Showing : deseq2 • reset
1
vote
4
replies
290
views
DESeq2 interactions
DESeq2
written 5 weeks ago by • 0
3
votes
14
replies
911
views
DESeq2 used with zinbwave weights - Differences on contrasts calculations
zinbwave DESeq2
written 11 weeks ago by • 0
0
votes
2
replies
177
views
3-factor DESeq2 trime-series analysis
time-series DESeq2
5 weeks ago gogeni5529 • 0
0
votes
3
replies
299
views
Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg?
RUVSeq DESeq2
updated 5 weeks ago by 43k • written 7 weeks ago by • 0
0
votes
1
reply
505
views
Which of apeglm and ashr may be more appropriate for pseudobulked DESeq2 analysis of single-cell RNA-seq data?
apeglm DESeq2
updated 6 weeks ago by 43k • written 8 weeks ago by • 0
3
votes
5
replies
1.0k
views
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
DESeq2
updated 7 weeks ago by 68k • written 7 weeks ago by ▴ 200
17
votes
45
replies
13k
views
Can NanoString data be analyzed using DESeq2?
NanoString Differential Expressed Genes Analysis DESeq2
updated 8 weeks ago by 68k • written 6.2 years ago by ▴ 60
0
votes
0
replies
132
views
DESeq2 on non-RNASeq counts data
DESeq2
8 weeks ago vs • 0
1
vote
10
replies
1.1k
views
Using DESeq2 on single cell RNA Seq data of same cell type but different conditions that were pseudo bulked
DESeq2 scRNAseq
updated 26 days ago by • 0 • written 9 weeks ago by • 0
0
votes
11
replies
531
views
Getting way too many DEGs with LRT for time-series RNA-seq!
TimeCourse DESeq2
9 weeks ago • updated 8 weeks ago Denise • 0
2
votes
6
replies
448
views
Very different log2 Fold changes with DESeq2 and explict calculation
DESeq2
9 weeks ago richardallenfriedmanbrooklyn ▴ 30
0
votes
3
replies
225
views
DESeq2 inconsistent fits depending on model design with interacting factors
des DESeq2
written 9 weeks ago by ▴ 10
0
votes
4
replies
815
views
Using shrunken LFC and s-value from DESeq2 as DGE results
apeglm s-value DESeq2
updated 11 weeks ago by 43k • written 3 months ago by • 0
1
vote
2
replies
353
views
Differential expression on the transcript-level
DESeq2
updated 12 weeks ago by ★ 1.4k • written 12 weeks ago by • 0
3
votes
11
replies
1.9k
views
Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 12 months ago by • 0
4
votes
8
replies
1.8k
views
Should Xenium pseudobulk experiments be analysed like microarrays (limma) or like RNASeq (edgeR,Deseq2, or limma-voom)
Deseq2 edgeR limma xenium Voom
3 months ago richardallenfriedmanbrooklyn ▴ 30
7
votes
9
replies
5.5k
views
competitive enrichment test yields too few significant results, self-contained too many
limma DESeq2 fry edgeR
3 months ago bbao ▴ 10
0
votes
2
replies
922
views
Install old version of DESeq2
apeglm Install DESeq2 version
updated 3 months ago by 68k • written 3 months ago by • 0
0
votes
1
reply
458
views
discrepancy in IDs from file and tx2gene (IDs don't match)
tximport DESeq2
updated 3 months ago by 68k • written 3 months ago by • 0
0
votes
2
replies
936
views
gene detection across experiments
DESeq2 Normalization
3 months ago Mara • 0
5
votes
11
replies
3.1k
views
parameters of filterByExpr
edgeR DESeq2 filterByExpr
written 5 months ago by ▴ 10
1
vote
5
replies
3.9k
views
Pre-filtering, adjusting independent filtering, or lfcthreshold() on DESeq2? Low counts and dropouts produce interesting volcano plots.
DESeq2
updated 12 weeks ago by 43k • written 4 months ago by • 0
1
vote
1
reply
2.1k
views
DESeq2 LRT: Testing Effects of Treatment1, Treatment2, and Their Interaction in a Four-Factor Design
DESeq2 multifactorialdesign interaction InteractionSet
updated 4 months ago by 43k • written 4 months ago by • 0
0
votes
2
replies
1.1k
views
6 groups to compare DESeq2 (Wald vs LRT)
DESeq2
updated 4 months ago by 43k • written 4 months ago by • 0
3
votes
2
replies
1.3k
views
Biological replicates consideration in DESeq2 design formula.
DESeq2 RNASeqData RNASeq
written 4 months ago by ▴ 20
1
vote
2
replies
2.6k
views
Deseq2 paired sample in the design is considered as "batch"?
DESeq2
written 4 months ago by • 0
3
votes
1
reply
3.7k
views
DESeq2 empirical bayes: variance of the prior for log fold changes (LFC)
DESeq2
updated 4 months ago by 43k • written 4 months ago by ▴ 10
0
votes
1
reply
461
views
DESeq2 results
result DESeq2 subsetting
updated 4 months ago by ★ 5.0k • written 4 months ago by • 0
0
votes
1
reply
389
views
Unclear DEseq2 replaceOutliers error message
DESeq2
updated 4 months ago by 43k • written 4 months ago by • 0
0
votes
1
reply
497
views
Difference in DESeq2 output and tidybulk DESeq2 method
DifferentialExpression DESeq2 tidybulk RNASeq
updated 4 months ago by 43k • written 5 months ago by • 0
3
votes
2
replies
2.0k
views
Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)
DESeq2
5 months ago • updated 4 months ago dudutchy ▴ 10
2
votes
3
replies
1.3k
views
Differential gene expression analysis on haplotype-resolved diploid assembly
edgeR DESeq2 haplotype limma
5 months ago • updated 4 months ago Paulito • 0
4
votes
4
replies
2.0k
views
Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatmap
DESeq2 ComplexHeatmap
5 months ago • updated 4 months ago caroline.zanchi ▴ 10
0
votes
1
reply
379
views
DESeq2 from phyloseq error
DESeq2 phyloseq
5 months ago asafpr • 0
3
votes
1
reply
592
views
DESeq2 Apeglm Coefficient Reordering / Log2FoldChange Comparison Change
DESeq2 apeglm
updated 5 months ago by 68k • written 5 months ago by • 0
1
vote
5
replies
1.3k
views
Heatmap of a transformed deseq object with pheatmap
DESeq2 heatmaps
updated 5 months ago by 68k • written 5 months ago by ▴ 10
8
votes
3
replies
3.0k
views
DESeq2 class error: superclass "ExpData" not defined in the environment of the object's class
DESeq2
updated 4 months ago by 43k • written 5 months ago by ▴ 40
2
votes
4
replies
1.6k
views
Filtering after DESeq
DESeq2 IHW
written 5 months ago by ▴ 10
0
votes
4
replies
1.2k
views
DESEQ2 - Correctly altering log2foldchange when switching comparison direction (HELP GREATLY APPRECIATED)
DESeq2
5 months ago sk • 0
0
votes
6
replies
1.7k
views
Discrepancies in normalised count data vs unnormalised
DESeq2
5 months ago • updated 4 months ago AMgroup • 0
0
votes
2
replies
666
views
Design formula for circadian time-course data for vst() function
DESeq2
5 months ago Vishnu • 0
0
votes
2
replies
792
views
Analyzing TnSeq data with DESeq2
DESeq2
written 6 months ago by • 0
0
votes
1
reply
1.1k
views
How do I set up my DESeq analysis when I know a few vehicle control samples provide background effects we don't want to see in any of the subsequent …
DESeq2 RUVSeq
updated 6 months ago by 43k • written 7 months ago by • 0
0
votes
2
replies
691
views
Differing results with DESeq2
DESeq2
updated 6 months ago by • 0 • written 6 months ago by • 0
0
votes
2
replies
568
views
RNA Seq using Lrt
DESeq2
6 months ago Rob • 0
0
votes
3
replies
974
views
Log2foldchange strange behavior
DESeq2
updated 6 months ago by ★ 5.0k • written 6 months ago by • 0
0
votes
1
reply
859
views
WGCNA
WGCNA DESeq2
updated 6 months ago by ★ 5.0k • written 6 months ago by • 0
0
votes
1
reply
1.0k
views
Comparison of results obtained from a subset of the data versus the complete dataset for a few selected genes.
DESeq2
updated 6 months ago by ★ 1.4k • written 6 months ago by ▴ 20
1
vote
1
reply
1.3k
views
PhD scholar
RNASeqAnalysis DESeq2
updated 6 months ago by 4.2k • written 6 months ago by • 0
0
votes
1
reply
464
views
DESeq2 - am I extracting results incorrectly?
DESeq2
updated 6 months ago by 68k • written 6 months ago by ▴ 30
4,835 results • Page 1 of 97
Recent ...
Replies
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
Oh. ``` > z <- read10xCounts(c(tmpdir, tmpdir), mtx.class = "SVT_SparseMatrix", delayed = TRUE) > class(counts(z)) [1] "DelayedMatrix" att…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
That's weird. Using the example data works for me. ``` > example(read10xCounts) rd10xC> # Mocking up some 10X genomics output. rd10xC> ex…
Comment: Join BOC Sciences at Drug Discovery Chemistry by teamardigen • 0
Sounds like an exciting event for anyone passionate about small molecule innovation. The focus on discovery and optimization really drives …
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0
I am, but perhaps I'm not understanding how it should work. > sse = DropletUtils::read10xCounts(curr_files[1], mtx.class = 'SVT_Sparse…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
Did you use the development version as Aaron suggested? There is an argument to read the market matrix file directly into an `SVT_SparseMat…
Votes
Join BOC Sciences at Drug Discovery Chemistry
Drug datasets for RNA-seq
Comment: Check removeBatchEffect effectiveness
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset?
Answer: DESeq2 design for haplotype MPRA
Awards • All
Popular Question to Hervé Pagès 16k
Popular Question to Gordon Smyth 53k
Popular Question to dan.gatti • 0
Popular Question to shepherl 4.2k
Popular Question to Steve Lianoglou ★ 13k
Locations • All
The city by the bay, 8 minutes ago
Seattle, WA, United States, 48 minutes ago
United States, 58 minutes ago
United States, 1 hour ago
United States, 1 hour ago
Traffic: 407 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