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sashimi
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Setting ylims in bam coverage plot and assigning compound sashimi numbers to overlay plots
Coverage
Gviz
sashimi
8 weeks ago
Marco
• 0
0
votes
1
reply
971
views
Extracting read coverage data from a Gviz AlignmentsTrack
gviz
sashimi
updated 5.2 years ago by
Robert Ivanek
▴ 750 • written 5.3 years ago by
willbradshaw
• 0
0
votes
3
replies
1.4k
views
Normalized sashimi plots with Gviz
Gviz
Sashimi
5.6 years ago
benjamin.carter
• 0
1
vote
4
replies
2.3k
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Gviz sashimi read count
Gviz
sashimi
sashimi plots
read counting
bam
updated 7.7 years ago by
Robert Ivanek
▴ 750 • written 7.7 years ago by
bernt.popp
• 0
0
votes
1
reply
1.2k
views
GVIZ junction plot without bam
gviz
intropolis
junction
sashimi
updated 8.2 years ago by
florian.hahne@novartis.com
★ 1.6k • written 8.3 years ago by
bernt.popp
• 0
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Comment: lfcShrink and alpha value
by
cropero
• 0
Thank you so much! Would that be equivalent to perform `res <- results(dds, contrast = c("conditions", "wild_type_114_2_no_carbon", "wild_t…
Comment: pathview - multiple states
by
Philippine
• 0
Thank you! Here a subset of genes that really works with "ame04145". data <- data.frame( EntrezID = c(100577548, 100577764, 406…
Comment: pathview - multiple states
by
Guido Hooiveld
★ 4.1k
A quick comment after I copied/pasted your code: when using `geneList1` in the 3rd code chunk I do **not** get a nice plot... I rather got …
Answer: scuttle::perFeatureQCMetrics runs very slow for big scRNA-seq data
by
Adam
• 0
Hi Aaron, Thanks a lot for your help! As you mentioned, I checked my data and it is "DelayedMatrix". I don't know the detailed differe…
Answer: scuttle::perFeatureQCMetrics runs very slow for big scRNA-seq data
by
Aaron Lun
★ 28k
You don't mention how your matrix data is being represented, but if it's a file-backed matrix (e.g., `HDF5Matrix` or one of its variants, b…
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Answer: contrast matrix design for a continuous variable
A: What's the difference between p.adjust and qvalue?
Answer: DESeq2- merging technical vs biological replicates
Comment: What type of counts data to import for performing Isoform analysis in edgeR
Answer: What type of counts data to import for performing Isoform analysis in edgeR
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