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Showing :
geneexpression
•
reset
0
votes
2
replies
220
views
FeatureCounts Output Counts at Exon Level Using Default Settings, want gene level
GeneExpression
5 weeks ago
CDSPARKS
• 0
0
votes
1
reply
150
views
Heatmap of two conditions from the normalized gene count data
GeneExpression
heatmaps
updated 12 weeks ago by
ATpoint
★ 2.9k • written 3 months ago by
Amazing570
• 0
0
votes
1
reply
546
views
DESeq2 after Seurat analysis on integrated datasets
DESeq2
SingleCell
GeneExpression
Seurat
updated 3 months ago by
ATpoint
★ 2.9k • written 3 months ago by
bio.boi
• 0
0
votes
3
replies
412
views
CountOverlap
GeneExpression
ChIPSeqData
updated 8 months ago by
James W. MacDonald
63k • written 8 months ago by
michela
▴ 20
2
votes
4
replies
744
views
Comparing different method for DESEQ2
DESeq2
GeneExpression
updated 8 months ago by
Michael Love
40k • written 8 months ago by
Vapin
• 0
0
votes
0
replies
214
views
Free Gibbson energy RNA doublex
GeneExpression
RNAinteract
9 months ago
Tamina
• 0
1
vote
0
replies
231
views
Error while running Case study n. 3: Integration of methylation and expression for ACC
geneexpression
methylation
10 months ago
hlee
▴ 10
0
votes
2
replies
478
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 11 months ago by
swbarnes2
★ 1.2k • written 11 months ago by
ac.mainul.mmb
• 0
0
votes
1
reply
265
views
Error "DESeqDataSetFromMatrix" function not found
GeneExpression
updated 11 months ago by
Basti
▴ 720 • written 11 months ago by
Iraide
• 0
0
votes
1
reply
325
views
Aggregate differentially expressed genes across all contrast results using DEVis
DifferentialExpression
NanoporeRNASeq
DESeq2
GeneExpression
DEVis
updated 12 months ago by
James W. MacDonald
63k • written 12 months ago by
Ana
• 0
1
vote
1
reply
465
views
Error while using champ.SVD function
GeneExpression
updated 13 months ago by
Basti
▴ 720 • written 13 months ago by
Afrin
• 0
0
votes
1
reply
1.2k
views
GDCprepare of STAR - counts
GeneExpression
TCGAbiolinks
updated 8 months ago by
Aurora
• 0 • written 13 months ago by
mahsa
• 0
0
votes
0
replies
475
views
Volcano plot: Putting calculated values in legend
GeneExpression
updated 13 months ago by
Kevin Blighe
3.8k • written 13 months ago by
Narender Singh
• 0
2
votes
2
replies
469
views
Could use some advice on analyzing ranks of expressed genes in two conditions,
GeneExpression
DESeq2
ExpressionData
updated 14 months ago by
fivescarynightsgames
• 0 • written 15 months ago by
reza
▴ 10
0
votes
2
replies
1.3k
views
Using DESeq2 for Differential Expression Analysis with Interaction Term
DifferentialExpression
GeneExpression
DESeq2
Design()
20 months ago
p.l.chen
• 0
2
votes
2
replies
4.5k
views
Deseq2 and log2foldchange cutoffs- How to get differentially expressed genes?
DifferentialExpression
GeneExpression
DESeq2
R
updated 20 months ago by
ATpoint
★ 2.9k • written 20 months ago by
janjoy
▴ 10
0
votes
2
replies
569
views
Gene expression in R
limma
edgeR
Biobase
GeneExpression
21 months ago
sogol.bouyeh
• 0
2
votes
2
replies
1.0k
views
DESeq2 - one groups with no replicates
DESeq2
rnaseqGene
DifferentialExpression
GeneExpression
23 months ago
SUMIT
• 0
5
votes
18
replies
1.7k
views
DESeq2 comparison two cell types and two genotypes
GeneExpressionWorkflow
DESeq2
GeneExpression
updated 2.1 years ago by
Michael Love
40k • written 2.1 years ago by
Yosapol
• 0
1
vote
3
replies
623
views
DESeq analysis with Biological replicate.
DESeq2
ExpressionData
GeneExpression
updated 2.3 years ago by
Michael Love
40k • written 2.3 years ago by
Javad_Sadeghi
• 0
1
vote
1
reply
517
views
Accounting for fish body mass in DE?
GeneExpression
edgeR
updated 2.4 years ago by
James W. MacDonald
63k • written 2.4 years ago by
michael.lawrence
• 0
0
votes
1
reply
541
views
Find significant genes related to a specific disease
GeneExpression
RNASeqR
limma
updated 2.5 years ago by
António Miguel de Jesus Domingues
▴ 490 • written 2.5 years ago by
Will
• 0
1
vote
3
replies
634
views
Troubles implementing LIMMA for paired samples (before/after treatment) comparaisons
GeneExpression
R
limma
MultipleComparison
updated 2.5 years ago by
James W. MacDonald
63k • written 2.5 years ago by
Gwénolé
• 0
0
votes
0
replies
413
views
Diffrential Gene expression in a group of specific methylated prometor patience
GeneExpression
methyAnalysis
MethylationArray
2.5 years ago
coobzie
• 0
1
vote
5
replies
8.9k
views
Calculating FPKM from raw counts data using fpkm() in deseq2
deseq2
r
fpkm()
geneexpression
updated 4.7 years ago by
Michael Love
40k • written 4.7 years ago by
Beginner
▴ 50
1
vote
4
replies
1.4k
views
Need help loading gene expression data into R using either ArrayExpress or GEOquery R packages
arrayexpress
geoquery
geneexpression
updated 5.1 years ago by
Sean Davis
21k • written 5.1 years ago by
arbet003
▴ 10
3
votes
1
reply
1.2k
views
Processing several GSM from GEO database using Barcode and fRMA
frma
barcode
geneexpression
gsm
ncbi geo
updated 5.5 years ago by
Matthew McCall
▴ 830 • written 5.6 years ago by
diana.elassal
• 0
1
vote
4
replies
1.5k
views
ddCT Package for StepOnePlus qPCR output
qPCR
ddCt
geneexpression
updated 5.9 years ago by
Zhang, Jitao David
▴ 120 • written 5.9 years ago by
rbronste
▴ 60
1
vote
3
replies
943
views
General suggestions regarding gene expression
geneexpression
updated 6.3 years ago by
Gordon Smyth
47k • written 6.3 years ago by
mariagiovannetti86
• 0
0
votes
0
replies
689
views
Where or how to find the gene interaction with itself?
microarray
gene interaction
geneexpression
6.4 years ago
shaheryar
• 0
0
votes
0
replies
944
views
Error in SAMseq analysis with R
r
samseq
microarray
rnaseq
geneexpression
6.8 years ago
namilio
• 0
0
votes
0
replies
922
views
Methylation and gene expression
methylation
geneexpression
6.8 years ago
Asma rabe
▴ 290
0
votes
2
replies
877
views
Methylation and gene expression data
methylation
geneexpression
updated 7.0 years ago by
arfranco
▴ 130 • written 7.0 years ago by
Asma rabe
▴ 290
0
votes
3
replies
1.3k
views
error in drawing MDS plot for eset
MDSplot
geneexpression
insilicomerging
updated 7.2 years ago by
James W. MacDonald
63k • written 7.2 years ago by
Shamim Sarhadi
▴ 20
1
vote
6
replies
1.5k
views
how to deal the effect of enormous gene expression?
deseq2
rnaseq
tomato
geneexpression
updated 7.3 years ago by
Michael Love
40k • written 7.3 years ago by
hamaor
• 0
0
votes
1
reply
1.0k
views
Error in MetaQC R package.
r
metaqc
microarray
geneexpression
7.5 years ago
Agaz Hussain Wani
▴ 260
0
votes
3
replies
1.4k
views
problem with WGCNA
geneexpression
updated 7.6 years ago by
Peter Langfelder
★ 2.8k • written 7.6 years ago by
nazaninhoseinkhan
• 0
2
votes
5
replies
1.3k
views
heatmap in R
r language
microarray
geneexpression
updated 7.8 years ago by
Axel Klenk
▴ 990 • written 7.8 years ago by
ifaizurahredzuan
• 0
1
vote
1
reply
934
views
gene expression data analysis
microarray
geneexpression
updated 7.8 years ago by
James W. MacDonald
63k • written 7.8 years ago by
ifaizurahredzuan
• 0
1
vote
1
reply
4.8k
views
NA p and p adjusted value
geneexpression
updated 7.8 years ago by
Peter Langfelder
★ 2.8k • written 7.8 years ago by
timarogger
• 0
1
vote
2
replies
5.0k
views
explanation of makeContrasts function of limma package
limma
microarray
R
geneexpression
updated 7.8 years ago by
Aaron Lun
★ 28k • written 7.8 years ago by
elisa.micarelli
▴ 10
0
votes
3
replies
10k
views
How to combine expression values of multiple probes for one gene
probe
convert
geneexpression
onechannelgui
updated 7.9 years ago by
svlachavas
▴ 810 • written 7.9 years ago by
ayanava18
▴ 10
0
votes
0
replies
886
views
Using segAnglePo() for a set of genes
geneexpression
genesetenrichment
segAnglePo
8.5 years ago
Peter.Wood
• 0
3
votes
5
replies
7.2k
views
limma voom accessing normalised counts tables
limma
rnaseq
geneexpression
voom
counts
updated 8.6 years ago by
Steve Lianoglou
13k • written 8.6 years ago by
Peter Crisp
▴ 10
9
votes
7
replies
8.6k
views
DESeq2 timecourse - How to set the experimental design
deseq2
geneexpression
timecourse
updated 8.6 years ago by
Wolfgang Huber
13k • written 8.7 years ago by
nafeesa
▴ 10
4
votes
2
replies
3.6k
views
Selecting genes based on expressional variance
geneexpression
wgcna
rnaseq
updated 8.7 years ago by
Laurent Gatto
1.6k • written 8.7 years ago by
Jon Bråte
▴ 250
0
votes
0
replies
1.2k
views
easyRNASeq: Number of total counts
GeneExpression
RNASeq
Genetics
Coverage
Normalization
BSgenome
Biobase
Biostrings
biomaRt
9.1 years ago
Guest User
★ 12k
47 results • Page
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Comment: Use with_go along with other filters in getBM function
by
RuBBiT0
▴ 10
Thank you! I think that makes much sense to me.
Comment: Interpret plot from DiffBind
by
Rory Stark
★ 4.8k
Not necessarily. It look to me like there is reconfiguring going on, with some chromatin that was open in the control becoming closed (the …
Comment: Interpret plot from DiffBind
by
Chris
• 0
Thanks Rory! So that means the diseased sample has chromatin more open then the control one, is that correct?
Answer: List of Deprecated Packages for Bioc3.17
by
shepherl
3.5k
lfa and gcatest have been reinstated.
Comment: Remove duplicate genera in DEseq output?
by
Lluís Revilla Sancho
▴ 710
How is your data before calculating the deg_DESeq? I see you use `phyloseq_to_deseq2` which should work well, but have you double checked t…
Votes
Answer: Use with_go along with other filters in getBM function
Answer: Use with_go along with other filters in getBM function
Answer: Interpret plot from DiffBind
A: Generating a proper TxDb instance from NCBI GFF Annotations File
A: VariantAnnotation non-model species
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