Last updated: 2023-08-25
Checks: 2 0
Knit directory: m6A_in_disease_genetics/
This reproducible R Markdown analysis was created with workflowr (version 1.7.0). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.
Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.
Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.
The results in this page were generated with repository version d0f5634. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.
Note that you need to be careful to ensure that all relevant files for
the analysis have been committed to Git prior to generating the results
(you can use wflow_publish or
wflow_git_commit). workflowr only checks the R Markdown
file, but you know if there are other scripts or data files that it
depends on. Below is the status of the Git repository when the results
were generated:
Ignored files:
Ignored: .ipynb_checkpoints/
Ignored: analysis/m6A_switch_to_disease_h2g.nb.html
Ignored: data/plots/
Untracked files:
Untracked: HMGCR_locus_gene_tracks.pdf
Untracked: Rplots.pdf
Untracked: analysis/.ipynb_checkpoints/
Untracked: analysis/IBD_E_S_m6A.Rmd
Untracked: analysis/IBD_E_S_m6A_output.Rmd
Untracked: analysis/LDL_E_S_m6A.Rmd
Untracked: analysis/LDL_m6A_output.Rmd
Untracked: analysis/RA_m6A_output.Rmd
Untracked: analysis/WhiteBlood_WholeBlood_E_M.Rmd
Untracked: analysis/identify_m6A_mechanisms_with_finemapping.Rmd
Untracked: analysis/lymph_m6A_output.Rmd
Untracked: analysis/pre_weights_m6AQTL.txt
Untracked: analysis/rbc_E_S_m6A_output.Rmd
Untracked: analysis/rbc_m6A_output.Rmd
Untracked: analysis/summarize_ctwas_m6A_results.Rmd
Untracked: analysis/wbc_E_S_m6A_output.Rmd
Untracked: code/.ipynb_checkpoints/
Untracked: code/all_m6a_sites_with_paired_cisNATs_summary.csv
Untracked: code/annotating_fine-mapped_m6A_QTLs.Rmd
Untracked: code/check_double_strand.ipynb
Untracked: code/check_double_strand_v2.ipynb
Untracked: code/ctwas/
Untracked: code/figure/
Untracked: code/learn_gviz.Rmd
Untracked: code/learn_gviz.html
Untracked: code/learn_gviz.nb.html
Untracked: code/m6AQTL_finemapping.Rmd
Untracked: code/plot_genomic_tracks_gviz.ipynb
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: data/.ipynb_checkpoints/
Untracked: data/ADCY7_gwas_input.tsv
Untracked: data/ADCY7_qtl_input.tsv
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/G_list.Rd
Untracked: data/HMGCR_ctwas_dat.Rd
Untracked: data/IBD_full_coloc.txt
Untracked: data/JointPeaks.bed
Untracked: data/Li2022_dsRNAs.xlsx
Untracked: data/Lupus_full_coloc.txt
Untracked: data/RA_full_coloc.txt
Untracked: data/TABLE1_hg19.txt
Untracked: data/TABLE1_hg19.txt.zip
Untracked: data/__MACOSX/
Untracked: data/coloc_blood_traits.csv
Untracked: data/crohns_disease_full_coloc.txt
Untracked: data/ctwas_m6a_joint_top_PIP.txt
Untracked: data/edit_sites_and_GE_neg_correlated.txt
Untracked: data/edit_sites_and_GE_pos_correlated.txt
Untracked: data/features
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/nasser_2021_ABC_IBD_genes.txt
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/test_locuscomparer.pdf
Untracked: data/ulcerative_colitis_full_coloc.txt
Untracked: data/wbc_full_coloc.txt
Untracked: data/zhao_silver_genes.csv
Untracked: output/.ipynb_checkpoints/
Untracked: output/HMGCR_gene_track_plot.pdf
Untracked: output/HMGCR_locus_plot.pdf
Untracked: output/IBD_DHX38_plot.pdf
Untracked: output/IBD_DHX38_plot_genetrack.pdf
Untracked: output/IBD_IP6K2_plot.pdf
Untracked: output/LDL_PMPCA_plot.pdf
Untracked: output/LDL_TMEM199_plot.pdf
Untracked: output/all_m6a_sites_with_cisNATs.csv
Untracked: output/all_m6a_sites_with_paired_cisNATs_summary.csv
Untracked: output/all_m6a_sites_with_paired_cisNATs_summary_PP40.3.csv
Untracked: output/all_m6a_sites_with_paired_cisNATs_summary_PP40.5.csv
Untracked: output/all_m6a_sites_with_paired_cis_NATs.csv
Untracked: output/asthma_GPR183_plot.pdf
Untracked: output/asthma_GPR183_plot2.pdf
Untracked: output/asthma_GPR183_plot_genetrack.pdf
Untracked: output/asthma_GPR183_plot_genetrack2.pdf
Untracked: output/asthma_SLC25A11_plot_genetrack.pdf
Untracked: output/asthma_ZMAT2_plot.pdf
Untracked: output/asthma_ZMAT2_plot2.pdf
Untracked: output/asthma_ZMAT2_plot_genetrack.pdf
Untracked: output/asthma_ZMAT2_plot_genetrack2.pdf
Untracked: output/ctwas_locus_plot_output_data.Rd
Untracked: output/ctwas_m6a_joint_m6a_PIP_0.8.csv
Untracked: output/ctwas_m6a_joint_m6a_PIP_0.8.txt
Untracked: output/ctwas_m6a_joint_pip_above_0.6.RData
Untracked: output/eosinoph_MEPCE_plot.pdf
Untracked: output/eosinoph_PTK2B_plot.pdf
Untracked: output/eosinoph_PTK2B_plot_genetrack.pdf
Untracked: output/eosinoph_SH2D3C_plot.pdf
Untracked: output/eosinoph_SLC43A3_plot.pdf
Untracked: output/eosinoph_ZER1_plot.pdf
Untracked: output/eosinoph_ZER1_plot_genetrack.pdf
Untracked: output/fine_mapped_m6AQTLs_TWAS_genes_highPP4.rds
Untracked: output/gene_summary.csv
Untracked: output/immune_related_m6A_targets.csv
Untracked: output/lupus_MIR210HG_IRF7_plot.pdf
Untracked: output/lupus_MIR210HG_IRF7_plot_genetrack.pdf
Untracked: output/lupus_MIR210HG_plot.pdf
Untracked: output/lupus_MIR210HG_plot_genetrack.pdf
Untracked: output/lymph_ADCY7_BRD7_plot.pdf
Untracked: output/lymph_ADCY7_BRD7_plot_genetrack.pdf
Untracked: output/lymph_ADCY7_NOD2_plot.pdf
Untracked: output/lymph_ADCY7_NOD2_plot_genetrack.pdf
Untracked: output/lymph_ADCY7_plot.pdf
Untracked: output/lymph_BAZ1B_plot.pdf
Untracked: output/lymph_EPC1_plot.pdf
Untracked: output/lymph_LAMTOR4_plot.pdf
Untracked: output/lymph_MDM2_plot.pdf
Untracked: output/lymph_RANGAP1_plot.pdf
Untracked: output/lymph_TAP2_plot.pdf
Untracked: output/lymph_THEMIS2_plot.pdf
Untracked: output/lymph_ZKSCAN5_plot.pdf
Untracked: output/lymph_ZSCAN25_plot.pdf
Untracked: output/m6aQTL_dsRNAs_PPP2R3C_PRORP.pdf
Untracked: output/m6a_QTL_genes.csv
Untracked: output/m6a_genes_PIP_0.6_blood_immune.csv
Untracked: output/m6a_genes_PIP_0.6_blood_immune.txt
Untracked: output/m6a_peaks_nearby_dsRNAs.csv
Untracked: output/m6a_sites_near_all_dsRNAs_twas.csv
Untracked: output/m6a_sites_near_dsRNAs_coloc.csv
Untracked: output/m6a_sites_near_dsRNAs_twas.csv
Untracked: output/m6a_sites_near_dsRNAs_twas_summary.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/platelet_AKAP8_plot.pdf
Untracked: output/platelet_C17orf62_plot.pdf
Untracked: output/platelet_GSDMD_plot.pdf
Untracked: output/platelet_PHF11_plot.pdf
Untracked: output/platelet_SLC25A11_plot.pdf
Untracked: output/platelet_TAOK1_plot.pdf
Untracked: output/platelet_THEMIS2_plot.pdf
Untracked: output/platelet_THEMIS2_plot_genetrack.pdf
Untracked: output/platelet_TRAF2_plot.pdf
Untracked: output/platelet_UBE2G2_plot.pdf
Untracked: output/platelet_ZSCAN25_plot.pdf
Untracked: output/postively_correlated_genes.txt
Untracked: output/rs1806261_RABEP1-NUP88_focused_locusview.pdf
Untracked: output/rs1806261_RABEP1-NUP88_locusview.pdf
Untracked: output/rs3177647_MAPKAPK5-AS1-MAPKAPK5_locusview.pdf
Untracked: output/rs3204541_DDX55-EIF2B1_locusview.pdf
Untracked: output/rs7184802_ADCY7-BRD7_locusview.pdf
Untracked: output/rs7184802_ADCY7_locuscompare.pdf
Untracked: output/twas_genes_PP4_0.3_immune_traits_trackplots.pdf
Untracked: output/twas_genes_PP4_0.5_blood_traits_trackplots.pdf
Untracked: output/twas_m6a_sites_with_all_cisNATs.RDS
Untracked: output/twas_m6a_sites_with_cisNATs_range.RDS
Untracked: output/twas_m6a_sites_with_the_nearest_cisNAT.RDS
Untracked: output/wbc_RABEP1_NUP88_plot.pdf
Untracked: output/wbc_RABEP1_NUP88_plot_genetrack.pdf
Untracked: output/wbc_SLC9A3R1_plot.pdf
Untracked: twas_genes_PP4_0.3_immune_traits_trackplots.pdf
Unstaged changes:
Deleted: analysis/learn_ctwas.Rmd
Modified: analysis/lymph_m6A_output_hg19.Rmd
Modified: analysis/m6A_switch_to_disease_h2g.Rmd
Modified: analysis/rbc_m6A_output_hg19.Rmd
Modified: analysis/wbc_m6A_output.Rmd
Modified: analysis/wbc_m6A_output_hg19.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 | d0f5634 | Jing Gu | 2023-08-25 | other traits |
| html | 571007e | Jing Gu | 2023-08-22 | Build site. |
| Rmd | 132a611 | Jing Gu | 2023-08-22 | wflow_publish("analysis/index.Rmd") |
| html | 866865b | Jing Gu | 2023-08-22 | Build site. |
| html | f4e6d93 | Jing Gu | 2023-08-22 | Build site. |
| Rmd | fb910fa | Jing Gu | 2023-08-22 | blood traits |
| html | bef698c | Jing Gu | 2023-08-17 | Build site. |
| Rmd | 06e2427 | Jing Gu | 2023-08-17 | added lupus |
| html | f11f68a | Jing Gu | 2023-08-16 | Build site. |
| Rmd | a1e2443 | Jing Gu | 2023-08-16 | added rbc |
| html | 992e835 | Jing Gu | 2023-08-16 | Build site. |
| Rmd | 22983a7 | Jing Gu | 2023-08-16 | wflow_publish("analysis/index.Rmd") |
| html | 3a4bab9 | Jing Gu | 2023-08-11 | Build site. |
| Rmd | c94ee10 | Jing Gu | 2023-08-11 | wflow_publish(c("analysis/wbc_m6A_output_hg19.Rmd", "analysis/index.Rmd", |
| html | 170a310 | Jing Gu | 2023-08-10 | gene-association with ctwas |
| html | 499f070 | Jing Gu | 2023-06-19 | visualize target sites |
| 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. |
Test the enrichment for dsRNAs formed by m6A-switch with GWAS variants