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RNA-SEQ
•
reset
9
votes
12
replies
7.8k
views
Multi factor design edgeR/Deseq2
deseq2
edgeR
rna-seq
updated 8 days ago by
Elizabeth
• 0 • written 8.8 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 11 months ago by
Gordon Smyth
50k • written 11 months ago by
mohammedtoufiq91
▴ 10
3
votes
3
replies
294
views
permutation test in edgeR
rna-seq
edgeR
updated 6 days ago by
Gordon Smyth
50k • written 18 days ago by
Netanel
• 0
3
votes
4
replies
854
views
lfcShrink() and batch effects in DESeq2
BatchEffect
lfcshrink
RNA-seq
DESeq2
8 months ago
Eva
▴ 10
2
votes
3
replies
1.5k
views
TPM from STAR mapped counts
GeneExpression
GenomicFeatures
RNA-Seq
TPM
updated 7 months ago by
Gordon Smyth
50k • written 7 months ago by
gingergeiger22
• 0
0
votes
4
replies
688
views
DESeq2 : standardising variation between treatments
RNA-seq
DESeq2
6 months ago
ar14g12
• 0
0
votes
10
replies
2.2k
views
Error in reading data on isoformswitchanalyzeR
isoformswitchanalyzeR
rna-seq
splice-variants
written 5.1 years ago by
saddamhusain77
• 0
0
votes
3
replies
671
views
Fishpond with unbalanced dataset
rna-seq
salmon
fishpond
swish
updated 10 months ago by
Michael Love
41k • written 10 months ago by
samuelcjx
• 0
0
votes
3
replies
702
views
Is the gene-specific PCR efficiency a serious concern for intrasample comparisons in RNA-Seq?
RNA-Seq
normalization
PCR_efficiency
bias
intrasample_comparison
updated 11 months ago by
James W. MacDonald
65k • written 11 months ago by
FedeXander
• 0
0
votes
3
replies
643
views
RNAseq (Deseq2 and Dexseq2) analysis on two time points with expected same effect
DEXSeq
RNA-seq
DESeq2
updated 7 months ago by
Alejandro Reyes
★ 1.9k • written 7 months ago by
Alice
• 0
0
votes
3
replies
841
views
Why is RNA-Seq library size not constant among samples?
RNA-Seq
sequencer
library_size
sequency_depth
multiplexing
offtopic
updated 11 months ago by
James W. MacDonald
65k • written 11 months ago by
FedeXander
• 0
0
votes
1
reply
903
views
Human genes correlation to Bacterial genes
correlation
pearsoncorrelation
rna-seq
differential gene expression
updated 4 months ago by
ATpoint
★ 4.0k • written 6.0 years ago by
saad_k6
• 0
0
votes
2
replies
303
views
WGCNA less samples
RNA-Seq
WGCNA
Worms
5 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 2.0 years ago by
cicely.day
• 0
0
votes
2
replies
1.2k
views
Pathway analysis using GAGE returns all NA values
gage
rna-seq
pathwayanalysis
updated 11 months ago by
Rob
• 0 • written 3.5 years ago by
microPhD
• 0
0
votes
2
replies
3.5k
views
Dealing with multi-overlapping and multi-mapping reads
RNA-seq
featureCounts
ht-seq
written 3.8 years ago by
ag1805x
▴ 80
16 results • Page
1 of 1
Recent ...
Replies
Answer: Dominance Index for Shotgun Metagenomics Data
by
Leo Lahti
▴ 40
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
pl23
• 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions
by
Michael Love
41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
by
ussarizona
▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative?
by
Michael Love
41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Votes
Answer: Dominance Index for Shotgun Metagenomics Data
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
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