixed ipynb links on site homepage |
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$", "html")
for(i in rmd_htmls){
cat("[", i, "](", i,")\n\n", sep="")
}
20200110_PickSamplesForGrowth.html
20200210_PickSamplesToOrder.html
20210604_CheckSampleGenotypes.html
20211207_ExploreColocalizations.html
20211217_GenewiseColocFirstLook.html
20220114_ColocalizationEffectSizeCorrelations.html
20220228_PickCutAndTagSamples.html
20220401_Cluster_CheckOutNA18855chRNA.html
202204012_Cluster_TestGwasHarmonisation.html
20220415_Cluster_CheckTehranchiConcordance.html
20220424_CheckH3K36me3SampleGenotypes.html
20220511_Cluster_CheckH3K36me3QC.html
20220511_ExploreColocsAtDifferentThresholds.html
20220518_Explore_eQTLColocsAtDifferentThresholds.html
20220524_CheckClosestPeakToTSS.html
20220527_ExploreCarlosChromatinSplicingData.html
20220606_PlotColocsForIntuitions.html
Also, a list of links to ipynb files that were incorporated into the snakemake. Since github renders ipynbs directly, this is not a relative link from the site folder, but rather links directly to the file to view on github (code here):
ipynbs <- list.files(path = "../docs/", pattern="^\\d+.+ipynb$")
for(i in ipynbs){
cat("[", i, "](","https://github.com/bfairkun/ChromatinSplicingQTLs/blob/master/docs/", i,")\n\n", sep="")
}
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