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RNA-Seq
•
reset
9
votes
12
replies
7.9k
views
Multi factor design edgeR/Deseq2
deseq2
edgeR
rna-seq
updated 4 weeks ago by
Elizabeth
• 0 • written 8.9 years ago by
gthm
▴ 30
5
votes
7
replies
1.2k
views
Question about setting threshold using filtering by expression on genes in edgeR
filtering
RNA-Seq
CPM
edgeR
filterByExpr
updated 12 months ago by
Gordon Smyth
50k • written 12 months ago by
mohammedtoufiq91
▴ 10
3
votes
4
replies
898
views
lfcShrink() and batch effects in DESeq2
BatchEffect
lfcshrink
RNA-seq
DESeq2
9 months ago
Eva
▴ 10
3
votes
3
replies
371
views
permutation test in edgeR
rna-seq
edgeR
updated 4 weeks ago by
Gordon Smyth
50k • written 6 weeks ago by
Netanel
• 0
2
votes
3
replies
1.7k
views
TPM from STAR mapped counts
GeneExpression
GenomicFeatures
RNA-Seq
TPM
updated 8 months ago by
Gordon Smyth
50k • written 8 months ago by
gingergeiger22
• 0
2
votes
4
replies
202
views
DESeq2- Mysterious interaction suppresses DEGs
DESeq2
PCAplot
RNA-Seq
DesignModel
updated 2 days ago by
Michael Love
42k • written 5 days ago by
shaunpeterson
• 0
2
votes
3
replies
265
views
Too many significant genes when integrating gtex and tcga
RNA-seq
DESeq2
updated 17 days ago by
ATpoint
★ 4.1k • written 19 days ago by
Reza
• 0
1
vote
2
replies
292
views
Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq
duplicateCorrelation
limma
voom
13 days ago • updated 12 days ago
Dylan.Sheerin
• 0
0
votes
4
replies
737
views
DESeq2 : standardising variation between treatments
RNA-seq
DESeq2
7 months ago
ar14g12
• 0
0
votes
2
replies
3.6k
views
Dealing with multi-overlapping and multi-mapping reads
RNA-seq
featureCounts
ht-seq
written 3.8 years ago by
ag1805x
▴ 80
0
votes
3
replies
714
views
Fishpond with unbalanced dataset
rna-seq
salmon
fishpond
swish
updated 11 months ago by
Michael Love
42k • written 11 months ago by
samuelcjx
• 0
0
votes
3
replies
699
views
RNAseq (Deseq2 and Dexseq2) analysis on two time points with expected same effect
DEXSeq
RNA-seq
DESeq2
updated 8 months ago by
Alejandro Reyes
★ 1.9k • written 8 months ago by
Alice
• 0
0
votes
1
reply
727
views
How to arrange multiple plots into one page in NOISeq?
noiseq
RNA-seq
quality control
updated 1 day ago by
baptiste.bidon
• 0 • written 4.7 years ago by
ag1805x
▴ 80
0
votes
2
replies
330
views
WGCNA less samples
RNA-Seq
WGCNA
Worms
6 months ago
davca
• 0
0
votes
2
replies
2.3k
views
Incorporating spike-ins to rna-seq analysis
Spike-in
RNASeqR
DESeq2
Normalization
rna-seq
updated 8 months ago by
manuel.fernandez
• 0 • written 2.1 years ago by
cicely.day
• 0
0
votes
10
replies
2.3k
views
Error in reading data on isoformswitchanalyzeR
isoformswitchanalyzeR
rna-seq
splice-variants
written 5.1 years ago by
saddamhusain77
• 0
0
votes
1
reply
921
views
Human genes correlation to Bacterial genes
correlation
pearsoncorrelation
rna-seq
differential gene expression
updated 5 months ago by
ATpoint
★ 4.1k • written 6.1 years ago by
saad_k6
• 0
17 results • Page
1 of 1
Recent ...
Replies
Answer: Help with infinite recursion - non-zero exit status in installation of GenomeInf
by
James W. MacDonald
66k
Maybe just try again? ``` > install("GenomeInfoDbData", force = TRUE) 'getOption("repos")' replaces Bioconductor standard repositorie…
Comment: Help with infinite recursion - non-zero exit status in installation of GenomeInf
by
Brandon
• 0
Hello, As an update, I am able to install and load GenomeInfoDb successfully in a fresh renv in my WSL distro. However, I'm not sure what …
Comment: slingshot: error with plot3d.SlingshotDataSet
by
Kelly Street
• 0
This issue has been addressed [on GitHub][1]. [1]: https://github.com/kstreet13/slingshot/issues/249
Comment: Slightly different count plots from R and spreadsheet
by
Michael Love
42k
Change timepoint to an integer in the data frame: ``` as.numeric(as.character( <factor> )) ``` Then it should make points instead of boxe…
Answer: WGNCA kME vs. kIM
by
Vitor
• 0
You can compare kIM and kME within module assignments. The plot below is for my network (I used Pearson correlation and signed network). !…
Votes
Including squared covariates to account for non-linear dependencies in differential gene expression analysis
DESeq2 DE gene expression of scRNA-seq pseudobulk
Answer: Multiple factor DSEq2 result generates weird volcano plot
DESeq2 for single cell pseudobulk processing
Simultaneously adding two different covariates in the model gives error in DESeq2.
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