Showing : DEseq2 • reset
0
votes
1
reply
527
views
Deseq2 design matrix
DESeq2 Designmatrix limma
updated 15 months ago by 68k • written 15 months ago by • 0
1
vote
1
reply
707
views
DESeq2 - vst() - log2FC - no replicates
DESeq2 log2FC vst()
updated 15 months ago by ★ 4.9k • written 15 months ago by • 0
1
vote
5
replies
1.0k
views
DESeq2 ML Query
DESeq2
updated 14 months ago by 43k • written 15 months ago by • 0
1
vote
3
replies
922
views
Test of Multiple Linear Combination on coefficients from Wald Test in Deseq2
Regression DESeq2
15 months ago • updated 13 months ago David W. H. • 0
0
votes
1
reply
636
views
Significant genes in DESeq2 analysis
DESeq2 RNASeq
updated 15 months ago by 68k • written 15 months ago by • 0
1
vote
3
replies
1.8k
views
Combining two bulk RNA seq datasets
RNASeqData DESeq2 Normalization
15 months ago Tanvi • 0
0
votes
1
reply
1.3k
views
In a 3 group DEG analysis with three batches, can I use 1 group in all three batches to correct for the batch effect?
DESeq2
updated 15 months ago by 43k • written 15 months ago by • 0
2
votes
1
reply
606
views
Design formula, numeric contrast, and lfcshrink in deseq2
DESeq2
updated 15 months ago by 43k • written 15 months ago by ▴ 10
2
votes
1
reply
756
views
DESeq2 returns results for group with just one replicate
DESeq2 DifferentialExpression
updated 15 months ago by 68k • written 15 months ago by ▴ 70
1
vote
9
replies
3.1k
views
Most enriched pathway is not expressed when modifying universe parameter
DESeq2 clusterProfiler Pathways RNASeq org.Mm.eg.db
updated 15 months ago by 68k • written 15 months ago by ▴ 10
1
vote
3
replies
924
views
Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 15 months ago by 68k • written 15 months ago by ▴ 50
3
votes
6
replies
3.4k
views
Multiple factor DSEq2 result generates weird volcano plot
DESeq2
updated 15 months ago by ★ 4.9k • written 2.5 years ago by ▴ 20
2
votes
2
replies
843
views
Double normalising when using sva and deseq2
DESeq2 Normalisation Bulkrnaseq Svaseq
15 months ago BioinfGuru ▴ 70
1
vote
2
replies
1.2k
views
Cohen's D calculation for differentially expressed genes via DESeq2 results summary stats
DESeq2
15 months ago a_p • 0
0
votes
1
reply
571
views
Can we compare 3 different experimental conditions with DESeq2?
DESeq2 StatisticalMethod
updated 15 months ago by ★ 1.4k • written 15 months ago by • 0
0
votes
1
reply
599
views
How to identify transcripts/genes with differential kinetics in two genotypes, using time-course RNA seq data?
RNASeqData DESeq2 DifferentialExpression
updated 15 months ago by 68k • written 15 months ago by • 0
1
vote
2
replies
2.6k
views
using tximport with STAR transcript-quantification output
tximport deseq2 STAR
updated 15 months ago by ▴ 40 • written 5.9 years ago by • 0
0
votes
1
reply
493
views
multiple condition issue running DESeq
DESeq2
updated 15 months ago by 43k • written 15 months ago by • 0
0
votes
3
replies
698
views
Ploting of normalized counts after batch removal
DESeq2
updated 15 months ago by 53k • written 15 months ago by ▴ 10
1
vote
1
reply
442
views
makeExampleDESeqDataSet using pilot data
DESeq2
updated 15 months ago by 43k • written 15 months ago by • 0
0
votes
2
replies
629
views
Best way to describe DEseq2 design
DESeq2
updated 15 months ago by ★ 1.4k • written 16 months ago by • 0
1
vote
2
replies
767
views
Deseq2
DESeq2 rnaseqGene
updated 15 months ago by ▴ 220 • written 16 months ago by • 0
1
vote
1
reply
534
views
LRT, pairwise comparisons and p-value adjustment
DESeq2
updated 16 months ago by 68k • written 16 months ago by ▴ 740
0
votes
6
replies
1.1k
views
Counter-directional LFC shrinkage
DESeq2
updated 16 months ago by 43k • written 16 months ago by • 0
0
votes
2
replies
1.2k
views
How to add Ensembl ids after Pseudobulk analysis by DESeq2
Seurat DESeq2 single-cell scRNA Pseudobulk
updated 16 months ago by ★ 4.1k • written 16 months ago by • 0
0
votes
3
replies
1.8k
views
GSVA function
DESeq2 GSVA ssGSEA
updated 16 months ago by ★ 3.4k • written 16 months ago by • 0
0
votes
2
replies
911
views
Normalisation using clinical traits in RNA seq using DESeq2
DESeq2 clinicaltraits Normalization batchnormalisation
16 months ago sukeshinik5 ▴ 20
0
votes
4
replies
2.1k
views
Volcano plot of scRNA-seq data not "centered"
DESeq2
updated 16 months ago by ★ 4.9k • written 16 months ago by • 0
1
vote
8
replies
1.2k
views
Slightly different count plots from R and spreadsheet
DESeq2 ggplot2
16 months ago boczniak767 ▴ 740
1
vote
3
replies
964
views
LRT, more than two conditions and pairwise comparisons
DESeq2
updated 16 months ago by 68k • written 16 months ago by ▴ 740
0
votes
6
replies
1.5k
views
Numerical differences in DESeq2 output depending on different design matrix construction
DESeq2
16 months ago Ken C • 0
2
votes
4
replies
1.0k
views
DESeq2- Mysterious interaction suppresses DEGs
DESeq2 PCAplot RNA-Seq DesignModel
updated 16 months ago by 43k • written 16 months ago by • 0
4
votes
9
replies
1.2k
views
Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2 timecoursedata GeneExpression
updated 16 months ago by ★ 4.9k • written 16 months ago by • 0
0
votes
3
replies
723
views
Assymetric MA plot with no overall trend
DESeq2 DifferentialExpression
updated 16 months ago by 43k • written 16 months ago by • 0
0
votes
1
reply
694
views
normalization across different species for DESeq2 analysis
DESeq2 normalization Normalization acrossspecies
updated 16 months ago by 43k • written 16 months ago by • 0
0
votes
9
replies
2.1k
views
Can I trust the differential expression analysis when the two groups overlap on the PCA?
DESeq2 pcaExplorer
updated 15 months ago by ▴ 70 • written 16 months ago by • 0
1
vote
2
replies
1.1k
views
How can I create a eigencorplot of pca created from deseq2 object with PCAtools
DESeq2 eigencorplot PCAtools
16 months ago BioinfGuru ▴ 70
0
votes
1
reply
580
views
Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 16 months ago by ★ 4.9k • written 16 months ago by • 0
0
votes
1
reply
663
views
normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 16 months ago by ★ 4.9k • written 16 months ago by • 0
2
votes
7
replies
1.8k
views
deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
16 months ago sajadahmad41454 • 0
2
votes
1
reply
783
views
Handling multiple differential expression comparisons
DESeq2
16 months ago • updated 15 months ago Zainab ▴ 20
0
votes
6
replies
1.1k
views
Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 16 months ago by ★ 1.4k • written 16 months ago by ▴ 130
2
votes
6
replies
2.1k
views
Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 6 months ago by • 0 • written 16 months ago by • 0
0
votes
2
replies
486
views
DESeq2 v1.35.0
DESeq2
updated 16 months ago by 43k • written 16 months ago by • 0
0
votes
2
replies
850
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
16 months ago kcarey • 0
0
votes
3
replies
1.4k
views
Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 16 months ago by ★ 4.9k • written 16 months ago by • 0
1
vote
3
replies
3.1k
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 16 months ago by ★ 4.9k • written 16 months ago by • 0
0
votes
3
replies
661
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 16 months ago by 43k • written 16 months ago by • 0
3
votes
1
reply
825
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 17 months ago by 43k • written 17 months ago by ▴ 10
0
votes
2
replies
938
views
Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
17 months ago • updated 16 months ago Aurora • 0
4,835 results • Page 5 of 97
Recent ...
Replies
Comment: GO.db and others package Download failure by James W. MacDonald 68k
Also, you never need to use anything but `BiocManager::install` to install any package, which has the beneficial side effect of ensuring th…
Comment: GO.db and others package Download failure by James W. MacDonald 68k
Yes. Your packages have odd Y version numbers (where the version is X.Y.Z). That means they are devel packages (release versions have even …
Comment: GO.db and others package Download failure by Skyler • 0
Am I using Bioc-devel?
Comment: GO.db and others package Download failure by James W. MacDonald 68k
Is there a reason to use Bioc-devel? If not, you should be using the release version (which I am, and which installs `GO.db` without compla…
Comment: GO.db and others package Download failure by Skyler • 0
Hi James, Below I have inserted all of my code. I have run r as an administrator and not as an administrator. I have changed my CRANmirror …
Votes
Comment: readDNAStringSet with non DNA characters
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Awards • All
Popular Question to Stephen Piccolo ▴ 600
Popular Question to Gordon Smyth 53k
Popular Question to Guangchuang Yu ★ 1.2k
Popular Question to Paulito • 0
Popular Question to geneprophet • 0
Locations • All
San Diego, 3 minutes ago
Seattle, WA, United States, 6 minutes ago
United States, 59 minutes ago
United States, 1 hour ago
United States, 1 hour ago
Traffic: 950 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