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Showing :
DESEQ2
•
reset
0
votes
4
replies
1.5k
views
DESeq2 : standardising variation between treatments
RNA-seq
DESeq2
2.1 years ago
ar14g12
• 0
0
votes
2
replies
855
views
Issues with ddseq2 for treatment response factoring in different KO clones
Clonality
RNASeq
DESeq2
updated 2.1 years ago by
swbarnes2
★ 1.4k • written 2.1 years ago by
Jules
• 0
0
votes
1
reply
910
views
DeSeq2 data comparison and extracting outputs
DESeq2
updated 2.1 years ago by
swbarnes2
★ 1.4k • written 2.1 years ago by
sedabarutcu.a
• 0
1
vote
5
replies
1.6k
views
Mixed up sample info with plotPCA
plotMA
ggplot2
plotPCA
DESeq2
updated 2.1 years ago by
Michael Love
43k • written 2.1 years ago by
sara.jacobson
• 0
0
votes
4
replies
1.0k
views
Extract LRT results for each comparison
LRT
DESeq2
updated 2.1 years ago by
ATpoint
★ 5.0k • written 2.1 years ago by
Yijing
• 0
2
votes
4
replies
1.6k
views
Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
RNASeqData
DifferentialExpression
SmallRNAData
DESeq2
2.1 years ago
Shihui
• 0
0
votes
5
replies
1.1k
views
DESeq2, results(dds, name = <reference>) interpretation results
DESeq2
2.1 years ago
Rockbar
• 0
0
votes
3
replies
1.0k
views
Deseq2, multifactor model design for comparing adult Mutant mouse versus pup Mutant mouse with normalization to the age difference of the Wildtype co…
DGE
DESeq2
2.2 years ago • updated 2.1 years ago
ruba-mahmoud
• 0
0
votes
5
replies
1.2k
views
DeSeq2 design fails (full model matrix is less than full rank)
DESeq2
updated 2.1 years ago by
James W. MacDonald
68k • written 2.2 years ago by
Theo
▴ 10
1
vote
3
replies
2.5k
views
How does DESeq2 calculate FPKM values when gene lengths are not supplied?
deseq2
written 5.6 years ago by
hasse.bossenbroek
• 0
0
votes
4
replies
1.5k
views
filtering out lowly expressed genes by groups
RNASeqData
DESeq2
updated 2.2 years ago by
James W. MacDonald
68k • written 2.2 years ago by
sohail.mbio
▴ 10
1
vote
3
replies
1.5k
views
Deseq2, enrichGO and ensembl ID
go
DESeq2
updated 10 months ago by
James W. MacDonald
68k • written 2.2 years ago by
Alvin
• 0
0
votes
3
replies
889
views
how to adjust other conditions when calling DEGs by DESeq2
DifferentialExpression
DESeq2
updated 2.2 years ago by
ATpoint
★ 5.0k • written 2.2 years ago by
xiaowen
• 0
0
votes
3
replies
971
views
The meaning of the analysis results when using a new metric in analysis
DESeq2
updated 2.2 years ago by
James W. MacDonald
68k • written 2.2 years ago by
SH
▴ 10
1
vote
1
reply
1.6k
views
Can I transform already normalized rna-seq data with Z-score?
Z-score
RNASeqData
Deseq
DESeq2
updated 2.2 years ago by
James W. MacDonald
68k • written 2.2 years ago by
khaserdene99
• 0
0
votes
1
reply
847
views
How to compared two groups out of twelve in DESeq2
DESeq2
updated 2.2 years ago by
James W. MacDonald
68k • written 2.2 years ago by
paige.ramkissoon
• 0
1
vote
7
replies
1.8k
views
Permutation test in DESeq2?
DESeq2
updated 2.2 years ago by
Michael Love
43k • written 2.2 years ago by
michellewei
• 0
3
votes
3
replies
1.1k
views
EdgeR and DESeq2, variance estimation and parametric test
parametrictest
edgeR
DESeq2
2.2 years ago
Nisha
• 0
3
votes
5
replies
2.2k
views
Getting batch corrected counts after RUVSeq
BatchEffect
RUVSeq
RNASeq
DESeq2
updated 2.2 years ago by
ATpoint
★ 5.0k • written 2.2 years ago by
Shashank
• 0
0
votes
1
reply
587
views
Run DESeq2 on chromosome and plasmids separately
DESeq2
updated 2.2 years ago by
ATpoint
★ 5.0k • written 2.2 years ago by
Laura
▴ 10
0
votes
1
reply
683
views
Unable to create ddf object
DESeqDataSetFromMatrix
dds
DESeq2
updated 2.2 years ago by
James W. MacDonald
68k • written 2.2 years ago by
naomi.croft
• 0
0
votes
2
replies
1.0k
views
RSubread DESeq2
RNASeqData
DifferentialExpression
DESeq2
2.2 years ago
Beyza
• 0
0
votes
3
replies
942
views
Dramatically different DESeq2 results in Mac and Linux computers
DESeq2
updated 2.2 years ago by
James W. MacDonald
68k • written 2.2 years ago by
jovel_juan
▴ 30
1
vote
2
replies
737
views
Setting up a multi-factor experiement
DESeq2
2.2 years ago • updated 2.1 years ago
jon50250
• 0
0
votes
1
reply
850
views
DESeq design and contrast with multiple factors
RNASeq
DESeq2
updated 2.2 years ago by
Michael Love
43k • written 2.2 years ago by
Adam
• 0
1
vote
1
reply
1.2k
views
results after deseq2 not showing gene ids and gene names but they are present in dds object
DESeq2
updated 2.2 years ago by
James W. MacDonald
68k • written 2.2 years ago by
Anup
• 0
0
votes
3
replies
1.5k
views
DESeq2 not full rank with paired patient samples and one control cohort
DESeq2
updated 2.2 years ago by
James W. MacDonald
68k • written 2.2 years ago by
The_T_cell_Guy
• 0
0
votes
3
replies
1.3k
views
RNAseq (Deseq2 and Dexseq2) analysis on two time points with expected same effect
DEXSeq
RNA-seq
DESeq2
updated 2.2 years ago by
Alejandro Reyes
★ 1.9k • written 2.2 years ago by
Alice
• 0
0
votes
1
reply
843
views
Is it possible to combine count gene expression data coming from one sequencing technology (RNA seq) with intensity gene expression data coming from …
DESeq2
RNASeqData
edgeR
limma
DifferentialExpression
updated 2.2 years ago by
ATpoint
★ 5.0k • written 2.2 years ago by
Sep
• 0
0
votes
1
reply
1.2k
views
How to properly compare the group-specific samples using DEseq2
DESeq2
updated 2.2 years ago by
swbarnes2
★ 1.4k • written 2.2 years ago by
sykbod
• 0
5
votes
13
replies
4.3k
views
Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport
DESeq2
updated 2.1 years ago by
Michael Love
43k • written 2.2 years ago by
Christian
• 0
0
votes
5
replies
1.6k
views
How to use contrast with multiple treatments?
RNASeqdataanalysis
DESeq2
updated 2.2 years ago by
swbarnes2
★ 1.4k • written 2.2 years ago by
Sreeja
• 0
2
votes
2
replies
1.6k
views
DESeq2 results - Annotating and exporting results
DESeq2
updated 2.2 years ago by
James W. MacDonald
68k • written 2.2 years ago by
Maka
• 0
3
votes
7
replies
1.7k
views
DESeq2 alternative hypyothesis: testing for genes NOT significantly downregulated
DESeq2
2.2 years ago
casco
▴ 10
0
votes
9
replies
1.7k
views
DESeq2: How to estimate effects of one factor controlling for other factors?
DESeq2
2.2 years ago
mjd275
• 0
1
vote
8
replies
4.2k
views
Significantly regulated genes produced by only a few affected samples
deseq2
written 7.7 years ago by
serpalma.v
▴ 60
2
votes
12
replies
2.9k
views
P-value inflation?
DESeq2
updated 2.2 years ago by
James W. MacDonald
68k • written 2.3 years ago by
dsambo
▴ 10
1
vote
2
replies
1.4k
views
DESeq2 batch design
DESeq2
updated 2.2 years ago by
swbarnes2
★ 1.4k • written 2.3 years ago by
Hope
▴ 10
0
votes
1
reply
1.1k
views
Getting NAs in both p-values (normal and adjusted) in DEseq2
DESeq2
updated 2.2 years ago by
ATpoint
★ 5.0k • written 2.2 years ago by
Juan Pablo
• 0
8
votes
15
replies
3.3k
views
PCA percent variance DESeq2
PCA
DESeq2
2.3 years ago • updated 2.2 years ago
IUH
• 0
1
vote
6
replies
3.4k
views
Time-series RNA-seq analysis using DESeq2
time-series
DESeq2
RNASeq
timecoursedata
TimeCourse
updated 2.3 years ago by
ATpoint
★ 5.0k • written 2.3 years ago by
Debebe
• 0
0
votes
1
reply
921
views
Comparing the effect of single drug and two-drug combination with control in RNA seq data
GeneExpressionWorkflow
DESeq2
updated 2.3 years ago by
Michael Love
43k • written 2.3 years ago by
Kent
• 0
0
votes
1
reply
632
views
DEG by deseq2 by Race
DESeq2
updated 2.3 years ago by
Kevin Blighe
★ 4.0k • written 2.3 years ago by
Sharif
• 0
0
votes
1
reply
737
views
the confuse issue in DEseq2 among multi group
DESeq2
updated 2.3 years ago by
James W. MacDonald
68k • written 2.3 years ago by
诗友
• 0
3
votes
2
replies
2.8k
views
ERROR in EnrichKEGG(), 'species should be listed' in, download method do not change
KEGG
DESeq2
biomaRt
clusterProfiler
org.Mm.eg.db
updated 2.3 years ago by
Guido Hooiveld
★ 4.1k • written 2.3 years ago by
Milan
▴ 10
5
votes
2
replies
1.8k
views
can't install DESeq2 ("unable to access index for repository")
biocmanager
DESeq2
2.3 years ago
Alessia
▴ 40
2
votes
5
replies
2.8k
views
removing the batch effect for vst counts and defining the batches in removeBatchEffect function
DESeq2
BatchEffect
limma
updated 2.3 years ago by
Gordon Smyth
53k • written 2.3 years ago by
Sara
• 0
0
votes
1
reply
856
views
FALSE error when checking a pre made sample data
Rstudio
scRNAseq
DESeq2
updated 2.3 years ago by
ATpoint
★ 5.0k • written 2.3 years ago by
DrFizz
• 0
0
votes
2
replies
721
views
No such file or directory DESeq2
rstudioScRNA
DESeq2
written 2.3 years ago by
DrFizz
• 0
2
votes
3
replies
3.0k
views
bulk RNA-seq analysis using R : batch effect : One question concerning Combat-seq and one question concerning DESeq2 design = batch + condition
BatchEffect
sva
DESeq2
RNASeqData
limma
updated 2.3 years ago by
James W. MacDonald
68k • written 2.3 years ago by
D-Bug
▴ 10
4,838 results • Page
10 of 97
Recent ...
Replies
Answer: Alternative to BrainArray custom CDF packages for Affymetrix chips?
by
Guido Hooiveld
★ 4.1k
It seems that through the Internet Archive these files can be obtained: https://web.archive.org/web/20240710102334/http://brainarray.mbn…
Comment: Alternative to BrainArray custom CDF packages for Affymetrix chips?
by
insuraasanaa3scetaxrealty
• 0
Lamento que el acceso a los paquetes BrainArray esté fallando; cuando ocurren estos problemas, es util contar con recursos alternativos bie…
Comment: Getting a large intercept with DESeq2
by
Denise
• 0
Hi, Thank you very much, James and Michael, for getting back to me! I noticed the large intercept when plotting the coefficients returned …
Comment: Error installing Seqinfo
by
shepherl
4.2k
Yes and we are working on getting the updated windows binaries distributed asap! We are hopeful by the end of this week
Comment: APAlyzer
by
shepherl
4.2k
We apologize for their unresponsiveness; you could try posting your question here to see if anyone in the community could assist in the me…
Votes
Answer: replace cat with message in glmTreat when lfc = 0
Answer: replace cat with message in glmTreat when lfc = 0
Comment: Issues with downloading biomaRt - SeqInfo and S4 Vectors
Answer: Issues with downloading biomaRt - SeqInfo and S4 Vectors
Answer: Issues with downloading biomaRt - SeqInfo and S4 Vectors
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