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degseq
•
reset
0
votes
3
replies
504
views
Are unequal sample sizes in differential gene expression (DGE) analysis a problem for edgeR, DESeq2, and NOISeq? Could you give me some advice on how…
RNA
RNASeqPower
DEGseq
written 9 months ago by
Jonathan
• 0
0
votes
9
replies
2.1k
views
limma fo continous variables
limma
DEGseq
updated 18 months ago by
James W. MacDonald
68k • written 18 months ago by
mia
• 0
0
votes
1
reply
922
views
Why was the number of DEG different between DESeq results and count by myself using excel?
RNASeqData
DEGseq
updated 2.0 years ago by
ATpoint
★ 4.9k • written 2.0 years ago by
sybyun419
• 0
0
votes
2
replies
922
views
RNA seq differential expression analysis
DEGseq
RNASeqData
limma
updated 2.2 years ago by
Gordon Smyth
52k • written 2.2 years ago by
Shaimaa Gamal
• 0
2
votes
5
replies
1.8k
views
Create the design matrix
DEGseq
edgeR
RNASeq
2.7 years ago • updated 2.6 years ago
Mohammad
• 0
0
votes
0
replies
1.3k
views
Extracting gene lists per timepoints using DEGPPatterns package and LRT
DEGseq
clusterProfiler
DEGreport
2.8 years ago
Rob
• 0
0
votes
2
replies
1.2k
views
RNA-Seq Reads Count
DESeq2
htseq
DEGseq
RNASeq
read
updated 2.8 years ago by
Michael Love
43k • written 2.8 years ago by
CP
• 0
0
votes
2
replies
1.3k
views
Seeking help in multifactor differential gene expression analysis using DESeq2. Can not get significance difference while comparing 3 time factor (…
DifferentialExpression
GeneExpression
R
enrichment
DEGseq
updated 3.1 years ago by
swbarnes2
★ 1.4k • written 3.1 years ago by
ac.mainul.mmb
• 0
1
vote
4
replies
1.4k
views
How to figure out the FC value from Limma
limma
DEGseq
DifferentialExpression
updated 3.2 years ago by
Kevin Blighe
★ 4.0k • written 3.3 years ago by
beslinail
• 0
0
votes
1
reply
1.2k
views
R CODE TO FIND AGGREGATE FOR DUPLICATES
aggregateBioVar
DEGseq
MicroarrayData
updated 3.7 years ago by
James W. MacDonald
68k • written 3.7 years ago by
biomyscience
• 0
0
votes
1
reply
926
views
Meta analysis
DEGseq
Metanalysis
updated 3.8 years ago by
Kevin Blighe
★ 4.0k • written 3.8 years ago by
biomyscience
• 0
1
vote
2
replies
1.2k
views
DESeq2 desing formula for cell fraction and siRNA scramble
DEGseq
DESeq2
Designformula
updated 4.3 years ago by
swbarnes2
★ 1.4k • written 4.3 years ago by
Nicolò
• 0
1
vote
7
replies
1.9k
views
how to make a contrast of uniquely DE genes
edgeR
limma
RNA-seq
DEGseq
4.4 years ago
decppced
• 0
0
votes
3
replies
1.5k
views
DeSeq2- design experiment
rnaseq
degseq
7.8 years ago
laksharikrish
• 0
0
votes
1
reply
1.5k
views
Problem with DEGseq/samWrapper
degseq
updated 8.2 years ago by
ab.tsubaki
• 0 • written 10.7 years ago by
jovel_juan
▴ 30
0
votes
0
replies
1.1k
views
Regarding q-value
DEGseq
DEGseq
12.2 years ago
deepika lakhwani
▴ 170
0
votes
1
reply
1.7k
views
Problems in running easyRNASeq
Annotation
Organism
DEGseq
easyRNASeq
Annotation
Organism
DEGseq
easyRNASeq
updated 12.6 years ago by
delhomme@embl.de
★ 1.2k • written 12.6 years ago by
Guest User
★ 13k
0
votes
3
replies
1.9k
views
Analysis of public GEO datasets - NGS
DEGseq
DEGseq
updated 12.9 years ago by
Aliaksei Holik
▴ 350 • written 12.9 years ago by
Guest User
★ 13k
0
votes
0
replies
1.5k
views
NGS public data analysis
Transcription
DEGseq
Transcription
DEGseq
12.9 years ago
Jill Pleasance
▴ 10
0
votes
1
reply
4.5k
views
RNA-seq analysis and two-way ANOVAs
edgeR
baySeq
DEGseq
DESeq
DEXSeq
edgeR
baySeq
DEGseq
DESeq
DEXSeq
updated 13.0 years ago by
Gordon Smyth
52k • written 13.0 years ago by
Elena Sorokin
▴ 160
0
votes
3
replies
1.5k
views
Help with plot comparison
baySeq
DEGseq
baySeq
DEGseq
13.5 years ago
Tina Asante Boahene
▴ 100
0
votes
0
replies
1.3k
views
DEGseq help
baySeq
DEGseq
baySeq
DEGseq
13.5 years ago
Tina Asante Boahene
▴ 100
0
votes
0
replies
1.4k
views
FDR (False Discovery Rate)
baySeq
DEGseq
baySeq
DEGseq
13.5 years ago
Tina Asante Boahene
▴ 100
0
votes
0
replies
1.2k
views
A question on baySeq
Normalization
DEGseq
DESeq
Normalization
DEGseq
DESeq
15.1 years ago
sunghee OH
▴ 50
0
votes
1
reply
1.3k
views
A question on DESeq
edgeR
DEGseq
DESeq
edgeR
DEGseq
DESeq
updated 15.1 years ago by
Simon Anders
★ 3.8k • written 15.1 years ago by
sunghee OH
▴ 50
0
votes
8
replies
2.7k
views
Experimental design for RNA-Seq
edgeR
DEGseq
DESeq
edgeR
DEGseq
DESeq
updated 15.2 years ago by
Naomi Altman
★ 6.0k • written 15.2 years ago by
michael watson IAH-C
★ 3.4k
0
votes
3
replies
2.0k
views
New package to identify differentially expressed genes from RNA-seq data
Annotation
DEGseq
Annotation
DEGseq
updated 15.9 years ago by
Ulrike Goebel
▴ 110 • written 15.9 years ago by
Naomi Altman
★ 6.0k
0
votes
0
replies
1.3k
views
New package to identify differentially expressed genes from RNA-seq data
Annotation
DEGseq
Annotation
DEGseq
15.9 years ago
Likun Wang
▴ 50
28 results • Page
1 of 1
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Replies
Comment: Are voomByGroup and voomLmFit compatible?
by
Gordon Smyth
52k
Your question is a bit cryptic, Rich. Are you trying to rewrite the voomByGroup() function yourself, to incorporate functionality that the …
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
by
Raya
• 0
Thank you for pointing this out James, it works now!
Answer: HMP_2019_t2d data origin
by
Levi Waldron
★ 1.1k
Dear @pleiramalls, @blann, sorry for the delay! We obtained fastq files for the HMP2 study from the HMP data portal (https://portal.hmpda…
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
by
ATpoint
★ 4.9k
I told you why, because you aggregate all cells into a single pseudobulk. You then need a pseudobulk per worm, but that assumes that in the…
Comment: Can NanoString data be analyzed using DESeq2?
by
ATpoint
★ 4.9k
There is nothing code-wise specific for Nanostring. The same workflow and code applies as if it was RNA-seq, ChIP-seq, any count dataset. R…
Votes
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
Can NanoString data be analyzed using DESeq2?
Comment: Are voomByGroup and voomLmFit compatible?
Comment: Updated Support Site Editor
Updated Support Site Editor
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