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RNA-Seq
•
reset
9
votes
12
replies
7.7k
views
Multi factor design edgeR/Deseq2
deseq2
edgeR
rna-seq
updated 8 hours ago by
Elizabeth
• 0 • written 8.8 years ago by
gthm
▴ 30
0
votes
10
replies
2.2k
views
Error in reading data on isoformswitchanalyzeR
isoformswitchanalyzeR
rna-seq
splice-variants
written 5.0 years ago by
saddamhusain77
• 0
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 10 months ago by
Gordon Smyth
50k • written 10 months ago by
mohammedtoufiq91
▴ 10
0
votes
4
replies
661
views
DESeq2 : standardising variation between treatments
RNA-seq
DESeq2
6 months ago
ar14g12
• 0
3
votes
4
replies
838
views
lfcShrink() and batch effects in DESeq2
BatchEffect
lfcshrink
RNA-seq
DESeq2
8 months ago
Eva
▴ 10
3
votes
3
replies
256
views
permutation test in edgeR
rna-seq
edgeR
updated 3 days ago by
Gordon Smyth
50k • written 10 days ago by
Netanel
• 0
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
3
replies
660
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
689
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
630
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
828
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
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 3.7 years ago by
ag1805x
▴ 80
0
votes
2
replies
295
views
WGCNA less samples
RNA-Seq
WGCNA
Worms
4 months ago
davca
• 0
0
votes
2
replies
2.2k
views
Incorporating spike-ins to rna-seq analysis
Spike-in
RNASeqR
DESeq2
Normalization
rna-seq
updated 7 months ago by
manuel.fernandez
• 0 • written 2.0 years ago by
cicely.day
• 0
0
votes
1
reply
894
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
16 results • Page
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Answer: OrgDb for maize
by
Guido Hooiveld
★ 3.9k
I notice the data you are working with is based on `ensembl` ids. This is important, because the `OrgDb` are annotation databases that are …
Comment: Theoretical WGCNA Question
by
Garrett
• 0
Thanks Peter!
Comment: FGSEA pre-ranked input in increasing order or decreasing
by
sropri
• 0
Thank you!
Comment: FGSEA pre-ranked input in increasing order or decreasing
by
alserg
▴ 240
They are reorder in the decreasing order.
Comment: significant difference of p-values with dream() after updating VariancePartition
by
Le
• 0
Thanks for your reply @gabrielhoffman ! I've been trying to isolate the changes, and v1.32.5 had the same results as v1.33.1 while v1.30.0…
Votes
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Comment: DEXSeq DEXSeqDataSet count matrix duplication
Comment: Error in champ.load(): The following specified files do not exist
Answer: Error in read.metharray(basenames = files, extended = extended, verbose = verbos
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