Showing : DESeq2 • reset
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Inclusion of non-coding portions of transcripts (UTR-regions and introns) within the DEX-seq dataset
dexseq deseq2 differential exon usage
updated 2 hours ago by • 0 • written 9.4 years ago by ▴ 10
0
votes
2
replies
109
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Subsetting DDS object for individual conditions over time
DESeq2
2 days ago • updated 1 day ago A ▴ 60
0
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1
reply
296
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[DESeq2] Changing dispersion estimates between runs of DESeq2
DESeq2
3 months ago • updated 23 days ago colinmccornack • 0
3
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3
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2.3k
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Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)
DESeq2
written 9 months ago by ▴ 10
1
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1
reply
243
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Subsetting data verses contrasts [DESeq2]?
DESeq2
updated 24 days ago by ★ 5.0k • written 24 days ago by • 0
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0
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113
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How to start learning RNA sequence analysis with DESeq2
DESeq2
25 days ago Syed • 0
1
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4
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419
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Bulk RNAseq analysis for
DESeq2 RNASeq edgeR limma
26 days ago Mariami • 0
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5
replies
2.3k
views
DESeq2 contrast cleaning problem
software error bugs deseq2
written 10.1 years ago by • 0
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1
reply
207
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DESeq2 for 16S rRNA Analysis
DESeq2
updated 5 weeks ago by 68k • written 5 weeks ago by • 0
0
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1
reply
198
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News: Online RNA-seq analysis course 26-29th Janury
EnhancedVolcano GSEABase pheatmap Workshop DESeq2
written 7 weeks ago by ▴ 20
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5
replies
315
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Lowly expressed genes reported as significant when using lfcThreshold in DESeq
RNASeq DESeq2 DifferentialExpression
updated 5 weeks ago by 43k • written 5 weeks ago by ▴ 10
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2
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264
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lfc shrinkage estimator in DESeq2
DESeq2
written 5 weeks ago by • 0
0
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13
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980
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Making a Full Rank Model for Allele-Specific Expression with DESeq2
DESeq2
updated 5 weeks ago by 53k • written 6 weeks ago by • 0
0
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1
reply
390
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DESeq2 - how to shrink LFC for pairwise comparisons having multiple groups
shrinkage DESeq2 contrast
updated 6 weeks ago by ★ 5.0k • written 7 weeks ago by • 0
0
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6
replies
800
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BiocParallel (and DESeq2) - wrong args for environment subassignment
BiocParallel DESeq2
updated 6 weeks ago by 25k • written 3 months ago by • 0
1
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4
replies
2.9k
views
Pairwise comparison of multiple groups with different base
deseq2 rna-seq r
updated 6 weeks ago by • 0 • written 5.8 years ago by ▴ 10
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3
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518
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DESeq2 - how many surrogate variables from svaseq, use of lfcshrink
sva lfcshrink DESeq2
11 weeks ago • updated 7 weeks ago ja569116 • 0
2
votes
5
replies
994
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Joining different datasets and analyzing using the group-specific condition effects strategy (DESeq2)
DESeq2
updated 7 weeks ago by 68k • written 3.1 years ago by • 0
0
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2
replies
467
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DESeq2 on non-RNASeq counts data
DESeq2
written 6 months ago by • 0
6
votes
6
replies
1.3k
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Highly similar RNA-seq samples in PCA - pooling or technical duplication?
RNASeq DESeq2 DifferentialExpression RNASeqData
written 3 months ago by ▴ 10
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1
reply
294
views
Question about DESeq2 Design for Paired Treatment Study
DESeq2
updated 3 months ago by ★ 5.0k • written 3 months ago by • 0
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2
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1.3k
views
Install old version of DESeq2
apeglm Install DESeq2 version
updated 3 months ago by ★ 4.0k • written 8 months ago by • 0
1
vote
11
replies
2.7k
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
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2
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424
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3-factor DESeq2 trime-series analysis
time-series DESeq2
updated 3 months ago by ★ 4.0k • written 5 months ago by • 0
0
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4
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397
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Getting a large intercept with DESeq2
DESeq2 DifferentialExpression TimeCourse
3 months ago Denise • 0
0
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2
replies
491
views
Setting up a DESeq2 Design with Paired Data
DESeq2
4 months ago Alexander • 0
3
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13
replies
2.4k
views
Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 17 months ago by • 0
31
votes
25
replies
65k
views
deseq2 filter the low counts
deseq2 lowcount
updated 4 months ago by 43k • written 11.0 years ago by ▴ 40
2
votes
4
replies
654
views
DESeq2 interactions
DESeq2
updated 4 months ago by 43k • written 5 months ago by • 0
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3
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1.5k
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PCA subset of genes vs DE
DESeq2 RNASeq
written 3.0 years ago by ▴ 20
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2
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1.4k
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Heat Map
ColData pheatmap DESeq2
written 2.7 years ago by • 0
0
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10
replies
2.1k
views
DESeq2 filtering vs edgeR filtering
DESeq2
written 24 months ago by • 0
3
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14
replies
1.6k
views
DESeq2 used with zinbwave weights - Differences on contrasts calculations
zinbwave DESeq2
written 7 months ago by • 0
0
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3
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491
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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
1
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2
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3.0k
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selecting result from deseq2
DESeq2
updated 5 months ago by 43k • written 5.9 years ago by • 0
0
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1
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1.1k
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Which of apeglm and ashr may be more appropriate for pseudobulked DESeq2 analysis of single-cell RNA-seq data?
apeglm DESeq2
updated 6 months ago by 43k • written 6 months ago by • 0
3
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5
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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
1
vote
2
replies
949
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DiffBind getting Fold values of near 0
DiffBind DESeq2
updated 6 months ago by ▴ 10 • written 2.3 years ago by • 0
17
votes
45
replies
14k
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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
9
votes
15
replies
7.7k
views
DESeq2 on NanoString Data
deseq2 nanostring
updated 6 months ago by 43k • written 7.8 years ago by ▴ 170
0
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11
replies
910
views
Getting way too many DEGs with LRT for time-series RNA-seq!
TimeCourse DESeq2
6 months ago Denise • 0
0
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3
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425
views
DESeq2 inconsistent fits depending on model design with interacting factors
des DESeq2
written 6 months ago by ▴ 10
2
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6
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738
views
Very different log2 Fold changes with DESeq2 and explict calculation
DESeq2
6 months ago richardallenfriedmanbrooklyn ▴ 30
1
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6
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1.6k
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heatmap with batch effect
DESeq2 BatchEffect
written 17 months ago by • 0
0
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4
replies
1.2k
views
Using shrunken LFC and s-value from DESeq2 as DGE results
apeglm s-value DESeq2
updated 7 months ago by 43k • written 7 months ago by • 0
1
vote
2
replies
623
views
Differential expression on the transcript-level
DESeq2
updated 7 months ago by ★ 1.4k • written 7 months ago by • 0
1
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5
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5.8k
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 9 months ago by • 0
1
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10
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11k
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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
7
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9
replies
6.0k
views
competitive enrichment test yields too few significant results, self-contained too many
limma DESeq2 fry edgeR
7 months ago bbao ▴ 10
4
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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
4,852 results • Page 1 of 98
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Comment: Inclusion of non-coding portions of transcripts (UTR-regions and introns) within by Pat • 0
Ill be honest, I didnt trust any of these services for a long time. Im a political science major and the pressure around writing is intense…
Comment: Question on processing compound protein groups in limpa by brianpeterson1210 • 0
Thank you[,][1] Appreciated! [1]: http://paint3d.org
Comment: Subsetting DDS object for individual conditions over time by A ▴ 60
Hi @atpoint Thank you for the quick reply! and this makes sense! I will confirm with a corr to see how the SFs differ but also how DE dif…
Answer: Subsetting DDS object for individual conditions over time by ATpoint ★ 5.0k
It would surprise my quite a bit if the size factors would differ notably between subset or not. I would always try to keep the size factor…
Comment: GSEA error by Adithi • 0
Thank you so much. That makes perfect sense to me. I will work on this.
Votes
Answer: RNA Seq using Lrt
Answer: DESeq2 LRT Reduced Formula
Answer: DESeq2: LRT or WALD guidance
Answer: GSEA error
Answer: OrgDb for maize
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