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RUVSeq
•
reset
1
vote
9
replies
2.6k
views
RUV: removing unwanted variation in RNA-seq
RUV
ruvseq
rnaseq
9.0 years ago
sergio.espeso-gil
• 0
3
votes
9
replies
5.1k
views
DESeq2 results with RUVSeq values
deseq2
ruvseq
sizefacotrs
updated 9.0 years ago by
davide risso
▴ 950 • written 9.0 years ago by
Assa Yeroslaviz
★ 1.5k
1
vote
8
replies
3.7k
views
Intepretation of RUVseq/edgeR logFC
RUVseq
logFC
edgeR
9.0 years ago
Marie
• 0
2
votes
12
replies
2.5k
views
LAPACK/BLAS error with edgeR GLM
glm
edger
lapack
segfault
ruvseq
8.8 years ago
Mark.Rogers
• 0
2
votes
6
replies
3.1k
views
RUVSeq DE analysis for data with replicate samples and 4 conditions
RUVSeq
updated 7.9 years ago by
anthonycolombo60
• 0 • written 8.7 years ago by
sharvari gujja
▴ 40
4
votes
16
replies
7.4k
views
Normalised counts from RUVg in RUVSeq
RUVg
ruvseq
rnaseq
updated 8 weeks ago by
Shaimaa Gamal
• 0 • written 9.0 years ago by
Pauly Lin
▴ 150
1
vote
4
replies
2.4k
views
RUVseq control genes - invalid subscript type 'list'
ruvseq
7.9 years ago
eteleeb
▴ 10
0
votes
5
replies
2.3k
views
RUVseq for microRNAs
ruvseq
ruv
microrna
8.8 years ago
sergio.espeso-gil
• 0
5
votes
3
replies
2.5k
views
edgeR: annotation and isoform analysis alternatives
edgeR
ruvseq
rnaseq
isoforms
9.0 years ago
sergio.espeso-gil
• 0
2
votes
8
replies
2.5k
views
Issue with RUVs
ruvseq
RUVs EDA
9.7 years ago
asif.zubair
• 0
6
votes
7
replies
3.9k
views
RUVseq PCA on raw data, whereas DESeq suggests stabilization
ruvseq
deseq
8.5 years ago
tonja.r
▴ 80
0
votes
6
replies
3.1k
views
How to use RUVseq with voom-limma for differential expression analysis?
ruvseq
limma
voom
updated 7.7 years ago by
davide risso
▴ 950 • written 7.7 years ago by
brainfood
• 0
1
vote
2
replies
2.4k
views
RUVseq using RUVg most non-differential expressed genes
ruvseq
updated 8.5 years ago by
davide risso
▴ 950 • written 8.5 years ago by
tonja.r
▴ 80
0
votes
4
replies
2.6k
views
DESeq2: Outliers, covariates and number of replicates
deseq2
ruvseq
cookscutoff
covariates
batch
7.5 years ago
j.viana
• 0
0
votes
4
replies
2.2k
views
Confused about using RUVg in getting negative control genes using RUVg
RUVnormalize
R
edgeR
RUVSeq
RUVnormalizeData
23 months ago
Mohamed
▴ 30
3
votes
7
replies
2.1k
views
Batch effects between controls
batch-effect
ruvseq
updated 6.6 years ago by
James W. MacDonald
66k • written 6.6 years ago by
llo
▴ 10
4
votes
14
replies
8.8k
views
Extracting custom post-normalization counts from DESeq2
deseq2
r
ruvseq
normalization
rnaseq
8.9 years ago • updated 8.8 years ago
nickp60
• 0
1
vote
2
replies
2.3k
views
RUVg or RUVs
ruvseq
updated 8.3 years ago by
g.atla
▴ 10 • written 8.3 years ago by
tonja.r
▴ 80
2
votes
6
replies
1.5k
views
effect of polyploidy level on RUVs normalisation
normalization
ruvseq
ruvnormalize
ruvs eda
8.1 years ago
thomas.wolfe
• 0
2
votes
9
replies
2.6k
views
Zero inflation in RUV normalization and DE for single cell data
ruv
ruvseq
ruvnormalize
single-cell
zero-inflated
updated 6.8 years ago by
davide risso
▴ 950 • written 6.8 years ago by
Nik Tuzov
▴ 80
0
votes
4
replies
656
views
DESeq2 & RUVseq model matrix is less than full rank
RUVSeq
DESeq2
9 months ago
anne.hoffrichter
• 0
1
vote
4
replies
3.8k
views
Number of co-variables k in RUVSeq (RUVr)
rnaseq
ruvseq
RUVr
edgeR
8.5 years ago
David R
▴ 90
0
votes
5
replies
3.6k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq
FPKM
removeBatchEffect
RNA-seq
sva
updated 2.4 years ago by
ATpoint
★ 4.1k • written 3.2 years ago by
Xiaojie Cheng
• 0
0
votes
1
reply
1.2k
views
Raw read count Vs EdgeR normzlized read count for RUVg normalization
rnaseq
ruvseq
normalization
updated 7.5 years ago by
davide risso
▴ 950 • written 7.5 years ago by
Venu Pullabhatla
▴ 40
0
votes
5
replies
1.6k
views
Can Normalized cpm values be used as RUVs input
rnaseq
ruvseq
updated 7.7 years ago by
davide risso
▴ 950 • written 7.7 years ago by
sooby
• 0
2
votes
1
reply
1.5k
views
RUVSeq empirical negative controls? how many to take to find the span set
ruvseq
RUV
ruvnormalize
ruvg
7.9 years ago
anthonycolombo60
• 0
1
vote
9
replies
2.7k
views
EDASeq, RUVSeq and edgeR together
edaseq
ruvseq
edgeR
updated 5.6 years ago by
davide risso
▴ 950 • written 5.7 years ago by
zoppoli pietro
▴ 10
2
votes
3
replies
1.3k
views
Design Matrix with paired and independent samples plus RUVg Spike-in normalization
edger
design matrix
paired samples
ruvseq
updated 5.8 years ago by
James W. MacDonald
66k • written 5.8 years ago by
ChrisM
• 0
1
vote
3
replies
1.5k
views
Global expression shift using RUVSeq
ruvseq
rnaseq
normalization
differential expression
updated 5.9 years ago by
davide risso
▴ 950 • written 5.9 years ago by
Leon
• 0
1
vote
2
replies
1.0k
views
RUVSeq and Generalised Linear Mixed Model
ruvseq
updated 7.9 years ago by
davide risso
▴ 950 • written 7.9 years ago by
dustar1986
▴ 10
3
votes
2
replies
2.6k
views
Normalisation before RUVg and RUV2?
ruvseq
ruv
updated 9.0 years ago by
davide risso
▴ 950 • written 9.0 years ago by
Pauly Lin
▴ 150
1
vote
2
replies
1.9k
views
RUVSEq and VSD integration
deseq2
ruvseq
covariates
continuous
vsd
updated 8.2 years ago by
Michael Love
42k • written 8.2 years ago by
Mattia
▴ 10
1
vote
1
reply
1.5k
views
Outputting batch-effect free normalized counts
ruvseq
svaseq
edaseq
updated 6.5 years ago by
davide risso
▴ 950 • written 6.5 years ago by
llo
▴ 10
4
votes
5
replies
2.6k
views
Removing unwanted variation (RUV) for paired analysis ?
ruvseq
edger
ruvg
removebatcheffect
updated 8.3 years ago by
Aaron Lun
★ 28k • written 8.3 years ago by
g.atla
▴ 10
0
votes
2
replies
2.0k
views
How to use RUVSeq in clustering problems?
ruvseq
rna-seq
clustering
updated 6.6 years ago by
davide risso
▴ 950 • written 6.6 years ago by
paul.alto
▴ 50
0
votes
1
reply
2.2k
views
RUVseq: How to implement to more complex time-course model?
ruvseq
deseq2
model.matrix
confounders
updated 6.8 years ago by
davide risso
▴ 950 • written 6.8 years ago by
heikki.sarin
▴ 10
2
votes
2
replies
1.6k
views
Paired analysis and batch effects ?
ruvseq
sva
edger
updated 8.3 years ago by
Ryan C. Thompson
★ 7.9k • written 8.3 years ago by
g.atla
▴ 10
1
vote
3
replies
2.3k
views
Does it make sense to consider RUVr normalization for single cell RNA analysis?
RUV
ruvseq
ruvr
ruvnormalize
single cell
6.8 years ago
Nik Tuzov
▴ 80
0
votes
1
reply
929
views
RNAseq Analysis using RUVs
rnaseq
ruvseq
r
updated 6.9 years ago by
davide risso
▴ 950 • written 6.9 years ago by
manish20072013
• 0
1
vote
1
reply
1.7k
views
RUVSeq installation problems
RUVSeq
bioconductor
biocinstaller
updated 8.3 years ago by
davide risso
▴ 950 • written 8.3 years ago by
plinsley
• 0
0
votes
1
reply
1.3k
views
How to generate heatmap for three groups
rnaseq
ruvseq
heatmap
updated 6.9 years ago by
James W. MacDonald
66k • written 6.9 years ago by
manish20072013
• 0
2
votes
1
reply
1.3k
views
Decide normalisation method in RUVseq for RNAseq data
edger
ruvseq
rnaseq
normalization
ruvnormalize
updated 6.9 years ago by
davide risso
▴ 950 • written 6.9 years ago by
manish20072013
• 0
2
votes
4
replies
1.8k
views
RUVseq design matrix for first pass of edger
ruvseq
written 8.4 years ago by
tonja.r
▴ 80
0
votes
3
replies
1.9k
views
How can I use DESeq2 for exploratory analysis after batch effect removal using RUVSeq?
deseq2
ruvseq
rna-seq
batch effect
updated 6.5 years ago by
Michael Love
42k • written 6.5 years ago by
dbouzo
• 0
7
votes
2
replies
3.2k
views
Incorporating RUVSeq factors of unwanted variation in DESeq2 time course analysis
deseq2
ruvseq
spike-in
time course
time series
updated 6.4 years ago by
davide risso
▴ 950 • written 6.4 years ago by
staceyborrego
▴ 20
2
votes
2
replies
2.0k
views
RUVg with differential transcript expression?
ruvseq
sleuth
updated 6.4 years ago by
davide risso
▴ 950 • written 6.4 years ago by
Brian Gudenas
• 0
5
votes
4
replies
2.4k
views
Fundamental questions about DESeq2 and RUVs in targeted gene set of 500
deseq2
ruvseq
updated 7.0 years ago by
davide risso
▴ 950 • written 7.0 years ago by
grashow
▴ 10
2
votes
3
replies
2.1k
views
How to determine a set of empirical control 'genes' using RUVSeq
RUVSeq
updated 23 months ago by
Mohamed
▴ 30 • written 7.2 years ago by
cguzman.roma
• 0
0
votes
1
reply
1.2k
views
Appropriate to apply RUVSeq to exon bin counts for DEXSeq?
dexseq
ruvseq
rnaseq
updated 7.3 years ago by
davide risso
▴ 950 • written 7.4 years ago by
Cornwell, Adam
▴ 110
0
votes
1
reply
2.3k
views
Can FPKM or TPM values be used as RUVs input ?
ruvseq
ruvg
ruv
updated 7.3 years ago by
davide risso
▴ 950 • written 7.4 years ago by
weiwsmiling
• 0
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