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

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Issues list

Recalc R-loop regions
#93 opened Apr 21, 2022 by millerh1
2 tasks
R-loop binding protein extension
#91 opened Apr 18, 2022 by millerh1
Compare the size of dEnh clusters to the amount of dRNH/S9.6 signal in them analysis needed This issue requires an analysis (e.g., Identification of gene expression changes with treatment) low-priority
#88 opened Apr 17, 2022 by millerh1
In a cell-line-specific manner, examine the relationship between TAD domains and dRNH-only signal analysis needed This issue requires an analysis (e.g., Identification of gene expression changes with treatment) high-priority
#84 opened Apr 1, 2022 by millerh1
Re-analyze the pathway enrichment analysis needed This issue requires an analysis (e.g., Identification of gene expression changes with treatment) high-priority
#82 opened Apr 1, 2022 by millerh1
Examine the KDM5B result more closely analysis needed This issue requires an analysis (e.g., Identification of gene expression changes with treatment) high-priority
#81 opened Apr 1, 2022 by millerh1
Alternative to downsampling: look only at cell lines found in both analysis needed This issue requires an analysis (e.g., Identification of gene expression changes with treatment) low-priority
#80 opened Apr 1, 2022 by millerh1
Idea for checking size of the peaks within each Tx Featurew analysis needed This issue requires an analysis (e.g., Identification of gene expression changes with treatment) mid-priority
#79 opened Apr 1, 2022 by millerh1
Idea for recentering S9.6 summits analysis needed This issue requires an analysis (e.g., Identification of gene expression changes with treatment) low-priority
#78 opened Apr 1, 2022 by millerh1
Compare stranded vs unstranded locations analysis needed This issue requires an analysis (e.g., Identification of gene expression changes with treatment) low-priority
#74 opened Feb 23, 2022 by millerh1
Analyze cis vs trans R-loops analysis needed This issue requires an analysis (e.g., Identification of gene expression changes with treatment) low-priority
#73 opened Feb 23, 2022 by millerh1
Additional support for RLFS analysis needed This issue requires an analysis (e.g., Identification of gene expression changes with treatment) mid-priority
#71 opened Dec 27, 2021 by millerh1
Analysis of S/N ratio analysis needed This issue requires an analysis (e.g., Identification of gene expression changes with treatment) low-priority
#70 opened Dec 27, 2021 by millerh1
Exploratory: compare R-loops with sites of chromosomal rearrangements and mutations analysis needed This issue requires an analysis (e.g., Identification of gene expression changes with treatment) mid-priority
#69 opened Dec 16, 2021 by millerh1
2 tasks
Exploratory: Establish method for finding proportion of Class I/II R-loops analysis needed This issue requires an analysis (e.g., Identification of gene expression changes with treatment) mid-priority
#68 opened Dec 16, 2021 by millerh1
Exploratory: Examine the variable R-loops in greater depth analysis needed This issue requires an analysis (e.g., Identification of gene expression changes with treatment) mid-priority
#67 opened Dec 16, 2021 by millerh1
Figure showing the "False NEG" data origins analysis needed This issue requires an analysis (e.g., Identification of gene expression changes with treatment) high-priority
#65 opened Dec 16, 2021 by millerh1
Response to rev 2: show downsampled S9.6 compared to dRNH samples analysis needed This issue requires an analysis (e.g., Identification of gene expression changes with treatment) high-priority
#64 opened Dec 16, 2021 by millerh1
Analysis: Binary clustering of R-loop regions and genomic annotations analysis needed This issue requires an analysis (e.g., Identification of gene expression changes with treatment) mid-priority
#62 opened Dec 13, 2021 by millerh1
5 tasks
How does the RLFS and consensus sites compare to where G4 quadruplexes are? analysis needed This issue requires an analysis (e.g., Identification of gene expression changes with treatment) mid-priority
#44 opened Aug 19, 2021 by millerh1
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