cruk-mi mesa issues - Githubissues

cruk-mi / mesa

mesa package for Methylation Enrichment Sequencing Analysis

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Add checks to ensure hmmCopy objects are correct

#29 SPPearce opened 6 days ago
0
Fix addMedipsEnrichmentFactors messages

#28 SPPearce closed 2 days ago
0
Typo when adding Medip enrichment values

#27 daonslog opened 6 days ago
1
Adding GC and mappability with incompatible bin sizes massively duplicates CNV regions in the resulting `qseaSet`

#26 lbeltrame opened 1 week ago
14
Memory usage can be excessive

#25 lbeltrame opened 1 week ago
7
Add sliceDMRs function

#24 SPPearce opened 3 weeks ago
0
plotRegionsHeatmap annotation working for duplicated windows

#23 SPPearce opened 4 weeks ago
0
The HMMcopy parameters (GC and mappability) are unclear

#22 SPPearce opened 1 month ago
0
Fix makeqset

#21 SPPearce opened 1 month ago
0
`makeQset` with CNV method `MeCap` does not properly pass fragment length to `qsea::addCNV`

#20 lbeltrame opened 2 months ago
2
`MeCap` is not mentioned as an available method in the help of the `makeQset` function.

#19 SPPearce opened 2 months ago
0
`plotRegionsHeatmap` fails if `regionsToOverlap` has multiple regions that overlap the same 300bp window.

#18 paddyharker1005 opened 3 months ago
0
Update README.md

#17 SPPearce opened 4 months ago
0
Update the mouse tests so that it skips on github if can't connect.

#16 SPPearce closed 4 months ago
0
Catch biomaRt errors in `plotGeneHeatmap`

#15 SPPearce opened 6 months ago
0
Updating vignettes and adding examples

#14 SPPearce opened 6 months ago
18
Function to select top DMRs between multiple comparisons

#13 ativey07 opened 6 months ago
0
Change default shape for PCA/UMAP plotting functions to filled circle (21)

#12 paddyharker1005 opened 6 months ago
0
Some minor tweaks to the pca functionality

#11 SPPearce closed 6 months ago
0
Remove `samples` from output of dimensionality reduction functions

#10 Steven-M-Hill opened 6 months ago
0
plotPCA fails if shape has an NA value but NAshape is not specified

#9 SPPearce opened 6 months ago
0
plotCorrelationMatrix should be swapped from pheatmap to ComplexHeatmap

#8 SPPearce opened 6 months ago
0
Create documentation for new object classes

#7 Steven-M-Hill opened 6 months ago
0
Merge dev branch into main having moved back to Github.

#6 SPPearce closed 6 months ago
0
Minor bug fixes

#5 SPPearce closed 6 months ago
3
Updated github actions for 2024, fix PCA issue related to newest ggplot version

#4 SPPearce closed 7 months ago
0
exceeding the memory limit when calculating DMRs

#3 shufanzhang closed 6 months ago
1
addMedipsEnrichmentFactors adapted to fix bug

#2 anjalisa closed 6 months ago
1
function addMedipsEnrichmentFactors() terminates with error

#1 anjalisa closed 6 months ago
2