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Showing :
RNAseq
•
reset
0
votes
8
replies
122
views
edgeR: Usage of estimated dispersion from replicates for pools of the same experiment
edgeR
RNAseq
20 hours ago • updated 1 hour ago
k.roelfs
• 0
2
votes
2
replies
139
views
Calculate transcriptional heterogeneity for a condition using DESeq2
RNASeq
19 days ago • updated 9 days ago
SciencyUsagi
▴ 10
0
votes
1
reply
119
views
Variance stabilization transformation (VST), blind=TRUE
DESeq2
Transcriptomics
RNASeq
updated 14 days ago by
Michael Love
39k • written 17 days ago by
Jayesh Kumar
• 0
3
votes
3
replies
143
views
Why is it better to count genes at the exon-level using subread::featureCounts()?
RNASeq
Rsubread
featureCounts
Quantification
updated 15 days ago by
Gordon Smyth
47k • written 15 days ago by
Sara
• 0
0
votes
3
replies
150
views
Gene TPM validity with STAR only quantification
RNASeq
updated 16 days ago by
Colby
• 0 • written 27 days ago by
SciencyUsagi
▴ 10
2
votes
5
replies
198
views
Create the design matrix
DEGseq
edgeR
RNASeq
29 days ago • updated 28 days ago
Mohammad
• 0
2
votes
4
replies
280
views
How to identify top most variable genes from log2 normalized data?
supervised
edgeR
variance
RNASeq
heatmaps
4 weeks ago
mohammedtoufiq91
▴ 10
0
votes
3
replies
153
views
DESeq2 Statistic - Padj NA
DESeq2
RNAseq123
rnaseq
deseq2
metatranscriptomic
updated 4 weeks ago by
Michael Love
39k • written 5 weeks ago by
irish.prg
• 0
0
votes
0
replies
81
views
A problem with Experimental Design for Limma
limma
RNASeq
6 weeks ago
ToReality
• 0
0
votes
3
replies
240
views
Unusual MA and volcano plots?
DESeq2
RNASeq
written 6 weeks ago by
BT
▴ 10
0
votes
1
reply
109
views
Job:
'Omics data analyst for HPCBio, University of Illinois
SingleCell
rnaseq
methylationArrayAnalysis
Spatial
written 6 weeks ago by
Jenny Drnevich
★ 2.0k
1
vote
2
replies
152
views
Extracting specific comparisons after fitting model in EdgeR
edgeR
limma
design
RNASeq
model.matrix
7 weeks ago
mohammedtoufiq91
▴ 10
0
votes
0
replies
92
views
RNA seq analysis
RNASeq
7 weeks ago
lesseyl
• 0
2
votes
3
replies
262
views
Error while reading rsem files in tximport
DESeq2
tximport
rsem
RNASeq
tximportData
8 weeks ago • updated 7 weeks ago
mohammedtoufiq91
▴ 10
0
votes
1
reply
98
views
TCGA RNAseq Normalization
normalization
RNASEQ
Normalization
TCGAutils
TCGA
updated 8 weeks ago by
ATpoint
★ 2.1k • written 8 weeks ago by
Deniz
• 0
2
votes
4
replies
328
views
Possibility of using TPM or FPKM values in edgeR for differential expression analysis?
DESeq2
R
edgeR
Normalization
RNASeq
8 weeks ago
mohammedtoufiq91
▴ 10
0
votes
1
reply
165
views
Interpretation of coefficient when using "~ grp + grp:ind.n + grp:cnd"
DESeq2
interaction
coefficient
LinearModel
RNASeq
updated 8 weeks ago by
Michael Love
39k • written 11 weeks ago by
Pedro Milanez-Almeida
▴ 10
1
vote
1
reply
169
views
Quantification of Genes with RSubread::featureCounts() at exon-level vs gene-level?
Subread
RNASeq
featureCounts
quantification
updated 8 weeks ago by
Gordon Smyth
47k • written 9 weeks ago by
Sara
• 0
0
votes
3
replies
226
views
Higher Dimensional RNASeq Clustering Significance
DESeq2
RNASeq
PrincipalComponent
pcaExplorer
updated 9 weeks ago by
oletaschmeler
• 0 • written 9 weeks ago by
James
• 0
1
vote
2
replies
187
views
How to process and analyze Total RNA-Seq data?
DESeq2
R
edgeR
Normalization
RNASeq
9 weeks ago
mohammedtoufiq91
▴ 10
0
votes
1
reply
118
views
Trouble with importing transcript counts with Salmon
Salmon
tximport
RNAseq
EdgeR
updated 9 weeks ago by
ATpoint
★ 2.1k • written 9 weeks ago by
Jenni
• 0
0
votes
0
replies
90
views
Job:
EPA Postdoctoral Fellowship in Bioinformatics and Computational Toxicology
MethylSeq
Transcriptomics
Pathways
Epigenetics
RNASeq
10 weeks ago
whduke
• 0
0
votes
1
reply
122
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell
RNASeq
RNASeqData
scRNAseq
updated 10 weeks ago by
Gordon Smyth
47k • written 10 weeks ago by
irvin.ng
• 0
0
votes
3
replies
142
views
Gene ontology enrichment analysis
rnaseq
rnaseqGene
geneontology
updated 10 weeks ago by
James W. MacDonald
62k • written 10 weeks ago by
acram
• 0
0
votes
1
reply
126
views
Analysing only significant genes from differential expression analysis in a replication cohort
RNASeq
updated 10 weeks ago by
swbarnes2
★ 1.2k • written 11 weeks ago by
S
• 0
2
votes
3
replies
183
views
Rsubread featureCounts outputs dozens of temp files, no counts
RNAseq
R
Rsubread
featurecounts
RNASeq
updated 11 weeks ago by
Gordon Smyth
47k • written 11 weeks ago by
Jon
• 0
0
votes
2
replies
206
views
RNA-Seq Reads Count
DESeq2
htseq
DEGseq
RNASeq
read
updated 12 weeks ago by
Michael Love
39k • written 3 months ago by
Paola
• 0
3
votes
7
replies
450
views
How to visaulize RNAseq data with edgeR, limma, ...?
r
rnaseq
DifferentialExpression
limma
edger
updated 12 weeks ago by
Gordon Smyth
47k • written 12 weeks ago by
jirkamanuel.petersen
• 0
1
vote
2
replies
201
views
Design formula with batch effects DESeq2 "Not full rank matrix" error.
DESeq2
BatchEffect
RNASeq
updated 3 months ago by
swbarnes2
★ 1.2k • written 3 months ago by
Flavio
• 0
0
votes
0
replies
94
views
Correct GFF3 translation for FeatureCounts
RNASeq
FeatureCounts
Rna
3 months ago
rridley3
• 0
3
votes
14
replies
722
views
Atena package - error (new user)
RNAseq
R
Atena
3 months ago • updated 7 days ago
lalanis1
• 0
2
votes
5
replies
1.5k
views
DESeq2 with two continuous variable in a design
DESeq2
RNASeq
R
design
updated 3 months ago by
Michael Love
39k • written 19 months ago by
sofia
• 0
0
votes
1
reply
275
views
Does DeSeq2 make comparisons between all samples vs. all controls, or between matched samples and controls in different groups?
DESeq2
RNAseq
bulk
DifferentialExpression
updated 3 months ago by
James W. MacDonald
62k • written 3 months ago by
Maria
• 0
0
votes
0
replies
121
views
question on the p value for VIPER results by dorothea
RNAseq
VIPER
Doth
4 months ago
snowmattin
• 0
0
votes
0
replies
119
views
WCGNA: Using Eigengenes when correlating modules to external features? What about PC2, PC3???
Network
Transcriptomics
MicrobiomeData
RNASEQ
WCGNA
4 months ago
Julieta
• 0
0
votes
0
replies
124
views
Simplify - clusterProfiler
RNASeq
simplify
clusterProfiler
enrichGO
simplifyEnrichment
4 months ago
estafana.t98
• 0
3
votes
4
replies
308
views
difference between txi$counts and txi$abundance when countsFromAbundance is true
RNAseq
tximport
updated 4 months ago by
ATpoint
★ 2.1k • written 4 months ago by
snowmattin
• 0
0
votes
1
reply
167
views
Confused about design for RNA seq experiment
RNAseq
ExperimentData
RNAseq123
RNA
ExperimentalDesign
updated 4 months ago by
ATpoint
★ 2.1k • written 4 months ago by
Mohamed
• 0
0
votes
1
reply
208
views
Reversing DEseq2 normalization
DESeq2
Normalization
RNASeq
updated 4 months ago by
Michael Love
39k • written 4 months ago by
adeizadavid
• 0
0
votes
0
replies
128
views
how to create PHENO_DATA
RNASeq
RNASeqData
RNASeqRData
4 months ago
marymshahi2021
• 0
0
votes
2
replies
1.4k
views
maSigPro: how to extract the genes in the same cluster
rnaseq
updated 4 months ago by
oseias.rf.junior
• 0 • written 6.8 years ago by
simonjean434
▴ 10
1
vote
2
replies
233
views
how to plot the union of the 100 most expressed genes
DESeq2
RNASEQ
updated 5 months ago by
ATpoint
★ 2.1k • written 5 months ago by
reem
• 0
0
votes
1
reply
196
views
Correlation between two different datasets: between results of RNAseq and absence/presence of Type3 Secretion System
RNASeq
Correlation
DESeq2
updated 5 months ago by
Michael Love
39k • written 5 months ago by
keshav.prasad.gubbi
• 0
2
votes
7
replies
458
views
Error in Create switchAnalyzeRlist
AlternativeSplicing
RNASeq
IsoformSwitchAnalyzeR
gtf
updated 5 months ago by
k.vitting.seerup
▴ 120 • written 5 months ago by
bpshtiwan
▴ 10
0
votes
2
replies
406
views
Error with TCGA package - TCGAbiolinks
TCGAbiolinks
RNASeq
CancerData
updated 5 months ago by
Tiago C. Silva
▴ 220 • written 7 months ago by
JAcky
• 0
0
votes
0
replies
140
views
DEXSeq aggregated genes/exons result in NA values
RNASeq
R
DEXSeq
5 months ago
osieman52
• 0
4
votes
5
replies
643
views
Which is the best type of data for correlation or survival analysis
TPM
RNASeq
RSEM
DESeq2
updated 5 months ago by
Michael Love
39k • written 5 months ago by
Yang Shi
• 0
1
vote
1
reply
174
views
Handling heterogeneous data in DESeq2: multiple covariates to control against
RNASeq
DESeq2
updated 5 months ago by
ATpoint
★ 2.1k • written 5 months ago by
seeta_rajpara
• 0
1
vote
5
replies
493
views
DESeq2 outlier options and LFC Shrinkage
DESeq2
RNASeq
RnaSeqSampleSize
apeglm
updated 5 months ago by
Michael Love
39k • written 5 months ago by
Riley
• 0
0
votes
6
replies
528
views
Is DESeq2 generating false postives when changing different pre-filtering thresholds?
RNASeq
DEG
DESeq2
6 months ago • updated 5 months ago
Weiqian
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper
by
k.roelfs
• 0
I felt that my way of analyzing this data set was a bit unfortunate. I was not involved in the experimental design myself and am now trying…
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper
by
k.roelfs
• 0
For tissue T1 and each time point, each replicate corresponds to a single plant. For tissue T2, we actually had to sample 5 plants per rep…
Answer: edgeR: Usage of estimated dispersion from replicates for pools of the same exper
by
Gordon Smyth
47k
> Due to the high degree of heterozygosity of the plants used for the experiment, we thought it best to pool the same tissue under the same…
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper
by
Gordon Smyth
47k
How many plants are used for each of the biological replicate samples? One plant or a few?
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper
by
k.roelfs
• 0
Yes you are right, we have 24 RNA-seq libraries in total. The replicates come from the same population of plants, but independent from tho…
Votes
DESeq2 pairwise comparisons w/ 3 factors
A: DESeq2 pairwise comparisons w/ 3 factors
A: DESeq2 pairwise comparisons w/ 3 factors
Comment: MA plot
Comment: MA plot
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