Showing : DESEQ2 • reset
17
votes
45
replies
14k
views
Can NanoString data be analyzed using DESeq2?
NanoString Differential Expressed Genes Analysis DESeq2
updated 6 months ago by 68k • written 6.6 years ago by ▴ 60
5
votes
30
replies
6.9k
views
DESeq2 model - How to test case/control time course model when taking account within sample variability?
deseq2 multiple time points time course casecontrol model design
updated 11 months ago by • 0 • written 8.7 years ago by ▴ 10
31
votes
25
replies
65k
views
deseq2 filter the low counts
deseq2 lowcount
updated 3 months ago by 43k • written 11.0 years ago by ▴ 40
38
votes
23
replies
19k
views
DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
deseq2
11.5 years ago • updated 11 months ago Michael Love 43k
9
votes
15
replies
7.6k
views
DESeq2 on NanoString Data
deseq2 nanostring
updated 6 months ago by 43k • written 7.7 years ago by ▴ 170
3
votes
14
replies
1.6k
views
DESeq2 used with zinbwave weights - Differences on contrasts calculations
zinbwave DESeq2
written 7 months ago by • 0
3
votes
13
replies
2.4k
views
Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 16 months ago by • 0
0
votes
13
replies
923
views
Making a Full Rank Model for Allele-Specific Expression with DESeq2
DESeq2
updated 4 weeks ago by 53k • written 5 weeks ago by • 0
0
votes
11
replies
2.8k
views
Question about using LRT test for time course experiments with DESeq2
DESeq2
updated 11 months ago by • 0 • written 16 months ago by • 0
5
votes
11
replies
4.2k
views
parameters of filterByExpr
edgeR DESeq2 filterByExpr
written 10 months ago by ▴ 10
1
vote
11
replies
2.5k
views
Using DESeq2 on single cell RNA Seq data of same cell type but different conditions that were pseudo bulked
DESeq2 scRNAseq
updated 3 months ago by ★ 4.0k • written 6 months ago by • 0
0
votes
11
replies
863
views
Getting way too many DEGs with LRT for time-series RNA-seq!
TimeCourse DESeq2
6 months ago Denise • 0
0
votes
10
replies
2.0k
views
DESeq2 filtering vs edgeR filtering
DESeq2
written 23 months ago by • 0
1
vote
10
replies
11k
views
DESeq2: Continuous and discreate variables in the design
deseq2 R rna-seq design
updated 7 months ago by 43k • written 6.3 years ago by • 0
8
votes
10
replies
18k
views
GSEA preranked analysis downstream of DEseq2
deseq2 gsea rnaseq
updated 10 months ago by ★ 5.0k • written 9.6 years ago by ▴ 20
7
votes
9
replies
5.9k
views
competitive enrichment test yields too few significant results, self-contained too many
limma DESeq2 fry edgeR
7 months ago bbao ▴ 10
1
vote
8
replies
3.0k
views
[ChIP-seq] DESeq2 on counts matrix from union set of called peaks
csaw ChIPseq DESeq2 DiffBind
11 months ago • updated 10 months ago Luca • 0
4
votes
8
replies
2.2k
views
Should Xenium pseudobulk experiments be analysed like microarrays (limma) or like RNASeq (edgeR,Deseq2, or limma-voom)
Deseq2 edgeR limma xenium Voom
7 months ago richardallenfriedmanbrooklyn ▴ 30
1
vote
8
replies
3.2k
views
DESeq: Gene is not flagged as differentially expressed despite count data showing differences
DifferentialExpression DESeq2
10 months ago ktz • 0
12
votes
7
replies
23k
views
DESEq2 comparison with mulitple cell types under 2 conditions
deseq2 multiple factor design
updated 9 months ago by ▴ 740 • written 10.8 years ago by ▴ 50
3
votes
7
replies
2.5k
views
Vertical line at A=0, nothing else, on MA plot
deseq2
updated 12 months ago by ▴ 10 • written 7.0 years ago by ▴ 20
1
vote
6
replies
1.6k
views
heatmap with batch effect
DESeq2 BatchEffect
written 17 months ago by • 0
0
votes
6
replies
1.9k
views
Discrepancies in normalised count data vs unnormalised
DESeq2
10 months ago • updated 9 months ago AMgroup • 0
2
votes
6
replies
3.0k
views
Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 12 months ago by • 0 • written 22 months ago by • 0
1
vote
6
replies
2.2k
views
how to analysis htseq-count
deseq2
written 8.1 years ago by ▴ 30
4
votes
6
replies
1.7k
views
Surprising behavior for DEXseq dispersion estimate plot?
DESeq2 DEXSeq
updated 11 months ago by ★ 5.0k • written 11 months ago by • 0
2
votes
6
replies
718
views
Very different log2 Fold changes with DESeq2 and explict calculation
DESeq2
6 months ago richardallenfriedmanbrooklyn ▴ 30
3
votes
6
replies
1.1k
views
Highly similar RNA-seq samples in PCA - pooling or technical duplication?
RNASeq DESeq2 DifferentialExpression RNASeqData
written 3 months ago by • 0
0
votes
6
replies
740
views
BiocParallel (and DESeq2) - wrong args for environment subassignment
BiocParallel DESeq2
updated 5 weeks ago by 25k • written 12 weeks ago by • 0
2
votes
5
replies
968
views
Joining different datasets and analyzing using the group-specific condition effects strategy (DESeq2)
DESeq2
updated 6 weeks ago by 68k • written 3.1 years ago by • 0
5
votes
5
replies
4.1k
views
Cannot extract size factor from DESeq2 analysis
deseq2 tximport
updated 9 months ago by 43k • written 5.8 years ago by • 0
0
votes
5
replies
2.3k
views
DESeq2 contrast cleaning problem
software error bugs deseq2
written 10.1 years ago by • 0
3
votes
5
replies
1.3k
views
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
DESeq2
updated 5 months ago by 68k • written 6 months ago by ▴ 200
1
vote
5
replies
1.9k
views
Heatmap of a transformed deseq object with pheatmap
DESeq2 heatmaps
updated 9 months ago by 68k • written 9 months ago by ▴ 10
0
votes
5
replies
303
views
Lowly expressed genes reported as significant when using lfcThreshold in DESeq
RNASeq DESeq2 DifferentialExpression
updated 4 weeks ago by 43k • written 4 weeks ago by • 0
1
vote
5
replies
5.6k
views
Pre-filtering, adjusting independent filtering, or lfcthreshold() on DESeq2? Low counts and dropouts produce interesting volcano plots.
DESeq2
updated 7 months ago by 43k • written 8 months ago by • 0
0
votes
5
replies
2.6k
views
DeSeq Strategies for run to run Replication
DESeq2 Normalization Clustering replicate
updated 9 months ago by 43k • written 3.5 years ago by • 0
1
vote
5
replies
4.8k
views
DESeq2 swap ensembl gene id rownames with gene symbol column
deseq2 dataframe ensembl gene id gene symbol entrezid
updated 11 months ago by • 0 • written 6.2 years ago by ▴ 10
2
votes
5
replies
1.5k
views
Group-specific condition effects with individuals nested: matrix is not full rank
DESeq2
12 months ago picasa1983 • 0
2
votes
4
replies
2.6k
views
deseq2 lfc shrinkage with few DEGs
RNASeq DESeq2
updated 11 months ago by 43k • written 3.7 years ago by ▴ 10
6
votes
4
replies
8.4k
views
DESeq2 with proteomics data
deseq2
updated 10 months ago by • 0 • written 7.6 years ago by ▴ 10
0
votes
4
replies
1.2k
views
Using shrunken LFC and s-value from DESeq2 as DGE results
apeglm s-value DESeq2
updated 6 months ago by 43k • written 7 months ago by • 0
0
votes
4
replies
1.7k
views
Guidance Needed: Best Practices for Handling Technical Replicates in RNA-seq Analysis
DESeq2 TechnicalReplicates RNASeq
written 11 months ago by • 0
2
votes
4
replies
2.0k
views
Filtering after DESeq
DESeq2 IHW
written 10 months ago by ▴ 10
2
votes
4
replies
624
views
DESeq2 interactions
DESeq2
updated 4 months ago by 43k • written 5 months ago by • 0
1
vote
4
replies
349
views
Bulk RNAseq analysis for
DESeq2 RNASeq edgeR limma
17 days ago • updated 16 days ago Mariami • 0
1
vote
4
replies
859
views
DESEQ2 looking at main effects while controlling for a continuous variable
DESeq2
11 months ago Lennie • 0
0
votes
4
replies
378
views
Getting a large intercept with DESeq2
DESeq2 DifferentialExpression TimeCourse
3 months ago Denise • 0
0
votes
4
replies
1.3k
views
DESEQ2 - Correctly altering log2foldchange when switching comparison direction (HELP GREATLY APPRECIATED)
DESeq2
9 months ago sk • 0
4
votes
4
replies
2.3k
views
Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatmap
DESeq2 ComplexHeatmap
9 months ago caroline.zanchi ▴ 10
111 results • Page 1 of 3
Recent ...
Replies
Comment: Can sample-level weights be used when analysing GSVA scores in limma? by A.Barden ▴ 20
Thanks both for this useful information.
Comment: Reproducibility of code in various Bioconductor versions by Gordon Smyth 53k
SNPlocs.Hsapiens.dbSNP155.GRCh38 is available for download from the same location as always. It has not changed since Bioc 3.20: Presumabl…
Comment: Changing multiple display parameters of a specific exon in GeneRegionTrack by a2a2hd42aa • 0
Similarly, for structural complexity in the [He777 Game][1] APK, having precise control over every detail is what makes a high-performance …
Answer: Issue loading and downloading Bioconductor 3.22 packages after update by strawberry3 • 0
Hi, thank you all for the advice. Using James's advice, I managed to install SNPlocs.Hsapiens.dbSNP155.GRCh38, but it took almost half an …
Answer: Issue loading and downloading Bioconductor 3.22 packages after update by James W. MacDonald 68k
As Robert and ATpoint have mentioned, you need to allow more time to download a large file like this. ``` > options(timeout = 5e5) > l…
Votes
Answer: Can sample-level weights be used when analysing GSVA scores in limma?
Answer: Can sample-level weights be used when analysing GSVA scores in limma?
Comment: Can sample-level weights be used when analysing GSVA scores in limma?
Answer: Issue loading and downloading Bioconductor 3.22 packages after update
Answer: Issue loading and downloading Bioconductor 3.22 packages after update
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