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DESEQ2
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15
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DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 58 minutes ago by
marka
• 0 • written 1 hour ago by
kcarey
• 0
1
vote
3
replies
66
views
Different Shrunk Log2FC according with reference
DESeq2
updated 6 hours ago by
Michael Love
41k • written 10 hours ago by
andrebolerbarros
▴ 20
0
votes
1
reply
41
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
updated 1 hour ago by
swbarnes2
★ 1.3k • written 10 hours ago by
winwater0928
• 0
2
votes
1
reply
139
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 16 hours ago by
Michael Love
41k • written 1 day ago by
i.sudbery
▴ 40
0
votes
4
replies
95
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 1 hour ago by
swbarnes2
★ 1.3k • written 1 day ago by
Aaliya
• 0
3
votes
3
replies
143
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 1 day ago by
Michael Love
41k • written 2 days ago by
WardDeb
• 0
0
votes
1
reply
87
views
rlog transformation
DESeq2
updated 6 days ago by
Michael Love
41k • written 6 days ago by
ishij9717
• 0
0
votes
1
reply
84
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 6 days ago by
Michael Love
41k • written 6 days ago by
09191919
• 0
0
votes
1
reply
94
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
updated 6 days ago by
Michael Love
41k • written 7 days ago by
ussarizona
• 0
0
votes
1
reply
108
views
covariate with negative and positive values
DESeq2
updated 6 days ago by
Michael Love
41k • written 7 days ago by
Brynn
• 0
0
votes
1
reply
111
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 6 days ago by
ATpoint
★ 4.0k • written 7 days ago by
quanah.hudson
• 0
0
votes
4
replies
191
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
7 days ago • updated 4 days ago
lonn
• 0
0
votes
3
replies
172
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 8 days ago by
Michael Love
41k • written 9 days ago by
andrebolerbarros
▴ 20
1
vote
2
replies
215
views
How to retrieve detailed regression results from deseq2
DESeq2
13 days ago • updated 4 days ago
Weiqian
▴ 10
0
votes
4
replies
228
views
DEG with low counts
DESeq2
updated 5 days ago by
Michael Love
41k • written 9 days ago by
Rajat
• 0
0
votes
1
reply
109
views
Deseq2 Rlog transformation
DESeq2
updated 9 days ago by
ATpoint
★ 4.0k • written 10 days ago by
Sahar
• 0
1
vote
2
replies
163
views
Design Matrix within group comparison more than two groups
DESeq2
12 days ago • updated 11 days ago
hemantcnaik
• 0
0
votes
1
reply
115
views
Bioinformatics student
Des
DESeq2
updated 12 days ago by
hemantcnaik
• 0 • written 12 days ago by
Sahar
• 0
0
votes
1
reply
154
views
DESeq2 gives an error and R crashes
DESeq2
13 days ago • updated 12 days ago
Shefali
• 0
0
votes
2
replies
191
views
Interaction term vs grouping variable design considerations
DESeq2
DifferentialExpression
updated 14 days ago by
Michael Love
41k • written 19 days ago by
nhaus
▴ 30
0
votes
1
reply
137
views
IgG control in RIP-seq with Deseq2
DESeq2
RIP-seq
updated 14 days ago by
Michael Love
41k • written 15 days ago by
Adelaide
• 0
0
votes
2
replies
219
views
Regressing out batch effects
DESeq2
updated 14 days ago by
Michael Love
41k • written 20 days ago by
kys91240
• 0
0
votes
2
replies
142
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2
timecourse
DifferentialExpression
updated 19 days ago by
James W. MacDonald
65k • written 19 days ago by
joshua.mannheimer
• 0
1
vote
1
reply
152
views
DESeq2 - Missing values in count matrix
DESeq2
updated 20 days ago by
James W. MacDonald
65k • written 20 days ago by
Hong Thu
• 0
1
vote
6
replies
400
views
DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2
Normalization
updated 20 days ago by
Michael Love
41k • written 21 days ago by
RL
• 0
1
vote
1
reply
135
views
DESeq2 , filter and theta arguments in resutlts()
DESeq2
22 days ago • updated 21 days ago
Layal
• 0
0
votes
2
replies
149
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2
sva
22 days ago • updated 21 days ago
michelafrancesconi8
• 0
0
votes
4
replies
229
views
Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 22 days ago by
Michael Love
41k • written 22 days ago by
Aidan
• 0
0
votes
1
reply
141
views
New genes that did not exist in dds object suddenly showed up after degPatterns
DESeq2
updated 26 days ago by
Michael Love
41k • written 26 days ago by
Mikushi
• 0
2
votes
3
replies
322
views
PCA of different bacterial species
DESeq2
updated 28 days ago by
Michael Love
41k • written 28 days ago by
Laura
▴ 10
0
votes
1
reply
157
views
collapseReplicates dimension error
DESeq2
Dese
updated 29 days ago by
Michael Love
41k • written 4 weeks ago by
Léa
• 0
3
votes
2
replies
196
views
How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2
Transcriptomics
4 weeks ago
Anita
▴ 10
1
vote
2
replies
211
views
DESeq2 "Contrast" option
DESeq2
contrast
DifferentialExpression
4 weeks ago • updated 28 days ago
Chanderkant Chaudhary
• 0
0
votes
2
replies
210
views
Filtering and Reference Level for DESeq2
DESeq2
GeneFiltering
RNAseq
4 weeks ago
kcarey
• 0
2
votes
3
replies
283
views
DESeq2 - Plot Nr. Genes vs Variance explained in PCA
DESeq2
updated 4 weeks ago by
Michael Love
41k • written 5 weeks ago by
andrebolerbarros
▴ 20
0
votes
3
replies
243
views
Help with Complex DESeq2 Design
DESeq2
updated 5 weeks ago by
ATpoint
★ 4.0k • written 5 weeks ago by
kelsey.beavers
• 0
1
vote
1
reply
163
views
Need help with creating and plotting temporal clustering analysis of DEGs
DESeq2
ctsGE
updated 5 weeks ago by
Michael Love
41k • written 5 weeks ago by
Emma
• 0
0
votes
1
reply
132
views
Help with DESeqDataSetFromHTSeqCount
DESeq2
RSeqAn
updated 5 weeks ago by
Michael Love
41k • written 5 weeks ago by
rahaf.nazzal9
• 0
0
votes
1
reply
163
views
lfcShrink error: the line search routine failed
apeglm
DESeq2
updated 5 weeks ago by
Michael Love
41k • written 5 weeks ago by
Yuqin
• 0
2
votes
2
replies
206
views
With DESeq2 "Not full rank" Error with design
DESeq2
DEs
5 weeks ago
feather-W
• 0
0
votes
2
replies
299
views
Missing Band on Volcano Plot from DESeq2
DESeq2
Visualization
DifferentialExpression
updated 5 weeks ago by
Michael Love
41k • written 6 weeks ago by
gglatzer
• 0
0
votes
4
replies
405
views
DESeq2: subtract effect of an isotope control before comparing to a baseline sample?
DESeq2
updated 5 weeks ago by
Michael Love
41k • written 5 weeks ago by
Jad
• 0
0
votes
7
replies
406
views
DESeq2 filtering vs edgeR filtering
DESeq2
6 weeks ago • updated 29 days ago
fr8712ca-s
• 0
0
votes
2
replies
236
views
RNA sequencing raw counts gene filtering
DESeq2
limma
RNAseq
5 weeks ago
kcarey
• 0
1
vote
1
reply
205
views
i'm not getting any differentially expressed genes.
DESeq2
updated 6 weeks ago by
ATpoint
★ 4.0k • written 6 weeks ago by
Marilyn
• 0
2
votes
1
reply
233
views
Creating data matrix in Deseq2 from tximport data invalid class SummarizedExperiment object
DESeq2
tximport
updated 6 weeks ago by
ATpoint
★ 4.0k • written 6 weeks ago by
hemantcnaik
• 0
1
vote
1
reply
195
views
Perform PCA for sample clustering using DESeq2
DESeq2
updated 6 weeks ago by
ATpoint
★ 4.0k • written 6 weeks ago by
synat.keam
• 0
0
votes
3
replies
358
views
Cross-species analysis - how to compute the mid parent value?
DESeq2
limma
edgeR
DifferentialExpression
written 11 weeks ago by
pl23
• 0
0
votes
2
replies
320
views
DESeq2: Comparing A Knockout to a Strain
DESeq2
6 weeks ago
Viktor Thiel
• 0
0
votes
1
reply
206
views
DESeq2 for pseudobulk analysis of scCITE-seq
DESeq2
scCITE-seq
updated 6 weeks ago by
ATpoint
★ 4.0k • written 6 weeks ago by
daiane.hemerichbrennan
• 0
50 results • Page
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Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
by
marka
• 0
As a single dad in Australia, finding time to unwind is rare, but [Lincoln Casino][1] has become my go-to escape after putting the kids to …
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
swbarnes2
★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error
by
James W. MacDonald
65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Comment: get BM error
by
Fara
• 0
Thank you for your response. The primary reason for translating Ensembl IDs into Entrez Gene IDs is to perform KEGG (Kyoto Encyclopedia of…
Votes
Answer: get BM error
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
Comment: Different Shrunk Log2FC according with reference
Reproducibility issue with scran together with lapply and BiocParallel
C: SGSeq: moving toward diffex from SGSeq analysis
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