Showing : DeSeq2 • reset
1
vote
1
reply
181
views
Subsetting data verses contrasts [DESeq2]?
DESeq2
updated 18 days ago by ★ 5.0k • written 18 days ago by • 0
0
votes
0
replies
98
views
How to start learning RNA sequence analysis with DESeq2
DESeq2
19 days ago Syed • 0
1
vote
4
replies
365
views
Bulk RNAseq analysis for
DESeq2 RNASeq edgeR limma
20 days ago • updated 19 days ago Mariami • 0
0
votes
5
replies
2.3k
views
DESeq2 contrast cleaning problem
software error bugs deseq2
written 10.1 years ago by • 0
0
votes
1
reply
198
views
DESeq2 for 16S rRNA Analysis
DESeq2
updated 4 weeks ago by 68k • written 4 weeks ago by • 0
0
votes
5
replies
308
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
0
votes
2
replies
255
views
lfc shrinkage estimator in DESeq2
DESeq2
written 4 weeks ago by • 0
0
votes
13
replies
945
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
6
replies
769
views
BiocParallel (and DESeq2) - wrong args for environment subassignment
BiocParallel DESeq2
updated 5 weeks ago by 25k • written 12 weeks ago by • 0
0
votes
1
reply
350
views
DESeq2 - how to shrink LFC for pairwise comparisons having multiple groups
shrinkage DESeq2 contrast
updated 5 weeks ago by ★ 5.0k • written 6 weeks ago by • 0
0
votes
1
reply
186
views
News: Online RNA-seq analysis course 26-29th Janury
EnhancedVolcano GSEABase pheatmap Workshop DESeq2
written 6 weeks ago by ▴ 20
0
votes
3
replies
485
views
DESeq2 - how many surrogate variables from svaseq, use of lfcshrink
sva lfcshrink DESeq2
10 weeks ago • updated 6 weeks ago ja569116 • 0
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
1
reply
285
views
Question about DESeq2 Design for Paired Treatment Study
DESeq2
updated 3 months ago by ★ 5.0k • written 3 months ago by • 0
0
votes
2
replies
1.3k
views
Install old version of DESeq2
apeglm Install DESeq2 version
updated 3 months ago by ★ 4.0k • written 7 months ago by • 0
1
vote
11
replies
2.6k
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
2
replies
453
views
DESeq2 on non-RNASeq counts data
DESeq2
written 6 months ago by • 0
0
votes
2
replies
419
views
3-factor DESeq2 trime-series analysis
time-series DESeq2
updated 3 months ago by ★ 4.0k • written 5 months ago by • 0
0
votes
1
reply
285
views
[DESeq2] Changing dispersion estimates between runs of DESeq2
DESeq2
3 months ago • updated 17 days ago colinmccornack • 0
0
votes
4
replies
386
views
Getting a large intercept with DESeq2
DESeq2 DifferentialExpression TimeCourse
3 months ago Denise • 0
0
votes
2
replies
448
views
Setting up a DESeq2 Design with Paired Data
DESeq2
3 months ago Alexander • 0
2
votes
4
replies
630
views
DESeq2 interactions
DESeq2
updated 4 months ago by 43k • written 5 months ago by • 0
3
votes
14
replies
1.6k
views
DESeq2 used with zinbwave weights - Differences on contrasts calculations
zinbwave DESeq2
written 7 months ago by • 0
0
votes
3
replies
482
views
Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg?
RUVSeq DESeq2
updated 5 months ago by 43k • written 6 months ago by • 0
0
votes
1
reply
1.0k
views
Which of apeglm and ashr may be more appropriate for pseudobulked DESeq2 analysis of single-cell RNA-seq data?
apeglm DESeq2
updated 5 months ago by 43k • written 6 months 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 6 months ago by 68k • written 6 months ago by ▴ 200
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
0
votes
11
replies
887
views
Getting way too many DEGs with LRT for time-series RNA-seq!
TimeCourse DESeq2
6 months ago Denise • 0
2
votes
6
replies
725
views
Very different log2 Fold changes with DESeq2 and explict calculation
DESeq2
6 months ago richardallenfriedmanbrooklyn ▴ 30
0
votes
3
replies
407
views
DESeq2 inconsistent fits depending on model design with interacting factors
des DESeq2
written 6 months 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
1
vote
2
replies
607
views
Differential expression on the transcript-level
DESeq2
updated 7 months ago by ★ 1.4k • 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 17 months ago by • 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
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
0
votes
1
reply
651
views
discrepancy in IDs from file and tx2gene (IDs don't match)
tximport DESeq2
updated 7 months ago by 68k • written 7 months ago by • 0
0
votes
2
replies
1.1k
views
gene detection across experiments
DESeq2 Normalization
8 months ago Mara • 0
5
votes
11
replies
4.3k
views
parameters of filterByExpr
edgeR DESeq2 filterByExpr
written 10 months ago by ▴ 10
1
vote
5
replies
5.7k
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
1
vote
1
reply
2.3k
views
DESeq2 LRT: Testing Effects of Treatment1, Treatment2, and Their Interaction in a Four-Factor Design
DESeq2 multifactorialdesign interaction InteractionSet
updated 8 months ago by 43k • written 8 months ago by • 0
0
votes
2
replies
1.3k
views
6 groups to compare DESeq2 (Wald vs LRT)
DESeq2
updated 8 months ago by 43k • written 8 months ago by • 0
3
votes
2
replies
1.6k
views
Biological replicates consideration in DESeq2 design formula.
DESeq2 RNASeqData RNASeq
written 8 months ago by ▴ 20
1
vote
2
replies
2.8k
views
Deseq2 paired sample in the design is considered as "batch"?
DESeq2
written 8 months ago by • 0
3
votes
1
reply
3.9k
views
DESeq2 empirical bayes: variance of the prior for log fold changes (LFC)
DESeq2
updated 8 months ago by 43k • written 9 months ago by ▴ 10
0
votes
1
reply
693
views
DESeq2 results
result DESeq2 subsetting
updated 9 months ago by ★ 5.0k • written 9 months ago by • 0
0
votes
1
reply
520
views
Unclear DEseq2 replaceOutliers error message
DESeq2
updated 9 months ago by 43k • written 9 months ago by • 0
0
votes
1
reply
696
views
Difference in DESeq2 output and tidybulk DESeq2 method
DifferentialExpression DESeq2 tidybulk RNASeq
updated 9 months ago by 43k • written 9 months ago by • 0
3
votes
3
replies
2.3k
views
Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)
DESeq2
written 9 months ago by ▴ 10
2
votes
3
replies
1.7k
views
Differential gene expression analysis on haplotype-resolved diploid assembly
edgeR DESeq2 haplotype limma
9 months ago Paulito • 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
4,851 results • Page 1 of 98
Recent ...
Replies
Answer: Inconsistencies between accessor functions for TxDb databases with selected seql by a2a2hd42aa • 0
Technical inconsistencies in database accessors can disrupt your workflow, but finding a reliable source to download online mobile games sh…
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 …
Votes
Do I map probes to gene symbols BEFORE or AFTER differentially expressed gene analysis?
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
Awards • All
Popular Question to Gordon Smyth 53k
Popular Question to Matan G. ▴ 60
Popular Question to Jaqueline • 0
Popular Question to Dario Strbenac ★ 1.6k
Popular Question to chirag.parsania ▴ 10
Locations • All
Melbourne, Australia, 15 minutes ago
Australia, 33 minutes ago
The city by the bay, 2 hours ago
WEHI, Melbourne, Australia, 4 hours ago
United States, 4 hours ago
Traffic: 1347 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