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Last updated: 2023-06-19

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Knit directory: m6A_in_disease_genetics/

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R Markdown file: uncommitted changes

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Repository version: 479f381

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The results in this page were generated with repository version 479f381. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.

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Ignored files:
    Ignored:    .ipynb_checkpoints/
    Ignored:    analysis/m6A_switch_to_disease_h2g.nb.html

Untracked files:
    Untracked:  analysis/.ipynb_checkpoints/
    Untracked:  code/.ipynb_checkpoints/
    Untracked:  code/check_double_strand.ipynb
    Untracked:  code/check_double_strand_v2.ipynb
    Untracked:  code/figure/
    Untracked:  code/learn_gviz.Rmd
    Untracked:  code/learn_gviz.nb.html
    Untracked:  code/m6AQTL_finemapping.Rmd
    Untracked:  code/summary_TWAS_coloc_m6A_2023.Rmd
    Untracked:  code/test_gviz.ipynb
    Untracked:  code/twas_genes_PP4_0.3_immune_traits_trackplots.pdf
    Untracked:  code/untitled.r
    Untracked:  data/.ipynb_checkpoints/
    Untracked:  data/Allergy_full_coloc.txt
    Untracked:  data/Asthma_full_coloc.txt
    Untracked:  data/CAD_full_coloc.txt
    Untracked:  data/Eosinophil_count_full_coloc.txt
    Untracked:  data/GSE125377_jointPeakReadCount.txt
    Untracked:  data/IBD_full_coloc.txt
    Untracked:  data/JointPeaks.bed
    Untracked:  data/Lupus_full_coloc.txt
    Untracked:  data/RA_full_coloc.txt
    Untracked:  data/coloc_blood_traits.csv
    Untracked:  data/crohns_disease_full_coloc.txt
    Untracked:  data/edit_sites_and_GE_neg_correlated.txt
    Untracked:  data/edit_sites_and_GE_pos_correlated.txt
    Untracked:  data/human_EERs.csv
    Untracked:  data/human_EERs.txt
    Untracked:  data/lymph_full_coloc.txt
    Untracked:  data/m6A_TWAS_results.csv
    Untracked:  data/m6a_TWAS_genes.txt
    Untracked:  data/m6a_joint_calling_peaks.csv
    Untracked:  data/nat_sense_pairs.csv
    Untracked:  data/plt_full_coloc.txt
    Untracked:  data/rbc_full_coloc.txt
    Untracked:  data/rdw_full_coloc.txt
    Untracked:  data/reported_AS_targets_S1.txt
    Untracked:  data/reported_AS_wanowska.txt
    Untracked:  data/sig_coloc_results/
    Untracked:  data/ulcerative_colitis_full_coloc.txt
    Untracked:  data/wbc_full_coloc.txt
    Untracked:  output/.ipynb_checkpoints/
    Untracked:  output/fine_mapped_m6AQTLs_TWAS_genes_highPP4.rds
    Untracked:  output/immune_related_m6A_targets.csv
    Untracked:  output/m6aQTL_dsRNAs_PPP2R3C_PRORP.pdf
    Untracked:  output/m6a_peaks_nearby_dsRNAs.csv
    Untracked:  output/m6a_sites_near_dsRNAs_coloc.csv
    Untracked:  output/m6a_sites_near_dsRNAs_twas.csv
    Untracked:  output/m6a_sites_overlapping_NAT_twas.csv
    Untracked:  output/m6a_sites_overlapping_dsRNAs_coloc.csv
    Untracked:  output/m6a_sites_overlapping_dsRNAs_twas.csv
    Untracked:  output/m6a_sites_overlapping_dsRegions.csv
    Untracked:  output/m6a_sites_overlapping_dsRegions_coloc.csv
    Untracked:  output/negatively_correlated_genes.txt
    Untracked:  output/postively_correlated_genes.txt
    Untracked:  output/twas_genes_PP4_0.3_immune_traits_trackplots.pdf
    Untracked:  output/twas_genes_PP4_0.5_blood_traits_trackplots.pdf
    Untracked:  twas_genes_PP4_0.3_immune_traits_trackplots.pdf

Unstaged changes:
    Modified:   analysis/index.Rmd
    Modified:   analysis/m6A_switch_to_disease_h2g.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
Rmd	b7a7aa3	Jing Gu	2023-05-09	update
html	bc330a2	Jing Gu	2023-04-12	update index page
html	98540ac	Jing Gu	2023-04-12	update index page
html	86b31ec	Jing Gu	2023-04-12	Build site.
Rmd	0e3b2a9	Jing Gu	2023-04-12	publish the initial files
Rmd	c558a6b	Jing Gu	2023-03-31	Start workflowr project.

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Backgrounds

Genetic variants may act through m6A-switch to cause disease

m6A informed fine-mapping