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Showing :
DESeq2
•
reset
1
vote
1
reply
195
views
Subsetting data verses contrasts [DESeq2]?
DESeq2
updated 19 days ago by
ATpoint
★ 5.0k • written 19 days ago by
js101
• 0
0
votes
0
replies
104
views
How to start learning RNA sequence analysis with DESeq2
DESeq2
20 days ago
Syed
• 0
1
vote
4
replies
379
views
Bulk RNAseq analysis for
DESeq2
RNASeq
edgeR
limma
21 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
john.hu
• 0
0
votes
1
reply
198
views
DESeq2 for 16S rRNA Analysis
DESeq2
updated 4 weeks ago by
James W. MacDonald
68k • written 4 weeks ago by
lizflor
• 0
0
votes
5
replies
309
views
Lowly expressed genes reported as significant when using lfcThreshold in DESeq
RNASeq
DESeq2
DifferentialExpression
updated 4 weeks ago by
Michael Love
43k • written 5 weeks ago by
Ahmed Salah
▴ 10
0
votes
2
replies
257
views
lfc shrinkage estimator in DESeq2
DESeq2
written 5 weeks ago by
julia_mcdonough
• 0
0
votes
13
replies
948
views
Making a Full Rank Model for Allele-Specific Expression with DESeq2
DESeq2
updated 5 weeks ago by
Gordon Smyth
53k • written 5 weeks ago by
chp265
• 0
0
votes
6
replies
776
views
BiocParallel (and DESeq2) - wrong args for environment subassignment
BiocParallel
DESeq2
updated 6 weeks ago by
Martin Morgan
25k • written 12 weeks ago by
Benjamin
• 0
0
votes
1
reply
363
views
DESeq2 - how to shrink LFC for pairwise comparisons having multiple groups
shrinkage
DESeq2
contrast
updated 5 weeks ago by
ATpoint
★ 5.0k • written 6 weeks ago by
ja569116
• 0
0
votes
1
reply
186
views
News:
Online RNA-seq analysis course 26-29th Janury
EnhancedVolcano
GSEABase
pheatmap
Workshop
DESeq2
written 7 weeks ago by
Frances Turner
▴ 20
0
votes
3
replies
495
views
DESeq2 - how many surrogate variables from svaseq, use of lfcshrink
sva
lfcshrink
DESeq2
10 weeks ago • updated 6 weeks ago
ja569116
• 0
6
votes
6
replies
1.2k
views
Highly similar RNA-seq samples in PCA - pooling or technical duplication?
RNASeq
DESeq2
DifferentialExpression
RNASeqData
written 3 months ago by
Ahmed Salah
▴ 10
0
votes
1
reply
289
views
Question about DESeq2 Design for Paired Treatment Study
DESeq2
updated 3 months ago by
ATpoint
★ 5.0k • written 3 months ago by
Junmo
• 0
0
votes
2
replies
1.3k
views
Install old version of DESeq2
apeglm
Install
DESeq2
version
updated 3 months ago by
Kevin Blighe
★ 4.0k • written 7 months ago by
Asma
• 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
Kevin Blighe
★ 4.0k • written 6 months ago by
Raya
• 0
0
votes
2
replies
458
views
DESeq2 on non-RNASeq counts data
DESeq2
written 6 months ago by
vs
• 0
0
votes
2
replies
421
views
3-factor DESeq2 trime-series analysis
time-series
DESeq2
updated 3 months ago by
Kevin Blighe
★ 4.0k • written 5 months ago by
gogeni5529
• 0
0
votes
1
reply
288
views
[DESeq2] Changing dispersion estimates between runs of DESeq2
DESeq2
3 months ago • updated 18 days ago
colinmccornack
• 0
0
votes
4
replies
387
views
Getting a large intercept with DESeq2
DESeq2
DifferentialExpression
TimeCourse
3 months ago
Denise
• 0
0
votes
2
replies
455
views
Setting up a DESeq2 Design with Paired Data
DESeq2
3 months ago
Alexander
• 0
2
votes
4
replies
634
views
DESeq2 interactions
DESeq2
updated 4 months ago by
Michael Love
43k • written 5 months ago by
Michael
• 0
3
votes
14
replies
1.6k
views
DESeq2 used with zinbwave weights - Differences on contrasts calculations
zinbwave
DESeq2
written 7 months ago by
Aurélie
• 0
0
votes
3
replies
485
views
Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg?
RUVSeq
DESeq2
updated 5 months ago by
Michael Love
43k • written 6 months ago by
yongjie.wang
• 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
Michael Love
43k • written 6 months ago by
KS
• 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
James W. MacDonald
68k • written 6 months ago by
snijesh
▴ 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
James W. MacDonald
68k • written 6.6 years ago by
lim6432
▴ 60
0
votes
11
replies
893
views
Getting way too many DEGs with LRT for time-series RNA-seq!
TimeCourse
DESeq2
6 months ago
Denise
• 0
2
votes
6
replies
728
views
Very different log2 Fold changes with DESeq2 and explict calculation
DESeq2
6 months ago
richardallenfriedmanbrooklyn
▴ 30
0
votes
3
replies
410
views
DESeq2 inconsistent fits depending on model design with interacting factors
des
DESeq2
written 6 months ago by
fedor.bezrukov
▴ 10
0
votes
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
Michael Love
43k • written 7 months ago by
Erika
• 0
1
vote
2
replies
609
views
Differential expression on the transcript-level
DESeq2
updated 7 months ago by
swbarnes2
★ 1.4k • written 7 months ago by
泓朴
• 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
bioshot.com
• 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
653
views
discrepancy in IDs from file and tx2gene (IDs don't match)
tximport
DESeq2
updated 7 months ago by
James W. MacDonald
68k • written 7 months ago by
IUH
• 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
caroline.zanchi
▴ 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
Michael Love
43k • written 8 months ago by
Alexander
• 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
Michael Love
43k • written 8 months ago by
Integrative
• 0
0
votes
2
replies
1.3k
views
6 groups to compare DESeq2 (Wald vs LRT)
DESeq2
updated 8 months ago by
Michael Love
43k • written 8 months ago by
Rocio
• 0
3
votes
2
replies
1.6k
views
Biological replicates consideration in DESeq2 design formula.
DESeq2
RNASeqData
RNASeq
written 9 months ago by
Christian
▴ 20
1
vote
2
replies
2.8k
views
Deseq2 paired sample in the design is considered as "batch"?
DESeq2
written 9 months ago by
corranna98
• 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
Michael Love
43k • written 9 months ago by
Chenghao
▴ 10
0
votes
1
reply
695
views
DESeq2 results
result
DESeq2
subsetting
updated 9 months ago by
ATpoint
★ 5.0k • written 9 months ago by
rajdeepboral00
• 0
0
votes
1
reply
520
views
Unclear DEseq2 replaceOutliers error message
DESeq2
updated 9 months ago by
Michael Love
43k • written 9 months ago by
Pak
• 0
0
votes
1
reply
699
views
Difference in DESeq2 output and tidybulk DESeq2 method
DifferentialExpression
DESeq2
tidybulk
RNASeq
updated 9 months ago by
Michael Love
43k • written 9 months ago by
s.malik
• 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
dudutchy
▴ 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
Comment: Unable to find ENTREZ IDs
by
Adithi
• 0
Hi James, Thank you so much for your reply. My main goal is to find ortholog genes from chinese hamster gene symbols to mouse gene symbols…
Comment: Unable to find ENTREZ IDs
by
Adithi
• 0
Hi James, Thank you so much for your reply. My main goal is to find ortholog genes from chinese hamster gene symbols to mouse gene symbols…
Answer: Unable to find ENTREZ IDs
by
James W. MacDonald
68k
Those are the 'symbols', and are a concatenation of LOC and the NCBI Gene ID (what used to be called an Entrez Gene ID). As an example:http…
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.
Votes
Answer: OrgDb for maize
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Do I map probes to gene symbols BEFORE or AFTER differentially expressed gene analysis?
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