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