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mirna
•
reset
1
vote
4
replies
551
views
controling for batch effect while preserving variation within repeated measures that unevenly distributed across batches
miRNA
BatchEffect
RNASeq
limma
4 months ago
Wending
• 0
1
vote
4
replies
617
views
How to annotate mir4.1 arrays?
AffymetrixChip
miRNA
oligo
10 months ago • updated 7 months ago
richardallenfriedmanbrooklyn
▴ 20
1
vote
1
reply
688
views
Library sizes of miRNA sequencing data and TMM normalization with Edge-R
edgeR
SequencingData
miRNA
TMM
Normalization
updated 13 months ago by
Gordon Smyth
50k • written 13 months ago by
tleona3
• 0
6
votes
6
replies
1.4k
views
Too many differentially expressed miRNA with limma
limma
miRNA
Microarray
16 months ago
Sara
▴ 10
1
vote
3
replies
1.6k
views
miRNA differential expression analysis - treat as transcript level?
tximport
DESeq2
edgeR
swish
miRNA
updated 21 months ago by
Michael Love
41k • written 21 months ago by
BG
• 0
0
votes
1
reply
563
views
miRNA analysis with DESeq2
mirna
DESeq2
updated 22 months ago by
Michael Love
41k • written 22 months ago by
Faith.omonijo
• 0
2
votes
2
replies
866
views
edgeR: How to display/plot individual miRNAs found to be differentialy expressed?
miRNAData
miRNA
DifferentialExpression
edgeR
23 months ago
Sarah
• 0
0
votes
3
replies
809
views
DESEQ PCA
DESeq2
miRNA
updated 2.6 years ago by
swbarnes2
★ 1.3k • written 2.6 years ago by
PJC
• 0
0
votes
1
reply
854
views
How to calculate high and low tumor mutational burden
SomaticMutation
miRNA
updated 2.8 years ago by
ATpoint
★ 4.0k • written 2.8 years ago by
lily
▴ 20
0
votes
1
reply
1.4k
views
edgeR on microRNA data
miRNA
edgeR
miRNA
edgeR
updated 2.8 years ago by
Gordon Smyth
50k • written 12.5 years ago by
Helena Persson
▴ 50
0
votes
1
reply
794
views
mircomb analysis from deg's list
mircomb
mrna
mirna
degs
interaction
3.8 years ago • updated 3.7 years ago
andreia
▴ 10
6
votes
4
replies
2.6k
views
Affymetrix miRNA4.1 / oligo package / pd.mirna.4.1
microarray
mirna
oligo package
pdinfobuilder
pd.mirna
updated 4.4 years ago by
soumyab.g
▴ 10 • written 6.8 years ago by
rolan.zauner
▴ 20
0
votes
2
replies
1.2k
views
Very high threshold for independent filtering
deseq2
mirna
independent filtering
updated 5.1 years ago by
Michael Love
41k • written 5.1 years ago by
thomas.deimel
• 0
0
votes
5
replies
1.4k
views
Hill shape p-value histogram after differential miRNA expression analysis with DESeq2
deseq2
mirna
fdrtool
updated 5.1 years ago by
Robert Castelo
★ 3.1k • written 5.1 years ago by
L_K
• 0
1
vote
8
replies
2.4k
views
Trying to map nucleotide position from a transcript to genomic location
genomicfeatures
mapfromtranscripts
mirna
updated 5.5 years ago by
Valerie Obenchain
★ 6.8k • written 5.5 years ago by
Victoria Perreau
▴ 20
1
vote
2
replies
1.1k
views
Whether "read_counts_miRNA" or "reads_per_million_miRNA" to use for DE expression analysis using DeSeq2
tcgadownload
deseq2
mirna
normalization
updated 5.8 years ago by
Lorena Pantano
▴ 120 • written 5.8 years ago by
Björn
• 0
0
votes
0
replies
1.2k
views
miR2Pathway Finite Observations
pathway analysis
mirna
parallel
6.0 years ago
genomic8328
▴ 10
2
votes
0
replies
1.2k
views
Job:
PhD Studentship - Investigating Regulation of Transcription and Translation in Prostate Cancer
mirna
riboseq
smallrna
differential gene expression
Job
6.0 years ago
Andy Lynch
▴ 120
0
votes
1
reply
1.2k
views
Best way to analyze multiple treatments using DESeq2?
deseq2
rna-seq
mirna
updated 6.1 years ago by
Michael Love
41k • written 6.1 years ago by
michael.frech
• 0
0
votes
0
replies
1.1k
views
Custom graphNEL object for pathview
pathview
mirintegrator
miRNA
6.5 years ago
drowsygoat
▴ 40
4
votes
3
replies
3.7k
views
EdgeR on miRNA data
edger
miRNA
updated 7.0 years ago by
Aaron Lun
★ 28k • written 7.0 years ago by
melmogy
• 0
0
votes
4
replies
4.4k
views
miRNA-seq data analysis
miRNA
mirna-seq
updated 7.0 years ago by
Jon Bråte
▴ 250 • written 7.1 years ago by
just
• 0
0
votes
0
replies
1.5k
views
miRNA target prediction tool(package) using R
mirna
prediction
target
7.1 years ago
Adam
• 0
1
vote
1
reply
1.0k
views
miRNA normalization for large amount of samples using LVSmiRNA
mirna
normalization
7.5 years ago • updated 7.3 years ago
carleshf
▴ 10
2
votes
5
replies
1.6k
views
miRNA Probe IDs
mirna
microarray
mirbase.db
updated 7.5 years ago by
Dario Strbenac
★ 1.5k • written 7.5 years ago by
snufkin002
• 0
1
vote
2
replies
1.7k
views
Rsubread align for miRNAseq?
rsubread
miRNA
updated 7.5 years ago by
Wei Shi
★ 3.6k • written 7.5 years ago by
Ina Hoeschele
▴ 620
0
votes
2
replies
934
views
Differential expression of one group agains all samples
deseq2
mirna
differential gene expression
updated 7.5 years ago by
Gavin Kelly
▴ 680 • written 7.5 years ago by
ofonov
▴ 10
0
votes
2
replies
2.0k
views
TPM for miRNA tags
mirna
7.5 years ago
manoharankumar01
• 0
0
votes
0
replies
1.3k
views
Normalizing miRNA-1_0 and miRNA-1_0_2Xgain type arrays simultaneously
mirna
microarray
normalization
7.5 years ago
arisarkar88
▴ 40
3
votes
6
replies
4.3k
views
Affymetrix miRNA 4.0 Normalization and Analysis
R
Limma
microarray
miRNA
updated 2.9 years ago by
S
▴ 10 • written 8.1 years ago by
Radek
▴ 90
4
votes
6
replies
2.7k
views
limma: within-array duplicates correlation
limma
mirna
microarray
updated 8.2 years ago by
Aaron Lun
★ 28k • written 8.2 years ago by
roser.navarro
• 0
0
votes
0
replies
1.3k
views
get precursor mirna from mature mirna
bioconductor
mirna
mir
mirbase.db
8.2 years ago
C T
▴ 140
3
votes
4
replies
1.8k
views
Network generation from adjacency matrix of zeroes and ones
R
adjacency matrix
mirna
8.3 years ago
alptaciroglu
▴ 50
0
votes
0
replies
1.4k
views
miRNA 3D-Gene chips Toray
Toray 3D-Gene
miRNA
limma
8.5 years ago
santi.cabellos
▴ 10
0
votes
0
replies
988
views
targetScan R errors
targetscan
R
error handling
miRNA
8.5 years ago
alptaciroglu
▴ 50
1
vote
5
replies
1.5k
views
normalization of a miRNA microarray
normalization
vsn
eximir
microarray
miRNA
updated 8.5 years ago by
Wolfgang Huber
★ 13k • written 8.5 years ago by
alptaciroglu
▴ 50
1
vote
1
reply
1.2k
views
How can get the GO and KEGG miRNA microarray Agilent?
go
kegg
limma
microarray
mirna
8.5 years ago
santi.cabellos
▴ 10
2
votes
5
replies
2.0k
views
Problems with "read.agiMicroRna"
read.agiMicroRna
agilent
limma
microarray
mirna
updated 8.5 years ago by
Jim Java
▴ 30 • written 8.5 years ago by
santi.cabellos
▴ 10
4
votes
2
replies
2.2k
views
Detect global differences in miRNA expression between tumor and normal using spike-ins
edger
limma
mirna
sequencing
updated 8.7 years ago by
Aaron Lun
★ 28k • written 8.7 years ago by
R
▴ 40
2
votes
5
replies
2.9k
views
miRNA expression analysis : annotation
miRNA
annotation
affymetrixchip
9.0 years ago • updated 8.9 years ago
aswathym
▴ 10
0
votes
0
replies
974
views
Invitation Research Collaborations
cancer
microarray
mirna
sequencing
9.0 years ago
alexandru.floares
• 0
0
votes
0
replies
1.7k
views
News:
RNAseq data analysis courses: Torino (Italy) : Beginner course March 17-19 2015 & Advance Course April 14-16 2015
rnaseq
mirna
onechannelgui
chimera
News
9.2 years ago
raffaele calogero
▴ 500
6
votes
2
replies
1.8k
views
Should I skip the eBayes step when using Limma for Affymetrix miRNA v1 chip?
miRNA
cdf
probe
limma
miRNA
cdf
probe
limma
updated 9.5 years ago by
Gordon Smyth
50k • written 9.6 years ago by
Guest User
★ 13k
3
votes
1
reply
1.3k
views
Bioinformatics researching Schizophrenia
miRNA
updated 9.5 years ago by
Valerie Obenchain
★ 6.8k • written 9.5 years ago by
Guest User
★ 13k
0
votes
5
replies
1.9k
views
Using custom CDF with 'make.cdf.env'
miRNA
cdf
probe
miRNA
cdf
probe
updated 9.6 years ago by
Scott Robinson
▴ 130 • written 9.6 years ago by
Guest User
★ 13k
0
votes
0
replies
4.0k
views
cpm cutoff (edgeR) [was: total count filter cutoff (edgeR)]
Sequencing
miRNA
edgeR
Sequencing
miRNA
edgeR
9.8 years ago
Gordon Smyth
50k
0
votes
0
replies
1.1k
views
total count filter cutoff (edgeR)
miRNA
edgeR
miRNA
edgeR
9.8 years ago
Daniel
▴ 10
0
votes
0
replies
1.2k
views
QuasR for miRNA
miRNA
QuasR
miRNA
QuasR
9.9 years ago
Michael Stadler
▴ 350
0
votes
4
replies
1.5k
views
combat error message
miRNA
Normalization
affy
miRNA
Normalization
affy
updated 9.9 years ago by
Guest User
★ 13k • written 9.9 years ago by
W. Evan Johnson
▴ 850
0
votes
0
replies
1.0k
views
ComBat error message, thanks
miRNA
Normalization
affy
miRNA
Normalization
affy
9.9 years ago
Guan
▴ 20
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Answer: New genes that did not exist in dds object suddenly showed up after degPatterns
by
Michael Love
41k
May be documented by the software you are using? https://github.com/lpantano/DEGreport
Answer: Doing comparison of RNA-seq data using Deseq2
by
Michael Love
41k
Take a look at our workflow, this starts from a beginner's level. You could export from Excel using CSV or TSV, then read into R. htt…
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by
James W. MacDonald
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This support site is meant to help people with questions about Bioconductor packages (WGCNA is not a Bioconductor package). You might try o…
Comment: miRTarRnaseq library
by
mercedeh.movassagh
▴ 10
Yes that is correct
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
by
Gordon Smyth
50k
It is the minimum group size rather than the total number of samples that is relevant. `min.prop` is more a biological parameter rather th…
Votes
A: Error object and replacement value dimnames differ, when changing column names o
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
DESeq2 normalization vs VST vs rlog
Answer: DESeq2 "Contrast" option
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