Showing : DEseq2 • reset
0
votes
0
replies
11
views
rlog transformation
DESeq2
1 hour ago ishij9717 • 0
0
votes
0
replies
8
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
1 hour ago 09191919 • 0
0
votes
0
replies
22
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
21 hours ago lonn • 0
0
votes
0
replies
28
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
21 hours ago • updated 19 hours ago ussarizona • 0
0
votes
0
replies
34
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
22 hours ago quanah.hudson • 0
0
votes
0
replies
43
views
covariate with negative and positive values
DESeq2
1 day ago Brynn • 0
0
votes
3
replies
128
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 1 day ago by 41k • written 2 days ago by ▴ 20
1
vote
1
reply
154
views
How to retrieve detailed regression results from deseq2
DESeq2
updated 2 days ago by 41k • written 7 days ago by ▴ 10
0
votes
3
replies
159
views
DEG with low counts
DESeq2
3 days ago • updated 1 day ago Rajat • 0
0
votes
1
reply
86
views
Deseq2 Rlog transformation
DESeq2
updated 3 days ago by ★ 4.0k • written 4 days ago by • 0
1
vote
2
replies
146
views
Design Matrix within group comparison more than two groups
DESeq2
5 days ago • updated 4 days ago hemantcnaik • 0
0
votes
1
reply
100
views
Bioinformatics student
Des DESeq2
updated 5 days ago by • 0 • written 5 days ago by • 0
0
votes
1
reply
140
views
DESeq2 gives an error and R crashes
DESeq2
7 days ago • updated 6 days ago Shefali • 0
0
votes
2
replies
177
views
Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 8 days ago by 41k • written 12 days ago by ▴ 30
0
votes
1
reply
122
views
IgG control in RIP-seq with Deseq2
DESeq2 RIP-seq
updated 8 days ago by 41k • written 8 days ago by • 0
0
votes
2
replies
210
views
Regressing out batch effects
DESeq2
updated 8 days ago by 41k • written 13 days ago by • 0
0
votes
2
replies
128
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 12 days ago by 65k • written 12 days ago by • 0
1
vote
1
reply
143
views
DESeq2 - Missing values in count matrix
DESeq2
updated 13 days ago by 65k • written 13 days ago by • 0
1
vote
6
replies
388
views
DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2 Normalization
updated 14 days ago by 41k • written 14 days ago by • 0
1
vote
1
reply
126
views
DESeq2 , filter and theta arguments in resutlts()
DESeq2
15 days ago Layal • 0
0
votes
2
replies
139
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2 sva
15 days ago michelafrancesconi8 • 0
0
votes
4
replies
210
views
Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 15 days ago by 41k • written 16 days ago by • 0
0
votes
1
reply
130
views
New genes that did not exist in dds object suddenly showed up after degPatterns
DESeq2
updated 20 days ago by 41k • written 20 days ago by • 0
2
votes
3
replies
309
views
PCA of different bacterial species
DESeq2
updated 21 days ago by 41k • written 22 days ago by ▴ 10
0
votes
1
reply
146
views
collapseReplicates dimension error
DESeq2 Dese
updated 23 days ago by 41k • written 26 days ago by • 0
3
votes
2
replies
186
views
How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2 Transcriptomics
23 days ago Anita ▴ 10
1
vote
2
replies
195
views
DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
27 days ago • updated 21 days ago Chanderkant Chaudhary • 0
0
votes
2
replies
195
views
Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
28 days ago • updated 27 days ago kcarey • 0
2
votes
3
replies
267
views
DESeq2 - Plot Nr. Genes vs Variance explained in PCA
DESeq2
updated 28 days ago by 41k • written 4 weeks ago by ▴ 20
0
votes
3
replies
223
views
Help with Complex DESeq2 Design
DESeq2
updated 29 days ago by ★ 4.0k • written 4 weeks ago by • 0
1
vote
1
reply
154
views
Need help with creating and plotting temporal clustering analysis of DEGs
DESeq2 ctsGE
updated 4 weeks ago by 41k • written 4 weeks ago by • 0
0
votes
1
reply
126
views
Help with DESeqDataSetFromHTSeqCount
DESeq2 RSeqAn
updated 4 weeks ago by 41k • written 4 weeks ago by • 0
0
votes
1
reply
157
views
lfcShrink error: the line search routine failed
apeglm DESeq2
updated 4 weeks ago by 41k • written 4 weeks ago by • 0
2
votes
2
replies
196
views
With DESeq2 "Not full rank" Error with design
DESeq2 DEs
4 weeks ago feather-W • 0
0
votes
2
replies
289
views
Missing Band on Volcano Plot from DESeq2
DESeq2 Visualization DifferentialExpression
updated 4 weeks ago by 41k • written 5 weeks ago by • 0
0
votes
4
replies
396
views
DESeq2: subtract effect of an isotope control before comparing to a baseline sample?
DESeq2
updated 4 weeks ago by 41k • written 5 weeks ago by • 0
0
votes
7
replies
394
views
DESeq2 filtering vs edgeR filtering
DESeq2
5 weeks ago • updated 22 days ago fr8712ca-s • 0
0
votes
2
replies
223
views
RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
5 weeks ago • updated 4 weeks ago kcarey • 0
1
vote
1
reply
198
views
i'm not getting any differentially expressed genes.
DESeq2
updated 5 weeks ago by ★ 4.0k • written 5 weeks ago by • 0
2
votes
1
reply
220
views
Creating data matrix in Deseq2 from tximport data invalid class SummarizedExperiment object
DESeq2 tximport
updated 5 weeks ago by ★ 4.0k • written 5 weeks ago by • 0
1
vote
1
reply
190
views
Perform PCA for sample clustering using DESeq2
DESeq2
updated 5 weeks ago by ★ 4.0k • written 5 weeks ago by • 0
0
votes
3
replies
350
views
Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 10 weeks ago by • 0
0
votes
2
replies
311
views
DESeq2: Comparing A Knockout to a Strain
DESeq2
5 weeks ago Viktor Thiel • 0
0
votes
1
reply
194
views
DESeq2 for pseudobulk analysis of scCITE-seq
DESeq2 scCITE-seq
updated 5 weeks ago by ★ 4.0k • written 5 weeks ago by • 0
0
votes
8
replies
362
views
DESeq and SVA for batch effect
DESeq2 BatchEffect sva
6 weeks ago • updated 5 weeks ago michelafrancesconi8 • 0
0
votes
1
reply
196
views
Unusually large fold-changes in Deseq2 results
DESeq2
updated 6 weeks ago by ★ 4.0k • written 6 weeks ago by • 0
1
vote
4
replies
279
views
DESeq2 Replicates
DESeq2 RNASeq
6 weeks ago kcarey • 0
2
votes
6
replies
307
views
Factor vs Character in design
DESeq2
6 weeks ago James Aiden • 0
1
vote
3
replies
298
views
Dispersion estimation step is very slow with latest DESeq2 and glmGamPoi
DESeq2 glmGamPoi
6 weeks ago I-Hsuan Lin ▴ 10
4
votes
7
replies
824
views
weird volcano plot
DESeq2
updated 6 weeks ago by • 0 • written 5 months ago by ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Comment: DESeq2 setting significant p-value by Dev • 0
after running DESeq2 does it sort the value on the basis of pvalue, or anything, or does it give the data back in the input format I have …
Comment: DESeq filtering specific to contrasts by Carlin95 • 0
But wouldn't this result in a different gene set for each analysis stratification? How can you then compare if maybe gene x comes up in Tim…
Comment: Reading huge bismark coverage files using bbseq::read.bismark by jacques.imbert • 0
Hello, Using nThread = 1L fixed the issue. Thank you for your time and help.
Comment: Error in champ.load(): The following specified files do not exist by Basti ▴ 760
The error stems from the Basename column, please see solution here : https://support.bioconductor.org/p/p132482/
Comment: FilterByExpr low counts with small sample size by Gordon Smyth 50k
As always, it helps to see code. Are you running `voom` or `voomLmFit`? Did you run `normLibSizes()` in edgeR prior to `voom`? Are you star…
Votes
Comment: Reading huge bismark coverage files using bbseq::read.bismark
Answer: Reading huge bismark coverage files using bbseq::read.bismark
Answer: Reading huge bismark coverage files using bbseq::read.bismark
Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
Awards • All
Popular Question to Alessia • 0
Popular Question to paria.alipour • 0
Popular Question to Eman • 0
Popular Question to James W. MacDonald 65k
Scholar to nhaus ▴ 30
Locations • All
France, just now
Spain, 7 minutes ago
UPF, Barcelona, Spain, 9 minutes ago
Wageningen University, Wageningen, the Netherlands, 15 minutes ago
India, 17 minutes ago
Traffic: 775 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6