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DESeq2
•
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0
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replies
15
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
11 hours ago
JalapenoCornbread
• 0
2
votes
9
replies
225
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 11 hours ago by
James W. MacDonald
65k • written 19 hours ago by
Alexandre
• 0
0
votes
1
reply
57
views
PCA plot suggestions
DESeq2
PCAtools
updated 17 hours ago by
JKim
• 0 • written 1 day ago by
Aaliya
• 0
0
votes
1
reply
75
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 1 day ago by
Michael Love
41k • written 1 day ago by
kcarey
• 0
1
vote
3
replies
101
views
Different Shrunk Log2FC according with reference
DESeq2
updated 1 day ago by
Michael Love
41k • written 1 day ago by
andrebolerbarros
▴ 20
1
vote
4
replies
136
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
1 day ago • updated 1 hour ago
winwater0928
• 0
3
votes
1
reply
213
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 2 days ago by
Michael Love
41k • written 2 days ago by
i.sudbery
▴ 40
0
votes
8
replies
235
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 1 day ago by
swbarnes2
★ 1.3k • written 2 days ago by
Aaliya
• 0
3
votes
3
replies
169
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 2 days ago by
Michael Love
41k • written 3 days ago by
WardDeb
• 0
0
votes
1
reply
90
views
rlog transformation
DESeq2
updated 7 days ago by
Michael Love
41k • written 7 days ago by
ishij9717
• 0
0
votes
1
reply
90
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 7 days ago by
Michael Love
41k • written 7 days ago by
09191919
• 0
0
votes
1
reply
99
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
updated 7 days ago by
Michael Love
41k • written 8 days ago by
ussarizona
• 0
0
votes
1
reply
115
views
covariate with negative and positive values
DESeq2
updated 7 days ago by
Michael Love
41k • written 9 days ago by
Brynn
• 0
0
votes
1
reply
118
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 7 days ago by
ATpoint
★ 4.0k • written 8 days ago by
quanah.hudson
• 0
0
votes
4
replies
199
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
8 days ago • updated 6 days ago
lonn
• 0
0
votes
3
replies
176
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 9 days ago by
Michael Love
41k • written 10 days ago by
andrebolerbarros
▴ 20
1
vote
2
replies
220
views
How to retrieve detailed regression results from deseq2
DESeq2
15 days ago • updated 6 days ago
Weiqian
▴ 10
0
votes
4
replies
230
views
DEG with low counts
DESeq2
updated 6 days ago by
Michael Love
41k • written 11 days ago by
Rajat
• 0
0
votes
1
reply
112
views
Deseq2 Rlog transformation
DESeq2
updated 10 days ago by
ATpoint
★ 4.0k • written 12 days ago by
Sahar
• 0
1
vote
2
replies
169
views
Design Matrix within group comparison more than two groups
DESeq2
13 days ago • updated 12 days ago
hemantcnaik
• 0
0
votes
1
reply
118
views
Bioinformatics student
Des
DESeq2
updated 13 days ago by
hemantcnaik
• 0 • written 13 days ago by
Sahar
• 0
0
votes
1
reply
158
views
DESeq2 gives an error and R crashes
DESeq2
15 days ago • updated 14 days ago
Shefali
• 0
0
votes
2
replies
196
views
Interaction term vs grouping variable design considerations
DESeq2
DifferentialExpression
updated 16 days ago by
Michael Love
41k • written 20 days ago by
nhaus
▴ 30
0
votes
1
reply
143
views
IgG control in RIP-seq with Deseq2
DESeq2
RIP-seq
updated 16 days ago by
Michael Love
41k • written 16 days ago by
Adelaide
• 0
0
votes
2
replies
225
views
Regressing out batch effects
DESeq2
updated 16 days ago by
Michael Love
41k • written 21 days ago by
kys91240
• 0
0
votes
2
replies
147
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2
timecourse
DifferentialExpression
updated 20 days ago by
James W. MacDonald
65k • written 20 days ago by
joshua.mannheimer
• 0
1
vote
1
reply
155
views
DESeq2 - Missing values in count matrix
DESeq2
updated 21 days ago by
James W. MacDonald
65k • written 21 days ago by
Hong Thu
• 0
1
vote
6
replies
407
views
DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2
Normalization
updated 22 days ago by
Michael Love
41k • written 22 days ago by
RL
• 0
1
vote
1
reply
139
views
DESeq2 , filter and theta arguments in resutlts()
DESeq2
23 days ago • updated 22 days ago
Layal
• 0
0
votes
2
replies
154
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2
sva
23 days ago • updated 22 days ago
michelafrancesconi8
• 0
0
votes
4
replies
234
views
Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 23 days ago by
Michael Love
41k • written 24 days ago by
Aidan
• 0
0
votes
1
reply
144
views
New genes that did not exist in dds object suddenly showed up after degPatterns
DESeq2
updated 28 days ago by
Michael Love
41k • written 28 days ago by
Mikushi
• 0
2
votes
3
replies
329
views
PCA of different bacterial species
DESeq2
updated 29 days ago by
Michael Love
41k • written 4 weeks ago by
Laura
▴ 10
0
votes
1
reply
161
views
collapseReplicates dimension error
DESeq2
Dese
updated 4 weeks ago by
Michael Love
41k • written 4 weeks ago by
Léa
• 0
3
votes
2
replies
202
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
216
views
DESeq2 "Contrast" option
DESeq2
contrast
DifferentialExpression
5 weeks ago • updated 29 days ago
Chanderkant Chaudhary
• 0
0
votes
2
replies
213
views
Filtering and Reference Level for DESeq2
DESeq2
GeneFiltering
RNAseq
5 weeks ago
kcarey
• 0
2
votes
3
replies
287
views
DESeq2 - Plot Nr. Genes vs Variance explained in PCA
DESeq2
updated 5 weeks ago by
Michael Love
41k • written 5 weeks ago by
andrebolerbarros
▴ 20
0
votes
3
replies
246
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
166
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
134
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
167
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
209
views
With DESeq2 "Not full rank" Error with design
DESeq2
DEs
5 weeks ago
feather-W
• 0
0
votes
2
replies
305
views
Missing Band on Volcano Plot from DESeq2
DESeq2
Visualization
DifferentialExpression
updated 6 weeks ago by
Michael Love
41k • written 6 weeks ago by
gglatzer
• 0
0
votes
4
replies
407
views
DESeq2: subtract effect of an isotope control before comparing to a baseline sample?
DESeq2
updated 6 weeks ago by
Michael Love
41k • written 6 weeks ago by
Jad
• 0
0
votes
7
replies
411
views
DESeq2 filtering vs edgeR filtering
DESeq2
6 weeks ago • updated 4 weeks ago
fr8712ca-s
• 0
0
votes
2
replies
243
views
RNA sequencing raw counts gene filtering
DESeq2
limma
RNAseq
6 weeks ago
kcarey
• 0
1
vote
1
reply
209
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
236
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
197
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
50 results • Page
1 of 1
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Replies
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
winwater0928
• 0
Thank you for your comment! I'll review my code from top to bottom.
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
James W. MacDonald
65k
So basically you are using HTML markup to set your subscripts and whatnot, and then `element_markdown` does the rest.
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
James W. MacDonald
65k
Oh snap. Foiled again. Here it is with spaces & ge ; and & lt ;
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
James W. MacDonald
65k
Oh LOL. My markdown got edited by the markdown editor! What is between the p and 50 in the first case is the HTML for greater than or equal…
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
James W. MacDonald
65k
Ah, good point. You could instead try ``` > library(ggtext) > keyvals.shape = c(rep(3,10), rep(2,8)) > names(keyvals.shape) = ifelse(keyva…
Votes
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Answer: Cross-species analysis - how to compute the mid parent value?
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
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