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rnaseq
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0
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5
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Using featureCounts and downloading Rsubread
Rsubread
featureCounts
DESeq2
R
RNASeq
17 minutes ago • updated 11 minutes ago
margo
• 0
0
votes
1
reply
146
views
Looking for a package that compares my RNA seq data to find published dataset with a similar expression pattern
RNASeq
updated 5 days ago by
Sehyun Oh
• 0 • written 13 days ago by
curiousmind007
• 0
0
votes
2
replies
82
views
How to properly use DESeq2 for an experiment
ExperimentalDesign
RNASeq
DifferentialExpression
DESeq2
updated 6 days ago by
Michael Love
36k • written 6 days ago by
Aurélien
• 0
3
votes
11
replies
352
views
RNA-seq: compare two technical replicates
RNASeq
updated 14 days ago by
Gordon Smyth
45k • written 20 days ago by
Marianna
• 0
1
vote
9
replies
805
views
Deseq2 normalization for WGCNA
RNASeq
Deseq2
DESeq2
WGCNA
updated 16 days ago by
Michael Love
36k • written 4 months ago by
jms2520
• 0
0
votes
2
replies
101
views
edgeR
rnaseq
edgeR
updated 27 days ago by
Gordon Smyth
45k • written 27 days ago by
edusbioinfo
• 0
12
votes
5
replies
4.6k
views
EDGE-R exact test vs QL F-test
edger
rnaseq
updated 28 days ago by
Sarah
• 0 • written 5.9 years ago by
kaihami
▴ 20
0
votes
3
replies
133
views
Best way to do RNA-seq analysis for a small number of samples obtained from 2 different batches
RNASeq
updated 28 days ago by
swbarnes2
★ 1.0k • written 29 days ago by
theemperor79
• 0
5
votes
6
replies
239
views
Large difference in PCA plot based on LCPM (log counts per million) and VST (variance stabilizing transformations)
PCAtools
edgeR
pcaExplorer
RNASeq
RNAseq123
4 weeks ago
Alan
• 0
0
votes
0
replies
70
views
Only 1 gene/ feature is present in module after WGCNA analysis
RNASeq
Clustering
cluster
WGCNA
4 weeks ago
chiwut.wong
• 0
0
votes
7
replies
285
views
DESeq2 on allelic reads
RNASeq
DifferentialExpression
DESeq2
updated 5 weeks ago by
Michael Love
36k • written 5 weeks ago by
Nayrouz
• 0
5
votes
13
replies
2.7k
views
Cross-species RNA-seq with DESeq2
deseq2
rnaseq
across species
updated 5 weeks ago by
petersearle94
• 0 • written 4.9 years ago by
vtartaglio
▴ 10
0
votes
0
replies
63
views
Pathway Analysis using GAGE
gage
RNASeq
gageData
Pathways
5 weeks ago
OST
• 0
2
votes
4
replies
163
views
confused with tximport counts abundance using salmon input
RNASeq
tximport
5 weeks ago
Al90
• 0
4
votes
4
replies
830
views
DESeq2: LRT or WALD guidance
DESeq2
RNASeq
DifferentialExpression
updated 6 weeks ago by
krushnach80
• 0 • written 8 months ago by
morgan.sobol
• 0
3
votes
3
replies
6.0k
views
GSEA preranked analysis downstream of DEseq2
deseq2
gsea
rnaseq
updated 6 weeks ago by
Michael Love
36k • written 5.8 years ago by
EJ
▴ 10
0
votes
1
reply
140
views
Rtracklayer
rtracklayer
RNASeq
gff
updated 6 weeks ago by
James W. MacDonald
59k • written 6 weeks ago by
edusbioinfo
• 0
0
votes
1
reply
122
views
Differential Expression Analysis-Input is DESeq Standardized
rnaseq
RNASeqData
limma
limmaGUI
updated 6 weeks ago by
Michael Love
36k • written 6 weeks ago by
sushimoto
• 0
1
vote
4
replies
634
views
Issues with scaling down enrichplot's dotplot and gseaplot2 plots
RNASeq
clusterProfiler
enrichplot
updated 6 weeks ago by
Lihe
• 0 • written 10 months ago by
jiro.becker
• 0
0
votes
3
replies
145
views
DEseq2 Analysis over multiple tissues and conditions only gives 16 coefficients
DESeq2
RNASeq
updated 7 weeks ago by
Michael Love
36k • written 7 weeks ago by
niko.fleischer
• 0
0
votes
2
replies
1.7k
views
DESeq2 counts distribution across both genes and samples
deseq2
rnaseq
updated 7 weeks ago by
BarryGutierrez
• 0 • written 5.7 years ago by
igor
▴ 40
5
votes
2
replies
3.1k
views
deseq2 LRT vs Wald test results for DE expression among 4 conditions
rnaseq
deseq2
lrt
wald
differential gene expression
updated 7 weeks ago by
krushnach80
• 0 • written 4.7 years ago by
chrysanthi.taxiarchi12
• 0
0
votes
0
replies
82
views
How to perform transcription factor enrichment analysis (TFEA) for RNA-seq counts data.
TFEA.ChIP
RNASeq
RNASeqData
7 weeks ago
treebig44
▴ 30
0
votes
4
replies
219
views
limma: Genes Associated with Continuous Predictor in Subsets of Samples
RNASeq
limma
8 weeks ago • updated 7 weeks ago
danphillips28
• 0
1
vote
0
replies
83
views
Is that possible to find if the sequence is enriched by specific motifs
MotifDiscovery
RNASeq
7 weeks ago
Liliian
• 0
0
votes
0
replies
85
views
Create a Gene Enrichment GO plot from goana output
goana
RNASeq
edgeR
RnaSeq
GO
7 weeks ago
Raito92
▴ 60
2
votes
2
replies
123
views
Make samples symbols bigger in PCA / MDS analysis with plotMDS function
plotMDS
PCA
RNASeq
MDS
updated 7 weeks ago by
Gordon Smyth
45k • written 8 weeks ago by
Raito92
▴ 60
0
votes
1
reply
137
views
GSEA using custom GO annotations
RNASeq
GSEA
updated 8 weeks ago by
Robert Castelo
★ 2.8k • written 8 weeks ago by
jms2520
• 0
0
votes
1
reply
125
views
Edge R Error in quantile.default(zresid, probs = prob) : missing values and NaN's not allowed if 'na.rm' is FALSE
diffSpliceDGE
RNASeq
DifferentialSplicingWorkflow
AlternativeSplicing
edgeR
updated 8 weeks ago by
Gordon Smyth
45k • written 8 weeks ago by
zhaoqiao1027
• 0
4
votes
1
reply
167
views
Finding significant up-regulated and down-regulated genes given a log2FoldChange threshold
DESeq2
RNASeq
RNASeqData
updated 8 weeks ago by
Michael Love
36k • written 8 weeks ago by
treebig44
▴ 30
1
vote
1
reply
102
views
Strange error while running DESeq() function.
DESeq2
RNASeq
RNASeqData
updated 8 weeks ago by
Michael Love
36k • written 8 weeks ago by
treebig44
▴ 30
2
votes
6
replies
249
views
How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
DESeq2
RNASeq
RNASeqData
9 weeks ago
treebig44
▴ 30
0
votes
0
replies
94
views
Gage pathway analysis of RNAseq graphical representation as dot plot
gage
plot
RNASeq
goseq
updated 9 weeks ago by
Michael Love
36k • written 9 weeks ago by
m.glymenaki
• 0
2
votes
2
replies
178
views
Complex contrasts in limma
RNASeq
limma
DifferentialExpression
10 weeks ago
tcalvo
▴ 70
0
votes
3
replies
339
views
EdgeR question: why I got discrepancy results for DEGs when using different ways setting up the models
RNAseq
edgeR
DEGs
updated 10 weeks ago by
Gordon Smyth
45k • written 9 months ago by
Ming
▴ 360
1
vote
5
replies
3.9k
views
limma-voom
RNASeq
Normalization
limma
edgeR
RNASeq
Normalization
limma
edgeR
updated 10 weeks ago by
Gordon Smyth
45k • written 8.3 years ago by
Ming
▴ 360
2
votes
6
replies
1.3k
views
Three way-interaction on voom (limma) data, including a factor with > 2 levels
RNASeq
limma
voom
anova
updated 10 weeks ago by
tcalvo
▴ 70 • written 4.9 years ago by
David Rengel
▴ 70
0
votes
2
replies
197
views
Differential expression in fixed windows
DESeq2
RNASeq
12 weeks ago • updated 11 weeks ago
anatmela
• 0
2
votes
1
reply
187
views
DESeq2 handling of replicates
DESeq2
RNASeq
limma
updated 12 weeks ago by
Michael Love
36k • written 12 weeks ago by
Eyal
• 0
0
votes
1
reply
140
views
Controlling for sex variance in Galaxy DESeq2
DESeq2
RNASeq
Galaxy
updated 3 months ago by
Michael Love
36k • written 3 months ago by
István
• 0
0
votes
1
reply
165
views
95% Confidence intervals for Fold Changes computed by DESeq2
DESeq2
RNASeq
updated 3 months ago by
ATpoint
★ 1.2k • written 3 months ago by
martin.kinisu
• 0
10
votes
3
replies
387
views
lfcShrink function for different comparison
DESeq2
RNASeq
updated 3 months ago by
molly_the_minotaur
▴ 20 • written 18 months ago by
bi.mi
▴ 50
0
votes
6
replies
395
views
Performing simple pairwise comparisons in DESEQ2
edgeR
DEG
RNASeq
DESEQ2
updated 3 months ago by
Michael Love
36k • written 3 months ago by
Raito92
▴ 60
0
votes
1
reply
168
views
Exporting org.*.*.db Gene Ontology annotations to excel sheet or txt
OrgDb
RNASeq
updated 3 months ago by
James W. MacDonald
59k • written 3 months ago by
Jonas
• 0
0
votes
4
replies
329
views
How do you get averages of each group in Limma output
RNASeq
limma
3 months ago
Matthew
• 0
0
votes
4
replies
315
views
Multi-factor paired RNAseq differential analysis with DEseq2
DESeq2
RNASeq
updated 3 months ago by
swbarnes2
★ 1.0k • written 3 months ago by
Matthew
• 0
3
votes
9
replies
1.4k
views
LOC gene IDs for characterised genes in annotation files
Annotation
RNAseq
updated 3 months ago by
Lan
• 0 • written 12 months ago by
Chris
• 0
0
votes
3
replies
314
views
DESeq2 contrast multiple treated conditions versus multiple control conditions
RNASeq
DESeq2
updated 3 months ago by
Basti
▴ 280 • written 3 months ago by
User000
• 0
0
votes
3
replies
394
views
using the goana function from edgeR
RNASeq
edgeR
GO
GOSemSim
updated 3 months ago by
Gordon Smyth
45k • written 3 months ago by
David Rengel
▴ 70
1
vote
2
replies
173
views
Correct use of Likelihood Ratio Test and LFC Shrinkage
RNASeq
LRT
DESeq2
lfcShrink
updated 3 months ago by
Michael Love
36k • written 3 months ago by
Emma
• 0
50 results • Page
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Answer: Using featureCounts and downloading Rsubread
by
James W. MacDonald
59k
You need to tell `BiocManager;;install` that you want to install the `Rsubread` package. ``` BiocManager::install("Rsubread") library(…
Comment: featureCounts: 0% successfully assigned fragments
by
KMS
• 0
Dear ATpoint I am exactly looking for read/gene count from BAM/SAM file either through ht-seq or feature count feature count giving me 0% s…
Answer: Get MANE transcripts from TxDb.Hsapiens.UCSC.hg38.knownGene
by
James W. MacDonald
59k
There is the ncbiRefSeqSelect table that has the MANE and RefSeq Select transcripts. It's not just the MANE though. ``` > z <- makeTxDb…
Comment: Handling of missing values in limma
by
AyHi
• 0
Thank you, Gordon, for your reply. I used sum(is.na(lmfit)) after lmFit, but somewhat it indicated there was no NA observations even when…
Comment: merging VCF files
by
lesefo6448
• 0
You can use this VCF Merger Software if you want to Merge VCF files into one file. this Software easily Merge your multiple VCF files with…
Votes
Answer: Load packages when using BatchtoolsParam
Comment: Load packages when using BatchtoolsParam
Answer: edgeR: the F-statistics changed after removing lowly expressed gene
Answer: edgeR: the F-statistics changed after removing lowly expressed gene
A: DESeq2: thousands of NA for pvalues?
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