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Showing :
RNASEQ
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0
votes
2
replies
50
views
Which genes are outliers in DESeq2?
DESeq2
RNAseq
outlier
updated 15 hours ago by
ATpoint
★ 2.1k • written 16 hours ago by
James
• 0
2
votes
10
replies
251
views
edgeR: Usage of estimated dispersion from replicates for pools of the same experiment
edgeR
RNAseq
updated 4 days ago by
Gordon Smyth
47k • written 8 days ago by
k.roelfs
• 0
2
votes
2
replies
147
views
Calculate transcriptional heterogeneity for a condition using DESeq2
RNASeq
27 days ago • updated 17 days ago
SciencyUsagi
▴ 10
0
votes
1
reply
145
views
Variance stabilization transformation (VST), blind=TRUE
DESeq2
Transcriptomics
RNASeq
updated 22 days ago by
Michael Love
39k • written 25 days ago by
Jayesh Kumar
• 0
3
votes
3
replies
165
views
Why is it better to count genes at the exon-level using subread::featureCounts()?
RNASeq
Rsubread
featureCounts
Quantification
updated 23 days ago by
Gordon Smyth
47k • written 23 days ago by
Sara
• 0
0
votes
3
replies
176
views
Gene TPM validity with STAR only quantification
RNASeq
written 5 weeks ago by
SciencyUsagi
▴ 10
2
votes
5
replies
218
views
Create the design matrix
DEGseq
edgeR
RNASeq
5 weeks ago
Mohammad
• 0
2
votes
4
replies
292
views
How to identify top most variable genes from log2 normalized data?
supervised
edgeR
variance
RNASeq
heatmaps
5 weeks ago
mohammedtoufiq91
▴ 10
0
votes
3
replies
162
views
DESeq2 Statistic - Padj NA
DESeq2
RNAseq123
rnaseq
deseq2
metatranscriptomic
updated 6 weeks ago by
Michael Love
39k • written 6 weeks ago by
irish.prg
• 0
0
votes
0
replies
85
views
A problem with Experimental Design for Limma
limma
RNASeq
7 weeks ago
ToReality
• 0
0
votes
3
replies
251
views
Unusual MA and volcano plots?
DESeq2
RNASeq
written 7 weeks ago by
BT
▴ 10
0
votes
1
reply
118
views
Job:
'Omics data analyst for HPCBio, University of Illinois
SingleCell
rnaseq
methylationArrayAnalysis
Spatial
written 8 weeks ago by
Jenny Drnevich
★ 2.0k
1
vote
2
replies
163
views
Extracting specific comparisons after fitting model in EdgeR
edgeR
limma
design
RNASeq
model.matrix
8 weeks ago
mohammedtoufiq91
▴ 10
0
votes
0
replies
95
views
RNA seq analysis
RNASeq
9 weeks ago
lesseyl
• 0
2
votes
3
replies
291
views
Error while reading rsem files in tximport
DESeq2
tximport
rsem
RNASeq
tximportData
9 weeks ago
mohammedtoufiq91
▴ 10
0
votes
1
reply
109
views
TCGA RNAseq Normalization
normalization
RNASEQ
Normalization
TCGAutils
TCGA
updated 9 weeks ago by
ATpoint
★ 2.1k • written 9 weeks ago by
Deniz
• 0
2
votes
4
replies
374
views
Possibility of using TPM or FPKM values in edgeR for differential expression analysis?
DESeq2
R
edgeR
Normalization
RNASeq
9 weeks ago
mohammedtoufiq91
▴ 10
0
votes
1
reply
183
views
Interpretation of coefficient when using "~ grp + grp:ind.n + grp:cnd"
DESeq2
interaction
coefficient
LinearModel
RNASeq
updated 9 weeks ago by
Michael Love
39k • written 12 weeks ago by
Pedro Milanez-Almeida
▴ 10
1
vote
1
reply
182
views
Quantification of Genes with RSubread::featureCounts() at exon-level vs gene-level?
Subread
RNASeq
featureCounts
quantification
updated 10 weeks ago by
Gordon Smyth
47k • written 10 weeks ago by
Sara
• 0
0
votes
3
replies
233
views
Higher Dimensional RNASeq Clustering Significance
DESeq2
RNASeq
PrincipalComponent
pcaExplorer
updated 10 weeks ago by
oletaschmeler
• 0 • written 10 weeks ago by
James
• 0
1
vote
2
replies
194
views
How to process and analyze Total RNA-Seq data?
DESeq2
R
edgeR
Normalization
RNASeq
11 weeks ago • updated 10 weeks ago
mohammedtoufiq91
▴ 10
0
votes
1
reply
133
views
Trouble with importing transcript counts with Salmon
Salmon
tximport
RNAseq
EdgeR
updated 11 weeks ago by
ATpoint
★ 2.1k • written 11 weeks ago by
Jenni
• 0
0
votes
0
replies
98
views
Job:
EPA Postdoctoral Fellowship in Bioinformatics and Computational Toxicology
MethylSeq
Transcriptomics
Pathways
Epigenetics
RNASeq
11 weeks ago
whduke
• 0
0
votes
1
reply
127
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell
RNASeq
RNASeqData
scRNAseq
updated 11 weeks ago by
Gordon Smyth
47k • written 11 weeks ago by
irvin.ng
• 0
0
votes
3
replies
170
views
Gene ontology enrichment analysis
rnaseq
rnaseqGene
geneontology
updated 11 weeks ago by
James W. MacDonald
62k • written 11 weeks ago by
acram
• 0
0
votes
1
reply
135
views
Analysing only significant genes from differential expression analysis in a replication cohort
RNASeq
updated 12 weeks ago by
swbarnes2
★ 1.2k • written 12 weeks ago by
S
• 0
2
votes
3
replies
191
views
Rsubread featureCounts outputs dozens of temp files, no counts
RNAseq
R
Rsubread
featurecounts
RNASeq
updated 12 weeks ago by
Gordon Smyth
47k • written 12 weeks ago by
Jon
• 0
0
votes
2
replies
215
views
RNA-Seq Reads Count
DESeq2
htseq
DEGseq
RNASeq
read
updated 3 months ago by
Michael Love
39k • written 3 months ago by
Paola
• 0
3
votes
7
replies
466
views
How to visaulize RNAseq data with edgeR, limma, ...?
r
rnaseq
DifferentialExpression
limma
edger
updated 3 months ago by
Gordon Smyth
47k • written 3 months ago by
jirkamanuel.petersen
• 0
1
vote
2
replies
206
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
98
views
Correct GFF3 translation for FeatureCounts
RNASeq
FeatureCounts
Rna
3 months ago
rridley3
• 0
3
votes
15
replies
754
views
Atena package - error (new user)
RNAseq
R
Atena
updated 21 hours ago by
beatriz.calvo
▴ 30 • written 3 months ago by
lalanis1
• 0
2
votes
5
replies
1.6k
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
296
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 4 months ago by
James W. MacDonald
62k • written 4 months ago by
Maria
• 0
0
votes
0
replies
129
views
question on the p value for VIPER results by dorothea
RNAseq
VIPER
Doth
4 months ago
snowmattin
• 0
0
votes
0
replies
126
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
130
views
Simplify - clusterProfiler
RNASeq
simplify
clusterProfiler
enrichGO
simplifyEnrichment
4 months ago
estafana.t98
• 0
3
votes
4
replies
315
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
172
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
216
views
Reversing DEseq2 normalization
DESeq2
Normalization
RNASeq
updated 4 months ago by
Michael Love
39k • written 5 months ago by
adeizadavid
• 0
0
votes
0
replies
132
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 5 months ago by
oseias.rf.junior
• 0 • written 6.8 years ago by
simonjean434
▴ 10
1
vote
2
replies
235
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
218
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
469
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
413
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
147
views
DEXSeq aggregated genes/exons result in NA values
RNASeq
R
DEXSeq
5 months ago
osieman52
• 0
4
votes
5
replies
659
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 6 months ago by
Yang Shi
• 0
1
vote
1
reply
177
views
Handling heterogeneous data in DESeq2: multiple covariates to control against
RNASeq
DESeq2
updated 6 months ago by
ATpoint
★ 2.1k • written 6 months ago by
seeta_rajpara
• 0
1
vote
5
replies
505
views
DESeq2 outlier options and LFC Shrinkage
DESeq2
RNASeq
RnaSeqSampleSize
apeglm
updated 6 months ago by
Michael Love
39k • written 6 months ago by
Riley
• 0
50 results • Page
1 of 1
Recent ...
Replies
Answer: struggling to create a heatmap
by
ATpoint
★ 2.1k
I am reluctant to read through that wall of code. Here is what would work. Note that prefiltering makes sense before, not after running `DE…
Answer: collapseReplicates error after tximeta
by
Michael Love
39k
The issue is that `collapseReplicates` just collapses `counts` and doesn't account for multiple assays which you need for e.g. Swish or oth…
Comment: Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it
by
ATpoint
★ 2.1k
That having said, I recommend to inspect the MA-plots (`plotMA()`), at best the ones produced right from `res <- results(dds); plotMA(res)`…
Answer: Which genes are outliers in DESeq2?
by
ATpoint
★ 2.1k
You can take over some of the lines from `results()` to find them easily: ```r suppressPackageStartupMessages(library(DESeq2)) set.s…
Answer: Which genes are outliers in DESeq2?
by
Michael Love
39k
Outliers will have high maxCooks values in `mcols(dds)` -- the threshold is `qf(.99, p, n - p)` where n is sample size and p is number of c…
Votes
Significant reporter activity with mpralm function
Answer: I cannot install annotables package in Rstudio (macOS)
Answer: log2 of normalized counts for further analyzes
Answer: Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it
Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it should *not* be used
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