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DESEQ2
•
reset
0
votes
4
replies
917
views
lfcShrink and alpha value
lfcShrink
DESeq2
11 months ago
anon
• 0
2
votes
1
reply
697
views
DESeq2- merging technical vs biological replicates
DESeq2
RNASeqData
updated 11 months ago by
Michael Love
43k • written 11 months ago by
Nikita
• 0
0
votes
2
replies
490
views
DESeq2 dispersion estimates fitting drastically different based on explanatory variable scaling
dispersionestimates
DESeq2
updated 11 months ago by
Michael Love
43k • written 11 months ago by
Sam
• 0
0
votes
2
replies
471
views
DESeq2 sizefactors counfounded with biological treatment
DESeq2
11 months ago
Anna
• 0
1
vote
2
replies
794
views
Deseq2 res Function
DESeq2
updated 11 months ago by
James W. MacDonald
68k • written 11 months ago by
sap275
▴ 10
0
votes
4
replies
736
views
Help with RSEM counts: do I transpose matrix?
RSEM
DESeq2
11 months ago
NB
• 0
0
votes
5
replies
761
views
Identical samples after deseq2 batch effect removal
DESeq2
updated 11 months ago by
Michael Love
43k • written 12 months ago by
maripane
• 0
0
votes
1
reply
568
views
DE analysis on Single cell RNA Seq time course data (using pseudotime) with 5 different genotypes
DESeq2
updated 12 months ago by
James W. MacDonald
68k • written 12 months ago by
Raya
• 0
1
vote
2
replies
484
views
Differene between the Wald and LRT test for time-series gene expression data
DESeq2
12 months ago
Denise
• 0
0
votes
1
reply
413
views
eRNAs count
RNASeq
DESeq2
updated 12 months ago by
ATpoint
★ 5.0k • written 12 months ago by
Irene
• 0
0
votes
1
reply
617
views
DESeq2 rerun returns different results
DESeq2
updated 12 months ago by
ATpoint
★ 5.0k • written 12 months ago by
wl1111
• 0
0
votes
1
reply
515
views
Is my time course analysis with DESeq2 valid?
GeneExpression
DESeq2
TimeCourse
updated 12 months ago by
Michael Love
43k • written 12 months ago by
Jason
• 0
0
votes
1
reply
581
views
DESeq2 "Not full rank" and "less than full rank" error
DESeq2
deseq
updated 12 months ago by
Guido Hooiveld
★ 4.1k • written 12 months ago by
Najla Abassi
• 0
2
votes
2
replies
1.1k
views
Handling biological replicates in DESeq2
DESeq2
updated 12 months ago by
ATpoint
★ 5.0k • written 12 months ago by
sk
• 0
5
votes
3
replies
29k
views
DESeq2: thousands of NA for pvalues?
deseq2
rna-seq
DEGs
cooks cutoff
written 6.9 years ago by
aishu.jp
▴ 30
1
vote
6
replies
1.6k
views
Volcano plot has many values around zero
RNA-seq
DESeq2
volcanoplot
updated 12 months ago by
Michael Love
43k • written 12 months ago by
nramakr
▴ 10
0
votes
2
replies
572
views
DESeq2 interaction between cancer cells and microenvironment cells
DESeq2
written 12 months ago by
ballackselma
• 0
4
votes
5
replies
1.3k
views
DESeq Input from Salmon + tximport/tximeta
tximportData
summarizeToGene
tximport
DESeq2
salmon
12 months ago
LuciaNhu
• 0
0
votes
1
reply
729
views
Average expression of genes across replicates
DESeq2
updated 12 months ago by
ATpoint
★ 5.0k • written 12 months ago by
James
• 0
0
votes
0
replies
408
views
News:
RNAseq data analysis with R/Bioconductor (4-15 November)
DESeq2
GenomicRanges
12 months ago
info
▴ 10
0
votes
11
replies
2.4k
views
Question about using LRT test for time course experiments with DESeq2
DESeq2
updated 7 months ago by
Rob
• 0 • written 12 months ago by
Denise
• 0
0
votes
1
reply
557
views
Deseq to output continous sequencing data
DESeq2
updated 12 months ago by
Michael Love
43k • written 13 months ago by
Neha
• 0
1
vote
4
replies
1.4k
views
Adjusted p-values become NA when sub-setting samples
DESeq2
13 months ago • updated 12 months ago
txema.heredia
• 0
3
votes
3
replies
1.5k
views
Robust way of dealing with low number of samples for Differential Gene Expression
limma
edgeR
DESeq2
MAST
written 12 months ago by
Satoshi
• 0
0
votes
2
replies
776
views
ESTMATE, MCPcounter, EPIC, xCell input
DESeq2
ESTIMATE
RNASeqData
MCPcounter
written 13 months ago by
Aleksandra
• 0
0
votes
1
reply
490
views
Should zero counts in some replicates lead to inflated p-values?
DESeq2
updated 13 months ago by
Michael Love
43k • written 13 months ago by
nicolettacommins
• 0
2
votes
3
replies
1.3k
views
Analysis of large RNA-Seq Datasets
DESeq2
updated 13 months ago by
Michael Love
43k • written 13 months ago by
KokiBio
• 0
1
vote
4
replies
1.1k
views
DESeq2 - interactions when using factors concatenated into group
DESeq2
13 months ago • updated 12 months ago
boczniak767
▴ 740
0
votes
1
reply
368
views
2 factor analysis using DESeq2 but the result is not what I expected from the design
DESeq2
13 months ago
JY
• 0
0
votes
1
reply
466
views
How does deseq2 address intra group variance when calculating log2foldchange
DESeq2
updated 13 months ago by
Michael Love
43k • written 13 months ago by
agamemnon
• 0
0
votes
2
replies
487
views
how to extract expression matrix post deseq2
DESeq2
written 13 months ago by
agamemnon
• 0
0
votes
2
replies
535
views
Using Normalized Counts in DESeq2
DESeq2
updated 13 months ago by
Michael Love
43k • written 13 months ago by
KokiBio
• 0
3
votes
2
replies
588
views
When running contrasts, does it use normalized read counts?
DESeq2
13 months ago
Katherine
▴ 20
0
votes
1
reply
417
views
How to adjust the DESeq2 formula when there is no control group for one factor?
DESeq2
updated 13 months ago by
swbarnes2
★ 1.4k • written 13 months ago by
Bingqian
• 0
3
votes
4
replies
1.2k
views
Are transformed values from rlog /vst log2 normalized counts?
Normalization
DESeq2
rlog
vst
13 months ago
Eva
▴ 10
1
vote
4
replies
1.3k
views
Mostly increased counts in differentially accessible peaks using DESeq2
ATAC-seq
DESeq2
Oddresults
updated 13 months ago by
ATpoint
★ 5.0k • written 13 months ago by
Ricardo Iván
• 0
0
votes
1
reply
519
views
How to set filtering standard for low-expression genes in ImpulseDE2
DifferentialExpression
ImpulseDE2
DESeq2
updated 13 months ago by
Michael Love
43k • written 13 months ago by
Jiahao Tian
• 0
2
votes
4
replies
881
views
RNASeq Time Course Question
DESeq2
RNASeq
TimeCourse
13 months ago
jihoon.kim.1495
▴ 10
0
votes
6
replies
1.4k
views
[DESeq2] Introduce a bias in DESeq2
DifferentialExpression
DESeq2
BatchEffect
updated 12 months ago by
Michael Love
43k • written 13 months ago by
CriticalPeriod
• 0
5
votes
4
replies
992
views
How to control batch effect if Group and batch are same?
limma
DESeq2
BatchEffect
updated 13 months ago by
ATpoint
★ 5.0k • written 13 months ago by
Bioinformagician
• 0
0
votes
2
replies
682
views
RNA-Seq p value range variation
DESeq2
pvalue
RNA-Seq
13 months ago
paul.meraner
• 0
0
votes
0
replies
590
views
News:
RNAseq data analysis with Bioconductor (online course)
DESeq2
SummarizedExperiment
13 months ago • updated 12 months ago
info
▴ 10
1
vote
6
replies
1.4k
views
heatmap with batch effect
DESeq2
BatchEffect
written 13 months ago by
tothuhien
• 0
0
votes
2
replies
735
views
How can I obtain DEGs that are resulted from using salmon in alignment-based mode or mapping-based mode?
tximport
DESeq2
updated 13 months ago by
Michael Love
43k • written 13 months ago by
oguzhankaraosmanoglu
• 0
1
vote
1
reply
1.0k
views
Deseq2 sfType
Microbiome
DESeq2
RNASeq
updated 13 months ago by
James W. MacDonald
68k • written 13 months ago by
Caroline
• 0
1
vote
1
reply
675
views
Normalization RNA-seq for multiple plates
Normalization
DESeq2
RNASeqData
edgeR
updated 13 months ago by
ATpoint
★ 5.0k • written 13 months ago by
Pimpa
• 0
1
vote
1
reply
590
views
DEseq 2 LFC shrinkage with apeglm in single-cell pseudobulk: strange volcano plot results
DESeq2
updated 13 months ago by
ATpoint
★ 5.0k • written 13 months ago by
picasa1983
• 0
1
vote
2
replies
874
views
Poor dispersion fit in DESeq2
limma
DESeq2
RNASeq
edgeR
updated 13 months ago by
Michael Love
43k • written 13 months ago by
Ben
▴ 10
0
votes
2
replies
996
views
DESeq2 analysis on 2 plant lines infected with virus, with 2 time points (days post infection)
DESeq2
updated 13 months ago by
Michael Love
43k • written 14 months ago by
duplessisantzel
• 0
1
vote
2
replies
1.0k
views
DESeq2 design and contrasts with 2 drug-treated and one control group
DESeq2
Bioconductor
updated 13 months ago by
Michael Love
43k • written 14 months ago by
JT
▴ 10
4,838 results • Page
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Comment: Guidance Requested on GCN Network Analysis and Module Enrichment in R
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• 0
Ensure your SummarizedExperiment object correctly incorporates the RPKM expression matrix, GTF gene annotation [link][1] , and sample metad…
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by
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If you re experiencing unexpected results while running your fitGAM function, it s important to check that your dataset s dimnames are cons…
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Using biomaRt to extract SNP information from genomic regions is as simple as setting the correct dataset in this case, and defining your …
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Answer: Issues with downloading biomaRt - SeqInfo and S4 Vectors
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Issues with downloading biomaRt - SeqInfo and S4 Vectors
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