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DEseq2
•
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0
votes
2
replies
1.0k
views
Install old version of DESeq2
apeglm
Install
DESeq2
version
updated 3 days ago by
Kevin Blighe
★ 4.0k • written 4 months ago by
Asma
• 0
1
vote
11
replies
1.2k
views
Using DESeq2 on single cell RNA Seq data of same cell type but different conditions that were pseudo bulked
DESeq2
scRNAseq
updated 3 days ago by
Kevin Blighe
★ 4.0k • written 3 months ago by
Raya
• 0
0
votes
1
reply
200
views
DESeq2 on non-RNASeq counts data
DESeq2
updated 4 days ago by
Kevin Blighe
★ 4.0k • written 3 months ago by
vs
• 0
2
votes
4
replies
164
views
Highly similar RNA-seq samples in PCA - pooling or technical duplication?
RNASeq
DESeq2
DifferentialExpression
RNASeqData
updated 9 hours ago by
ATpoint
★ 5.0k • written 4 days ago by
Ahmed Salah
• 0
0
votes
2
replies
269
views
3-factor DESeq2 trime-series analysis
time-series
DESeq2
updated 6 days ago by
Kevin Blighe
★ 4.0k • written 10 weeks ago by
gogeni5529
• 0
0
votes
0
replies
82
views
[DESeq2] Changing dispersion estimates between runs of DESeq2
DESeq2
updated 6 days ago by
Kevin Blighe
★ 4.0k • written 11 days ago by
colinmccornack
• 0
0
votes
4
replies
155
views
Getting a large intercept with DESeq2
DESeq2
DifferentialExpression
TimeCourse
10 days ago • updated 7 days ago
Denise
• 0
0
votes
2
replies
182
views
Setting up a DESeq2 Design with Paired Data
DESeq2
18 days ago • updated 17 days ago
Alexander
• 0
2
votes
4
replies
456
views
DESeq2 interactions
DESeq2
updated 26 days ago by
Michael Love
43k • written 10 weeks ago by
Michael
• 0
3
votes
14
replies
1.1k
views
DESeq2 used with zinbwave weights - Differences on contrasts calculations
zinbwave
DESeq2
written 3 months ago by
Aurélie
• 0
0
votes
3
replies
358
views
Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg?
RUVSeq
DESeq2
updated 10 weeks ago by
Michael Love
43k • written 11 weeks ago by
yongjie.wang
• 0
0
votes
1
reply
672
views
Which of apeglm and ashr may be more appropriate for pseudobulked DESeq2 analysis of single-cell RNA-seq data?
apeglm
DESeq2
updated 11 weeks ago by
Michael Love
43k • written 3 months ago by
KS
• 0
3
votes
5
replies
1.1k
views
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
DESeq2
updated 11 weeks ago by
James W. MacDonald
68k • written 12 weeks ago by
snijesh
▴ 200
17
votes
45
replies
13k
views
Can NanoString data be analyzed using DESeq2?
NanoString
Differential Expressed Genes Analysis
DESeq2
updated 3 months ago by
James W. MacDonald
68k • written 6.3 years ago by
lim6432
▴ 60
0
votes
11
replies
610
views
Getting way too many DEGs with LRT for time-series RNA-seq!
TimeCourse
DESeq2
3 months ago
Denise
• 0
2
votes
6
replies
566
views
Very different log2 Fold changes with DESeq2 and explict calculation
DESeq2
3 months ago
richardallenfriedmanbrooklyn
▴ 30
0
votes
3
replies
267
views
DESeq2 inconsistent fits depending on model design with interacting factors
des
DESeq2
written 3 months ago by
fedor.bezrukov
▴ 10
0
votes
4
replies
852
views
Using shrunken LFC and s-value from DESeq2 as DGE results
apeglm
s-value
DESeq2
updated 3 months ago by
Michael Love
43k • written 4 months ago by
Erika
• 0
1
vote
2
replies
398
views
Differential expression on the transcript-level
DESeq2
updated 3 months ago by
swbarnes2
★ 1.4k • written 4 months ago by
泓朴
• 0
3
votes
13
replies
2.1k
views
Highly DE genes but small count difference within conditions
RNASeq
DESeq2
RNASeqData
written 13 months ago by
bioshot.com
• 0
4
votes
8
replies
1.9k
views
Should Xenium pseudobulk experiments be analysed like microarrays (limma) or like RNASeq (edgeR,Deseq2, or limma-voom)
Deseq2
edgeR
limma
xenium
Voom
4 months ago
richardallenfriedmanbrooklyn
▴ 30
7
votes
9
replies
5.6k
views
competitive enrichment test yields too few significant results, self-contained too many
limma
DESeq2
fry
edgeR
4 months ago
bbao
▴ 10
0
votes
1
reply
515
views
discrepancy in IDs from file and tx2gene (IDs don't match)
tximport
DESeq2
updated 4 months ago by
James W. MacDonald
68k • written 4 months ago by
IUH
• 0
0
votes
2
replies
972
views
gene detection across experiments
DESeq2
Normalization
4 months ago
Mara
• 0
5
votes
11
replies
3.2k
views
parameters of filterByExpr
edgeR
DESeq2
filterByExpr
written 6 months ago by
caroline.zanchi
▴ 10
1
vote
5
replies
4.4k
views
Pre-filtering, adjusting independent filtering, or lfcthreshold() on DESeq2? Low counts and dropouts produce interesting volcano plots.
DESeq2
updated 4 months ago by
Michael Love
43k • written 5 months ago by
Alexander
• 0
1
vote
1
reply
2.2k
views
DESeq2 LRT: Testing Effects of Treatment1, Treatment2, and Their Interaction in a Four-Factor Design
DESeq2
multifactorialdesign
interaction
InteractionSet
updated 5 months ago by
Michael Love
43k • written 5 months ago by
Integrative
• 0
0
votes
2
replies
1.2k
views
6 groups to compare DESeq2 (Wald vs LRT)
DESeq2
updated 5 months ago by
Michael Love
43k • written 5 months ago by
Rocio
• 0
3
votes
2
replies
1.4k
views
Biological replicates consideration in DESeq2 design formula.
DESeq2
RNASeqData
RNASeq
written 5 months ago by
Christian
▴ 20
1
vote
2
replies
2.7k
views
Deseq2 paired sample in the design is considered as "batch"?
DESeq2
written 5 months ago by
corranna98
• 0
3
votes
1
reply
3.7k
views
DESeq2 empirical bayes: variance of the prior for log fold changes (LFC)
DESeq2
updated 5 months ago by
Michael Love
43k • written 5 months ago by
Chenghao
▴ 10
0
votes
1
reply
591
views
DESeq2 results
result
DESeq2
subsetting
updated 5 months ago by
ATpoint
★ 5.0k • written 5 months ago by
rajdeepboral00
• 0
0
votes
1
reply
416
views
Unclear DEseq2 replaceOutliers error message
DESeq2
updated 5 months ago by
Michael Love
43k • written 5 months ago by
Pak
• 0
0
votes
1
reply
568
views
Difference in DESeq2 output and tidybulk DESeq2 method
DifferentialExpression
DESeq2
tidybulk
RNASeq
updated 6 months ago by
Michael Love
43k • written 6 months ago by
s.malik
• 0
3
votes
2
replies
2.0k
views
Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)
DESeq2
6 months ago
dudutchy
▴ 10
2
votes
3
replies
1.5k
views
Differential gene expression analysis on haplotype-resolved diploid assembly
edgeR
DESeq2
haplotype
limma
6 months ago
Paulito
• 0
4
votes
4
replies
2.0k
views
Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatmap
DESeq2
ComplexHeatmap
6 months ago
caroline.zanchi
▴ 10
0
votes
1
reply
412
views
DESeq2 from phyloseq error
DESeq2
phyloseq
6 months ago
asafpr
• 0
3
votes
1
reply
633
views
DESeq2 Apeglm Coefficient Reordering / Log2FoldChange Comparison Change
DESeq2
apeglm
updated 6 months ago by
James W. MacDonald
68k • written 6 months ago by
sk
• 0
1
vote
5
replies
1.5k
views
Heatmap of a transformed deseq object with pheatmap
DESeq2
heatmaps
updated 6 months ago by
James W. MacDonald
68k • written 6 months ago by
caroline.zanchi
▴ 10
8
votes
3
replies
3.0k
views
DESeq2 class error: superclass "ExpData" not defined in the environment of the object's class
DESeq2
updated 5 months ago by
Michael Love
43k • written 6 months ago by
Cassia
▴ 40
2
votes
4
replies
1.8k
views
Filtering after DESeq
DESeq2
IHW
written 7 months ago by
caroline.zanchi
▴ 10
0
votes
4
replies
1.2k
views
DESEQ2 - Correctly altering log2foldchange when switching comparison direction (HELP GREATLY APPRECIATED)
DESeq2
6 months ago
sk
• 0
0
votes
6
replies
1.8k
views
Discrepancies in normalised count data vs unnormalised
DESeq2
6 months ago
AMgroup
• 0
0
votes
2
replies
692
views
Design formula for circadian time-course data for vst() function
DESeq2
6 months ago
Vishnu
• 0
0
votes
2
replies
823
views
Analyzing TnSeq data with DESeq2
DESeq2
written 7 months ago by
newfunland
• 0
0
votes
1
reply
1.2k
views
How do I set up my DESeq analysis when I know a few vehicle control samples provide background effects we don't want to see in any of the subsequent …
DESeq2
RUVSeq
updated 7 months ago by
Michael Love
43k • written 8 months ago by
Simran
• 0
0
votes
2
replies
718
views
Differing results with DESeq2
DESeq2
updated 7 months ago by
JKim
• 0 • written 7 months ago by
hampsdiv
• 0
0
votes
2
replies
593
views
RNA Seq using Lrt
DESeq2
7 months ago
Rob
• 0
0
votes
3
replies
1.0k
views
Log2foldchange strange behavior
DESeq2
updated 7 months ago by
ATpoint
★ 5.0k • written 7 months ago by
RambakKulit
• 0
4,839 results • Page
1 of 97
Recent ...
Replies
Comment: Large logFC but somewhat high FDR
by
Gordon Smyth
53k
I don't know what `tp1` is. The relevant histogram would be: ``` hist(fit2$p.value[,"KO_vs_WT"]) ```
Answer: p.adjust BH Question
by
Gordon Smyth
53k
Duplicate of https://support.bioconductor.org/p/41077/
Answer: Large logFC but somewhat high FDR
by
Gordon Smyth
53k
Glad you're getting good use out of the package. The results that you show seem pretty much as one would expect, with nothing surprising. …
Comment: After running samtools, the featureCounts command crashed.
by
MarcHintz99
• 0
Thanks for shairng https://subread.sourceforge.net/
Comment: Senior Teaching Fellow (MSc Computational Biomedicine)
by
eja.ger.m
• 0
Opportunities like this remind me how digital learning is evolving, much like modern mobile games. With programmes becoming fully online an…
Votes
Comment: upstream git branches of bioc-release
A: p.adjust BH generates duplicate values
Answer: gene Set with high AUC score but no cells assigned to cell type
Answer: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
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