Last updated: 2022-09-29

Checks: 7 0

Knit directory: ChromatinSplicingQTLs/analysis/

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Ignored files:
    Ignored:    .DS_Store
    Ignored:    .Rhistory
    Ignored:    .Rproj.user/
    Ignored:    analysis/.Rhistory
    Ignored:    code/.DS_Store
    Ignored:    code/.RData
    Ignored:    code/._.DS_Store
    Ignored:    code/._README.md
    Ignored:    code/._report.html
    Ignored:    code/.ipynb_checkpoints/
    Ignored:    code/.snakemake/
    Ignored:    code/APA_Processing/
    Ignored:    code/Alignments/
    Ignored:    code/ChromHMM/
    Ignored:    code/ENCODE/
    Ignored:    code/ExpressionAnalysis/
    Ignored:    code/FastqFastp/
    Ignored:    code/FastqFastpSE/
    Ignored:    code/Genotypes/
    Ignored:    code/IntronSlopes/
    Ignored:    code/Misc/
    Ignored:    code/MiscCountTables/
    Ignored:    code/Multiqc/
    Ignored:    code/Multiqc_chRNA/
    Ignored:    code/NonCodingRNA_annotation/
    Ignored:    code/PeakCalling/
    Ignored:    code/Phenotypes/
    Ignored:    code/PlotGruberQTLs/
    Ignored:    code/PlotQTLs/
    Ignored:    code/ProCapAnalysis/
    Ignored:    code/QC/
    Ignored:    code/QTL_SNP_Enrichment/
    Ignored:    code/QTLs/
    Ignored:    code/ReferenceGenome/
    Ignored:    code/Rplots.pdf
    Ignored:    code/Session.vim
    Ignored:    code/SplicingAnalysis/
    Ignored:    code/TODO
    Ignored:    code/Tehranchi/
    Ignored:    code/bigwigs/
    Ignored:    code/bigwigs_FromNonWASPFilteredReads/
    Ignored:    code/config/.DS_Store
    Ignored:    code/config/._.DS_Store
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    Ignored:    code/debug_python.ipynb
    Ignored:    code/deepTools/
    Ignored:    code/featureCounts/
    Ignored:    code/gwas_summary_stats/
    Ignored:    code/hyprcoloc/
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    Ignored:    code/scratch/
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    Ignored:    code/scripts/__pycache__/
    Ignored:    code/scripts/liftOverBedpe/liftOverBedpe.py
    Ignored:    code/snakemake.log
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    Untracked:  code/snakemake_profiles/slurm/__pycache__/

Unstaged changes:
    Modified:   code/scripts/GenometracksByGenotype

Staged changes:
    New:        analysis/20220928_ExploreIntronSum.Rmd

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 f94d014 Benjmain Fair 2022-09-22 edit index
html a80e66e Benjmain Fair 2022-09-22 update site
html bfb625e Benjmain Fair 2022-08-09 added finemapping snp enrichment rules
html 125a583 Benjmain Fair 2022-06-08 update site
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 2021-12-28 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 1.3.0 ──
✔ 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   1.3.1     ✔ forcats 0.4.0
── 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

202204012_Cluster_TestGwasHarmonisation.html

20220401_Cluster_CheckOutNA18855chRNA.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

20220622_QuantifyColocRateMoreInterpretableWay.html

20220623_CalculatePi1.html

20220623_CalculatePi1_AllTraits.html

20220627_CalculatePi1_AllTraits_AndCompareToColoc.html

20220628_exploretiertwomethods.html

20220713_PlotHeatmapManyWays.html

20220713_RPKM_v_TPM.html

20220728_CheckFinemapSNPEnrichments.html

20220920_Explore_chRNA_sQTLs.html

20220928_ExploreIntronSum.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 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

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         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_0.4.0   stringr_1.4.0   dplyr_1.0.9     purrr_0.3.4    
[5] readr_1.3.1     tidyr_1.2.0     tibble_3.1.7    ggplot2_3.3.6  
[9] tidyverse_1.3.0

loaded via a namespace (and not attached):
 [1] tidyselect_1.1.2 xfun_0.31        haven_2.3.1      colorspace_1.4-1
 [5] vctrs_0.4.1      generics_0.1.3   htmltools_0.5.3  yaml_2.2.0      
 [9] utf8_1.1.4       rlang_1.0.5      later_0.8.0      pillar_1.7.0    
[13] withr_2.5.0      glue_1.6.2       DBI_1.1.0        dbplyr_1.4.2    
[17] readxl_1.3.1     modelr_0.1.8     lifecycle_1.0.1  cellranger_1.1.0
[21] munsell_0.5.0    gtable_0.3.0     workflowr_1.6.2  rvest_0.3.5     
[25] evaluate_0.15    knitr_1.39       fastmap_1.1.0    httpuv_1.5.1    
[29] fansi_0.4.0      broom_1.0.0      Rcpp_1.0.5       promises_1.0.1  
[33] backports_1.4.1  scales_1.1.0     jsonlite_1.6     fs_1.5.2        
[37] hms_0.5.3        digest_0.6.20    stringi_1.4.3    rprojroot_2.0.2 
[41] grid_3.6.1       cli_3.3.0        tools_3.6.1      magrittr_1.5    
[45] crayon_1.3.4     whisker_0.3-2    pkgconfig_2.0.2  ellipsis_0.3.2  
[49] xml2_1.3.2       reprex_0.3.0     lubridate_1.7.4  assertthat_0.2.1
[53] rmarkdown_1.13   httr_1.4.4       rstudioapi_0.14  R6_2.4.0        
[57] git2r_0.26.1     compiler_3.6.1