Bishop-Laboratory RLoop-QC-Meta-Analysis-Miller-2022 issues

Bishop-Laboratory / RLoop-QC-Meta-Analysis-Miller-2022

Generates figures for "Quality-controlled R-loop meta-analysis reveals the characteristics of R-loop consensus regions"

https://doi.org/10.1093/nar/gkac537

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Recalc R-loop regions

#93 millerh1 opened 2 years ago
0
Show a genome browser picture of pausing at top dRNH-specific genes

#92 millerh1 closed 2 years ago
1
R-loop binding protein extension

#91 millerh1 opened 2 years ago
0
Fix labels on the RLRegions meta object

#90 millerh1 closed 2 years ago
1
Change proportion plot of enhancer types

#89 millerh1 closed 2 years ago
1
Compare the size of dEnh clusters to the amount of dRNH/S9.6 signal in them

#88 millerh1 opened 2 years ago
0
Reorder the signal track in the tornado & GenomeBrowser plots

#87 millerh1 closed 2 years ago
1
Size difference in S9.6-only and dRNH-only

#86 millerh1 closed 2 years ago
5
Look at a specific tissue's dRNH R-loop data and comapare with dEnh from GH -- what pathways are targeted?

#85 millerh1 closed 2 years ago
1
In a cell-line-specific manner, examine the relationship between TAD domains and dRNH-only signal

#84 millerh1 opened 2 years ago
1
Discussion: dRNH cannot access TSS if other factors there

#83 millerh1 closed 2 years ago
1
Re-analyze the pathway enrichment

#82 millerh1 opened 2 years ago
0
Examine the KDM5B result more closely

#81 millerh1 opened 2 years ago
0
Alternative to downsampling: look only at cell lines found in both

#80 millerh1 opened 2 years ago
0
Idea for checking size of the peaks within each Tx Featurew

#79 millerh1 opened 2 years ago
0
Idea for recentering S9.6 summits

#78 millerh1 opened 2 years ago
0
Exploratory analysis of CCREs and dRNH/S96 consensus peaks

#77 millerh1 closed 2 years ago
2
Drill down into intergenic dRNH peaks

#76 millerh1 closed 2 years ago
1
Analysis of shared vs unique dRNH and S9.6 sites

#75 millerh1 closed 2 years ago
3
Compare stranded vs unstranded locations

#74 millerh1 opened 2 years ago
0
Analyze cis vs trans R-loops

#73 millerh1 opened 2 years ago
0
Regenerate previous figures with updated datasets included

#72 millerh1 closed 2 years ago
1
Additional support for RLFS

#71 millerh1 opened 2 years ago
0
Analysis of S/N ratio

#70 millerh1 opened 2 years ago
0
Exploratory: compare R-loops with sites of chromosomal rearrangements and mutations

#69 millerh1 opened 2 years ago
0
Exploratory: Establish method for finding proportion of Class I/II R-loops

#68 millerh1 opened 2 years ago
0
Exploratory: Examine the variable R-loops in greater depth

#67 millerh1 opened 2 years ago
1
Exploratory: Is there a size difference in dRNH that do/do not overlap with S9.6?

#66 millerh1 closed 2 years ago
1
Figure showing the "False NEG" data origins

#65 millerh1 opened 2 years ago
0
Response to rev 2: show downsampled S9.6 compared to dRNH samples

#64 millerh1 opened 2 years ago
0
Analysis benefit of QC on downstream analysis

#63 millerh1 closed 2 years ago
1
Analysis: Binary clustering of R-loop regions and genomic annotations

#62 millerh1 opened 2 years ago
1
Jebriel

#61 millerh1 closed 3 years ago
0
Need conservation analysis to answer questions (listed)

#60 millerh1 closed 2 years ago
1
Need to refactor notebook for maintainability

#59 millerh1 closed 2 years ago
0
Need a summary of the datasets used with QC info included

#58 millerh1 closed 3 years ago
1
Need to set up a consistent color pallete and ggplot prototypes

#53 millerh1 closed 2 years ago
0
Before we go to the gene features -- need to have the summary of all the QC of all the datasets

#50 millerh1 closed 3 years ago
1
Remove the astrix on the FFT data

#47 millerh1 closed 3 years ago
1
Try using the transformer to scale the Zscores for plotting the peak enrichment plots

#45 millerh1 closed 3 years ago
1
How does the RLFS and consensus sites compare to where G4 quadruplexes are?

#44 millerh1 opened 3 years ago
0
Need to recreate model using full dataset

#42 millerh1 closed 3 years ago
1
It would be interesting to be able to say what the top hits are (in terms of repetitive elements) and then what you see once you get rid of rep elements

#40 millerh1 closed 3 years ago
1
Get the genome browser track for NEAT1 with new BW

#39 millerh1 closed 3 years ago
1
Need a radial label for the dendrogram for the heatmap

#38 millerh1 closed 3 years ago
1
What evidence do we have that the R-ChIP, RDIP, and RR-ChIP are performing as expected?

#37 millerh1 closed 3 years ago
1
Need to make figures and flow chart for the FFT analysis

#36 millerh1 closed 3 years ago
1
Need account of RMap Samples

#35 millerh1 closed 3 years ago
2
Once the datasets are ready, finish building the schemas for the refactored API/DB

#34 millerh1 closed 3 years ago
0
Rmapdb tables

#33 millerh1 closed 3 years ago
0