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Showing :
pcaExplorer
•
reset
0
votes
3
replies
735
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Higher Dimensional RNASeq Clustering Significance
DESeq2
RNASeq
PrincipalComponent
pcaExplorer
written 17 months ago by
James
• 0
0
votes
3
replies
1.1k
views
I got error when visualizing my PCA
PCAtools
pcaExplorer
pcaMethods
updated 22 months ago by
Federico Marini
▴ 150 • written 22 months ago by
m610110001
• 0
5
votes
6
replies
2.4k
views
Large difference in PCA plot based on LCPM (log counts per million) and VST (variance stabilizing transformations)
PCAtools
edgeR
pcaExplorer
RNASeq
RNAseq123
2.0 years ago
Alan
• 0
4
votes
7
replies
1.9k
views
Updating org.Sc.sgd.db, and integration with topGO
GeneTonic
org.Sc.sgd.db
pcaExplorer
topGO
EnrichmentBrowser
updated 2.2 years ago by
Federico Marini
▴ 150 • written 2.2 years ago by
chase.mateusiak
• 0
9
votes
6
replies
27k
views
DESeq2 / PCA Analysis of RNA-seq Data - Best Explanatory Resource?
DESeq2
pcaExplorer
updated 3.1 years ago by
Michael Love
41k • written 3.1 years ago by
vanbelj
▴ 30
2
votes
4
replies
1.5k
views
Comparing discrete variable to PCA
EDA
pcaExplorer
PCAtools
PCA
updated 2.4 years ago by
Miguel
▴ 10 • written 3.7 years ago by
k.vitting.seerup
▴ 120
0
votes
7
replies
1.8k
views
go_bp table in custom OrgDb package
annotation
go
pcaExplorer
AnnotationForge
updated 5.1 years ago by
James W. MacDonald
65k • written 5.1 years ago by
psutton
• 0
0
votes
1
reply
1.1k
views
PCA on deseq2 gene data set
pcaexplorer
genespca
deseq2
updated 6.4 years ago by
Michael Love
41k • written 6.4 years ago by
sally_b86
• 0
0
votes
8
replies
2.1k
views
pcaEcplorer PCA2go function crashing
pca2go
pcaexplorer
updated 6.7 years ago by
Federico Marini
▴ 150 • written 6.7 years ago by
reubenmcgregor88
• 0
1
vote
2
replies
1.3k
views
Error in pcaplot3d from pcaExplorer, when running Deseq2 since update of packages
deseq2
pcaexplorer
6.7 years ago
reubenmcgregor88
• 0
1
vote
2
replies
1.5k
views
pcaExplorer error displaying PCA plot
pcaExplorer
pca
updated 7.4 years ago by
Federico Marini
▴ 150 • written 7.4 years ago by
swaegers.janne
• 0
11 results • Page
1 of 1
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Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
Alexandre
• 0
My code for the sessionInfo() . If the pictures are too big, I will downsize them. THank you again for reading my post ! ```r > sessionInf…
Comment: Reproducibility issue with scran together with lapply and BiocParallel
by
ATpoint
★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
winwater0928
• 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Answer: Reproducibility issue with scran together with lapply and BiocParallel
by
Aaron Lun
★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Votes
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
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