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mirna
•
reset
1
vote
4
replies
553
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
618
views
How to annotate mir4.1 arrays?
AffymetrixChip
miRNA
oligo
10 months ago • updated 7 months ago
richardallenfriedmanbrooklyn
▴ 20
1
vote
1
reply
689
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
564
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
871
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
810
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
855
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
795
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
935
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
989
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
975
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
50 results • Page
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Recent ...
Replies
Comment: limma models out of memory issue on Slurm HPC
by
Jitendra
▴ 10
thanks Gordon, but our methylation epic array input file is quite big and we can't read it in R by just using laptop memory so we need to …
Comment: Doing comparison of RNA-seq data using EdgeR
by
Michael Love
41k
Just to clarify, when I originally posted the title and tags had listed "DESeq2" and then the post was changed after my answer was added. …
Comment: fgsea fork
by
shepherl
3.8k
Not quite sure what you mean by clone or fork the package on latest version of R. Bioconductor runs all builds on the latest version of R.…
Answer: Doing comparison of RNA-seq data using EdgeR
by
Gordon Smyth
50k
It's pretty easy to do a two-group comparison using edgeR, but you seem to be stuck at the initial stage of reading data into R. If you exp…
Answer: Differing results from plotMDS and PCAtools
by
Gordon Smyth
50k
The reason why the two plots are different is that the first plot is a PCA plot while the second is a biplot. Quite different plots. The P…
Votes
transcript name mapping between human and mouse
transcript name mapping between human and mouse
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
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