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DESEQ2
•
reset
0
votes
0
replies
4
views
Couldn't connect to server while using "pathways"
DESeq2
10 minutes ago
fduguchunhui
• 0
1
vote
1
reply
71
views
Handling multiple differential expression comparisons
DESeq2
updated 19 hours ago by
Michael Love
41k • written 2 days ago by
Zainab
▴ 10
0
votes
6
replies
191
views
Once again a "Model matrix not full rank"
DESeq2
design
coldata
updated 2 days ago by
swbarnes2
★ 1.3k • written 3 days ago by
arfranco
▴ 130
2
votes
3
replies
156
views
Too many significant genes when integrating gtex and tcga
RNA-seq
DESeq2
updated 21 hours ago by
ATpoint
★ 4.1k • written 2 days ago by
Reza
• 0
0
votes
2
replies
94
views
DESeq2 v1.35.0
DESeq2
updated 3 days ago by
Michael Love
41k • written 3 days ago by
Espresso
• 0
0
votes
2
replies
127
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
4 days ago • updated 3 days ago
kcarey
• 0
0
votes
3
replies
131
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 3 days ago by
ATpoint
★ 4.1k • written 4 days ago by
james.zhang20
• 0
0
votes
1
reply
134
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 4 days ago by
ATpoint
★ 4.1k • written 4 days ago by
angelathuynh5
• 0
0
votes
3
replies
244
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 4 days ago by
Michael Love
41k • written 5 days ago by
HAK
• 0
1
vote
1
reply
105
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 5 days ago by
Michael Love
41k • written 5 days ago by
marcusn
• 0
0
votes
2
replies
119
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
5 days ago • updated 2 days ago
Aurora
• 0
0
votes
1
reply
100
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 5 days ago by
Michael Love
41k • written 6 days ago by
Agung
• 0
0
votes
1
reply
102
views
putting my own expression data in deseq2
DESeq2
updated 5 days ago by
ATpoint
★ 4.1k • written 5 days ago by
Dev
• 0
3
votes
3
replies
225
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2
contrasts
updated 6 days ago by
ATpoint
★ 4.1k • written 7 days ago by
bioinf
▴ 10
0
votes
2
replies
205
views
PCA plot suggestions
DESeq2
PCAtools
updated 9 days ago by
Michael Love
41k • written 11 days ago by
Aaliya
• 0
1
vote
3
replies
214
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
updated 9 days ago by
Michael Love
41k • written 10 days ago by
JalapenoCornbread
• 0
2
votes
9
replies
388
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 10 days ago by
James W. MacDonald
65k • written 10 days ago by
Alexandre
• 0
0
votes
1
reply
153
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 11 days ago by
Michael Love
41k • written 11 days ago by
kcarey
• 0
1
vote
3
replies
211
views
Different Shrunk Log2FC according with reference
DESeq2
updated 11 days ago by
Michael Love
41k • written 11 days ago by
andrebolerbarros
▴ 20
1
vote
4
replies
325
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
11 days ago • updated 10 days ago
winwater0928
• 0
3
votes
1
reply
310
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 12 days ago by
Michael Love
41k • written 12 days ago by
i.sudbery
▴ 40
0
votes
8
replies
345
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 11 days ago by
swbarnes2
★ 1.3k • written 12 days ago by
Aaliya
• 0
3
votes
3
replies
227
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 12 days ago by
Michael Love
41k • written 13 days ago by
WardDeb
• 0
0
votes
1
reply
136
views
rlog transformation
DESeq2
updated 17 days ago by
Michael Love
41k • written 17 days ago by
ishij9717
• 0
0
votes
1
reply
112
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 17 days ago by
Michael Love
41k • written 17 days ago by
09191919
• 0
1
vote
2
replies
710
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
18 days ago • updated 9 days ago
ussarizona
▴ 10
0
votes
1
reply
133
views
covariate with negative and positive values
DESeq2
updated 17 days ago by
Michael Love
41k • written 19 days ago by
Brynn
• 0
0
votes
1
reply
148
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 17 days ago by
ATpoint
★ 4.1k • written 18 days ago by
quanah.hudson
• 0
0
votes
4
replies
236
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
18 days ago • updated 16 days ago
lonn
• 0
0
votes
3
replies
205
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 19 days ago by
Michael Love
41k • written 20 days ago by
andrebolerbarros
▴ 20
1
vote
2
replies
243
views
How to retrieve detailed regression results from deseq2
DESeq2
25 days ago • updated 16 days ago
Weiqian
▴ 10
0
votes
4
replies
269
views
DEG with low counts
DESeq2
updated 16 days ago by
Michael Love
41k • written 21 days ago by
Rajat
• 0
0
votes
1
reply
130
views
Deseq2 Rlog transformation
DESeq2
updated 20 days ago by
ATpoint
★ 4.1k • written 22 days ago by
Sahar
• 0
1
vote
2
replies
193
views
Design Matrix within group comparison more than two groups
DESeq2
23 days ago • updated 22 days ago
hemantcnaik
• 0
0
votes
1
reply
132
views
Bioinformatics student
Des
DESeq2
updated 23 days ago by
hemantcnaik
• 0 • written 23 days ago by
Sahar
• 0
0
votes
1
reply
175
views
DESeq2 gives an error and R crashes
DESeq2
25 days ago • updated 24 days ago
Shefali
• 0
0
votes
2
replies
220
views
Interaction term vs grouping variable design considerations
DESeq2
DifferentialExpression
updated 26 days ago by
Michael Love
41k • written 4 weeks ago by
nhaus
▴ 30
0
votes
1
reply
162
views
IgG control in RIP-seq with Deseq2
DESeq2
RIP-seq
updated 26 days ago by
Michael Love
41k • written 26 days ago by
Adelaide
• 0
0
votes
2
replies
247
views
Regressing out batch effects
DESeq2
updated 26 days ago by
Michael Love
41k • written 4 weeks ago by
kys91240
• 0
0
votes
2
replies
171
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2
timecourse
DifferentialExpression
updated 4 weeks ago by
James W. MacDonald
65k • written 4 weeks ago by
joshua.mannheimer
• 0
1
vote
1
reply
167
views
DESeq2 - Missing values in count matrix
DESeq2
updated 4 weeks ago by
James W. MacDonald
65k • written 4 weeks ago by
Hong Thu
• 0
1
vote
6
replies
433
views
DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2
Normalization
updated 4 weeks ago by
Michael Love
41k • written 4 weeks ago by
RL
• 0
1
vote
1
reply
156
views
DESeq2 , filter and theta arguments in resutlts()
DESeq2
4 weeks ago
Layal
• 0
0
votes
2
replies
173
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2
sva
4 weeks ago
michelafrancesconi8
• 0
0
votes
4
replies
262
views
Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 4 weeks ago by
Michael Love
41k • written 4 weeks ago by
Aidan
• 0
0
votes
1
reply
160
views
New genes that did not exist in dds object suddenly showed up after degPatterns
DESeq2
updated 5 weeks ago by
Michael Love
41k • written 5 weeks ago by
Mikushi
• 0
2
votes
3
replies
351
views
PCA of different bacterial species
DESeq2
updated 5 weeks ago by
Michael Love
41k • written 5 weeks ago by
Laura
▴ 10
0
votes
1
reply
170
views
collapseReplicates dimension error
DESeq2
Dese
updated 5 weeks ago by
Michael Love
41k • written 6 weeks ago by
Léa
• 0
3
votes
2
replies
216
views
How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2
Transcriptomics
5 weeks ago
Anita
▴ 10
1
vote
2
replies
235
views
DESeq2 "Contrast" option
DESeq2
contrast
DifferentialExpression
6 weeks ago • updated 5 weeks ago
Chanderkant Chaudhary
• 0
50 results • Page
1 of 1
Recent ...
Replies
Answer: Method to find pathways different between 2 groups
by
Gordon Smyth
50k
> When I search camera limma on pubmed, I found 2 papers I am unclear what point you are trying to make. limma's camera method has been fo…
Comment: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
limma most certainly is available. It installs in R 4.4.0 and Bioc 3.19 for all platforms without any issues. It has not had any period of …
Comment: package goseq seems to be not available on the latest version of R
by
Patrycja
▴ 20
limma package also isn't available.Is there any information when these packages will be available?
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
41k
Check the number of bootstrapped data per chromosome compared to the original, and then you can also look at its distribution. For this it'…
Comment: DNAString: Standard checksum function?
by
Henrik Bengtsson
★ 2.4k
For completeness: SEGUID v2 (https://www.seguid.org/), implemented in CRAN package **[seguid](https://cran.r-project.org/package=seguid)*…
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Handling multiple differential expression comparisons
Answer: fgsea significant result
Answer: fgsea significant result
package goseq seems to be not available on the latest version of R
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