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RnaSeq
•
reset
0
votes
6
replies
2.3k
views
DESeq2 Normalization with 4 Groups
Normalization
RNASeq
DESeq2
2.1 years ago
erika.maldonado-rosado
• 0
0
votes
0
replies
738
views
is Dada2 biased toward a particular sequence ?
virology
dada2
amplican
Sequencing
RNASeq
2.1 years ago
Sara
• 0
0
votes
2
replies
1.1k
views
Will DESeq2 be appropriate tool for analysis?
RNASeq
DESeq2
2.1 years ago
Karthik
• 0
0
votes
0
replies
723
views
Dual species RNA-seq, Library size and normalization
Normalization
edgeR
RNASeq
DESeq2
2.1 years ago
Florian
• 0
0
votes
0
replies
994
views
Pysam pileup and Rsamtools pileup output discrepancy
Pysam
pileup
Rsamtools
RNASeq
2.1 years ago
Xinqi
• 0
0
votes
0
replies
870
views
Using DADA2 for finding viral sequence variants
VariantDetection
dada2
RNASeq
2.1 years ago
Sara
• 0
1
vote
1
reply
1.0k
views
Multiple comparison using DESeq2
RNASeqData
RNASeq
DESeq2
updated 2.1 years ago by
James W. MacDonald
68k • written 2.1 years ago by
fuqichen1
• 0
1
vote
7
replies
1.8k
views
DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition
RNASeqData
limma
BulkRNAseq
RNASeq
updated 23 months ago by
Gordon Smyth
53k • written 2.1 years ago by
Gimena
• 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
1.1k
views
Comparing RNASeq data from multiple studies
RNASeqData
RnaSeqSampleSize
RNASeqPower
RNASeq
updated 2.1 years ago by
Basti
▴ 780 • written 2.1 years ago by
Luke
• 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
1
vote
1
reply
916
views
bulk RNA-Seq batch correction
RNASeqData
rnaseqcomp
RNASeq
updated 2.2 years ago by
ATpoint
★ 5.0k • written 2.2 years ago by
jg0428
• 0
0
votes
1
reply
849
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
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
6
votes
7
replies
1.5k
views
Adding a group of samples reduces DEGs in other groups
RNASeq
limma
updated 2.3 years ago by
Gordon Smyth
53k • written 2.3 years ago by
Jonathan
▴ 10
0
votes
1
reply
5.1k
views
Is it proper to compare two WGCNA matrixes if they were raised to different power (soft threshold)?
Network
cluster
WGCNA
RNASeq
updated 2.3 years ago by
James W. MacDonald
68k • written 2.3 years ago by
chiwut.wong
• 0
2
votes
1
reply
1.2k
views
Grouping DEGs yields varying results
RNASeq
limma
updated 2.3 years ago by
Gordon Smyth
53k • written 2.3 years ago by
Jonathan
▴ 10
2
votes
5
replies
2.1k
views
Question about RNAseq analysis in EdgeR to identify common and donor specific differentially expressed genes
R
edgeR
RNASeq
2.3 years ago
mohammedtoufiq91
▴ 10
0
votes
2
replies
1.3k
views
Correct DESeq2 design for tumoral stage differences in tumoral and matched-normal samples
DifferentialExpression
RNASeq
DESeq2
2.3 years ago
Matteo
• 0
4
votes
2
replies
3.2k
views
Gene set analysis: GSVA, Z-Score, and fold-changes
GSVA
RNASeq
limma
updated 2.4 years ago by
Gordon Smyth
53k • written 2.4 years ago by
Jonathan
▴ 10
0
votes
3
replies
1.6k
views
Multiple Testing When Using Multiple Contrasts/Comparisons in DESEQ2
MultipleComparison
DESeq2
Genetics
contrasts
RNASeq
updated 2.4 years ago by
James W. MacDonald
68k • written 2.4 years ago by
a26fd14e
• 0
3
votes
11
replies
4.8k
views
Adjusting for baseline when having longitudinal data, mixed model and no treatment
RNAseq
mixedmodels
baselineadjustement
limma
2.5 years ago
Anna
▴ 20
2
votes
9
replies
7.0k
views
how to control age and gender effect in expression data using DESeq2
deseq2
rnaseq
mirna-seq
differential gene expression
written 7.7 years ago by
klalit1803
▴ 10
0
votes
1
reply
876
views
CI for logCPM (fitted values)
RNAseq
edgeR
updated 2.5 years ago by
Gordon Smyth
53k • written 2.5 years ago by
Lina
▴ 10
3
votes
4
replies
1.1k
views
Anova table edgeR limma
limma
RNASeq
edgeR
2.5 years ago
KATHERINE CHUERE NUNES
• 0
1
vote
2
replies
1.1k
views
Obtention of the binomial transformed count table with edgeR
DESeq2
edgeR
RNASeq
DifferentialExpression
updated 2.5 years ago by
Gordon Smyth
53k • written 2.5 years ago by
Sofía
• 0
0
votes
3
replies
1.4k
views
Account for heteroscedasticity when fitting gene expression data
RNAseq
updated 2.5 years ago by
Michael Love
43k • written 2.5 years ago by
Alberto
• 0
1
vote
3
replies
1.6k
views
Is it okay to increase filtering to get more significant Adjusted P Values for DEGs found using Limma?
RNASeqPower
edgeR
DifferentialExpression
limma
RNASeq
updated 2.5 years ago by
Gordon Smyth
53k • written 2.5 years ago by
Sara
• 0
0
votes
2
replies
2.5k
views
model matrix not full rank
DESeq2
RNASeq
updated 2.5 years ago by
garryfrenchgarry
• 0 • written 2.6 years ago by
Simran
• 0
0
votes
1
reply
1.0k
views
What is the correct way to split genex_high and genex_low groups for DE analysis?
DESeq2
RNASeq
updated 2.6 years ago by
Michael Love
43k • written 2.6 years ago by
rohanphn
• 0
2
votes
3
replies
857
views
RNA seq with edgeR with several factors
RNAseq
factors
2.6 years ago
Nathalie
▴ 20
0
votes
3
replies
1.3k
views
edgeR DEGs multilevel
edgeR
RNASeq
DifferentialRegulation
updated 2.6 years ago by
Gordon Smyth
53k • written 2.6 years ago by
bioinfoWanderer
• 0
8
votes
10
replies
17k
views
GSEA preranked analysis downstream of DEseq2
deseq2
gsea
rnaseq
updated 6 months ago by
ATpoint
★ 5.0k • written 9.3 years ago by
EJ
▴ 20
0
votes
4
replies
1.7k
views
Combine RNA-seq
BatchEffect
R
rnaseq
updated 2.6 years ago by
swbarnes2
★ 1.4k • written 2.6 years ago by
Young Tae
• 0
1
vote
1
reply
718
views
Using R to measure differential gene expression of one gene due to different treatments using RNASeq counts
DESeq2
edgeR
RNAseq
updated 2.6 years ago by
Gordon Smyth
53k • written 2.6 years ago by
cmareevicars
• 0
3
votes
12
replies
2.9k
views
Unwanted variation observed on PCA for transcript level data
salmon
RUVSeq
cqn
PCA
RNASeq
updated 2.6 years ago by
Michael Love
43k • written 2.6 years ago by
urwah
▴ 10
0
votes
1
reply
756
views
Sample expression calculation in rna seq
Rnaseq
updated 2.6 years ago by
ATpoint
★ 5.0k • written 2.6 years ago by
zaid ur
• 0
1
vote
1
reply
903
views
Can I run deseq2 on two separate experiments at once?
rnaseq
deseq2
updated 2.6 years ago by
ATpoint
★ 5.0k • written 2.6 years ago by
lunarskye222
• 0
0
votes
0
replies
961
views
WGCNA approach on multiregional brain transcriptomes
Neurotranscriptome
RNAseq
WGCNA
2.6 years ago
Levi
• 0
4
votes
8
replies
6.1k
views
Interpreting ellipses in PCAtools for bulk RNAseq
ellipse
RNAseq
PCAtools
updated 2.6 years ago by
CP
• 0 • written 4.5 years ago by
elizabethe819
• 0
1
vote
2
replies
1.0k
views
RNA-Seq normalization of pre and post treatment groups
Normalization
RNASeq
written 2.6 years ago by
Sarah
• 0
2
votes
4
replies
1.4k
views
limma with or without intercept gives different results
limma
rnaseq
2.6 years ago
Sydney
• 0
1
vote
2
replies
1.8k
views
RUVSeq and DESeq2 -- all variables in design formula must be columns in colData
DESeq2
RNAseq
RUVSeq
2.7 years ago
garbuzov
• 0
0
votes
2
replies
1.2k
views
Compare and filter three BAM files
RNAseq
10X
2.7 years ago
wt215
• 0
0
votes
5
replies
1.6k
views
hill-shaped p-value distributions using EdgeR
edgeR
p-valuedistribution
RNAseq
hill-shaped
updated 2.7 years ago by
Gordon Smyth
53k • written 2.7 years ago by
Giuseppe
• 0
5
votes
7
replies
1.7k
views
different number of DEG because of outliers
DESeq2
RNASeq
updated 22 months ago by
Gordon Smyth
53k • written 2.7 years ago by
Ilya
• 0
0
votes
2
replies
1.6k
views
GO analysis in R vs website
GO
RNASeq
2.7 years ago
Nitro
• 0
1
vote
4
replies
1.3k
views
Repeated Measures-Cross Over Study for RNAseq data using variancePartition::dream
RNAseq
variancePartition
edgeR
dream
2.7 years ago
DH
• 0
1
vote
0
replies
1.2k
views
Job:
Seeking collaborator/contractor (paid) for Bioconductor package development
RNASeq
JobPosting
2.7 years ago
Jamie Walters
▴ 10
3
votes
2
replies
1.5k
views
Batch question Bulk RNA-Seq
BatchEffect
RNASeq
2.7 years ago
chf
• 0
1,409 results • Page
3 of 29
Recent ...
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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…
Answer: Error installing Seqinfo
by
fabio.marroni
• 0
I am answering my own question. I found the solution thanks to [this post][1], and I am writing here the very simple procedure: 1) Instal…
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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