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DESeq2
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2
votes
3
replies
164
views
Too many significant genes when integrating gtex and tcga
RNA-seq
DESeq2
updated 1 day ago by
ATpoint
★ 4.1k • written 3 days ago by
Reza
• 0
1
vote
1
reply
96
views
Handling multiple differential expression comparisons
DESeq2
updated 1 day ago by
Michael Love
41k • written 3 days ago by
Zainab
▴ 10
0
votes
6
replies
206
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
0
votes
2
replies
102
views
DESeq2 v1.35.0
DESeq2
updated 4 days ago by
Michael Love
41k • written 4 days ago by
Espresso
• 0
0
votes
2
replies
135
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
4 days ago • updated 3 days ago
kcarey
• 0
0
votes
3
replies
135
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 4 days ago by
ATpoint
★ 4.1k • written 4 days ago by
james.zhang20
• 0
0
votes
1
reply
139
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
250
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
108
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 6 days ago by
Michael Love
41k • written 6 days ago by
marcusn
• 0
0
votes
1
reply
109
views
putting my own expression data in deseq2
DESeq2
updated 6 days ago by
ATpoint
★ 4.1k • written 6 days ago by
Dev
• 0
0
votes
2
replies
122
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
6 days ago • updated 3 days ago
Aurora
• 0
0
votes
1
reply
103
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 6 days ago by
Michael Love
41k • written 6 days ago by
Agung
• 0
3
votes
3
replies
233
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2
contrasts
updated 7 days ago by
ATpoint
★ 4.1k • written 7 days ago by
bioinf
▴ 10
1
vote
3
replies
220
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
updated 10 days ago by
Michael Love
41k • written 10 days ago by
JalapenoCornbread
• 0
2
votes
9
replies
392
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 11 days ago by
Alexandre
• 0
0
votes
2
replies
210
views
PCA plot suggestions
DESeq2
PCAtools
updated 10 days ago by
Michael Love
41k • written 11 days ago by
Aaliya
• 0
0
votes
1
reply
155
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 11 days ago by
Michael Love
41k • written 12 days ago by
kcarey
• 0
1
vote
3
replies
215
views
Different Shrunk Log2FC according with reference
DESeq2
updated 12 days ago by
Michael Love
41k • written 12 days ago by
andrebolerbarros
▴ 20
1
vote
4
replies
326
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
12 days ago • updated 10 days ago
winwater0928
• 0
3
votes
1
reply
315
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 13 days ago by
i.sudbery
▴ 40
0
votes
8
replies
347
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 11 days ago by
swbarnes2
★ 1.3k • written 13 days ago by
Aaliya
• 0
3
votes
3
replies
228
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 13 days ago by
Michael Love
41k • written 14 days ago by
WardDeb
• 0
0
votes
1
reply
137
views
rlog transformation
DESeq2
updated 18 days ago by
Michael Love
41k • written 18 days ago by
ishij9717
• 0
0
votes
1
reply
113
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 18 days ago by
Michael Love
41k • written 18 days ago by
09191919
• 0
0
votes
4
replies
238
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
19 days ago • updated 16 days ago
lonn
• 0
1
vote
2
replies
713
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
19 days ago • updated 10 days ago
ussarizona
▴ 10
0
votes
1
reply
149
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 18 days ago by
ATpoint
★ 4.1k • written 19 days ago by
quanah.hudson
• 0
0
votes
1
reply
134
views
covariate with negative and positive values
DESeq2
updated 18 days ago by
Michael Love
41k • written 19 days ago by
Brynn
• 0
0
votes
3
replies
206
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 20 days ago by
Michael Love
41k • written 21 days ago by
andrebolerbarros
▴ 20
0
votes
4
replies
270
views
DEG with low counts
DESeq2
updated 17 days ago by
Michael Love
41k • written 21 days ago by
Rajat
• 0
0
votes
1
reply
132
views
Deseq2 Rlog transformation
DESeq2
updated 21 days ago by
ATpoint
★ 4.1k • written 22 days ago by
Sahar
• 0
1
vote
2
replies
197
views
Design Matrix within group comparison more than two groups
DESeq2
24 days ago • updated 23 days ago
hemantcnaik
• 0
0
votes
1
reply
133
views
Bioinformatics student
Des
DESeq2
updated 24 days ago by
hemantcnaik
• 0 • written 24 days ago by
Sahar
• 0
0
votes
1
reply
177
views
DESeq2 gives an error and R crashes
DESeq2
25 days ago • updated 24 days ago
Shefali
• 0
1
vote
2
replies
245
views
How to retrieve detailed regression results from deseq2
DESeq2
25 days ago • updated 17 days ago
Weiqian
▴ 10
0
votes
1
reply
165
views
IgG control in RIP-seq with Deseq2
DESeq2
RIP-seq
updated 26 days ago by
Michael Love
41k • written 27 days ago by
Adelaide
• 0
0
votes
2
replies
172
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
0
votes
2
replies
222
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
2
replies
249
views
Regressing out batch effects
DESeq2
updated 26 days ago by
Michael Love
41k • written 4 weeks ago by
kys91240
• 0
1
vote
1
reply
169
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
435
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
157
views
DESeq2 , filter and theta arguments in resutlts()
DESeq2
4 weeks ago
Layal
• 0
0
votes
2
replies
174
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2
sva
4 weeks ago
michelafrancesconi8
• 0
0
votes
4
replies
264
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
162
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
354
views
PCA of different bacterial species
DESeq2
updated 5 weeks ago by
Michael Love
41k • written 5 weeks ago by
Laura
▴ 10
3
votes
2
replies
218
views
How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2
Transcriptomics
6 weeks ago
Anita
▴ 10
0
votes
1
reply
171
views
collapseReplicates dimension error
DESeq2
Dese
updated 5 weeks ago by
Michael Love
41k • written 6 weeks ago by
Léa
• 0
1
vote
2
replies
238
views
DESeq2 "Contrast" option
DESeq2
contrast
DifferentialExpression
6 weeks ago • updated 5 weeks ago
Chanderkant Chaudhary
• 0
0
votes
2
replies
232
views
Filtering and Reference Level for DESeq2
DESeq2
GeneFiltering
RNAseq
6 weeks ago
kcarey
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
I am working with mouse data. I don't know how to do this, but I will go through it. Can you help me with the second question? how do we …
Comment: [Mfuzz] Error in cmeans(exprs(eset)
by
Caio
• 0
You can have this problem (lines with variance equal to zero) when you run experiments and obtain the data with more samples and use fewer …
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
41k
The left plot indicates you should use genome segmentation. It is what is called "nonstationary" meaning it looks like there are distinct r…
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
gene_bioconductor
▴ 10
Thanks for your thoughtful and detailed comment, Gordon
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
I looked into the genomic distributions. Please see the screenshot attatched ![ distrubution for female loci, boot1 and boot2][1] how do …
Votes
Answer: Method to find pathways different between 2 groups
Answer: Method to find pathways different between 2 groups
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: Method to find pathways different between 2 groups
Comment: Trying to use enrichGO
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