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2
votes
7
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1.4k
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distanceToNearest
rtracklayer
ranges
distanceToNearest
23 months ago
robjohn70000
• 0
1
vote
0
replies
809
views
News:
Ensembl 111 has been released
Ensembl
biomaRt
23 months ago
Benjamin
▴ 30
0
votes
1
reply
685
views
Conversion of .sf to .rgel format for the salmon processed files with transcript to gene mapping.
RnaSeqSampleSize
updated 23 months ago by
ATpoint
★ 5.0k • written 23 months ago by
Anudev
• 0
0
votes
0
replies
821
views
News:
Online course - Flow cytometry data analysis with R/Bioconductor
flowDensity
flowCore
23 months ago
info
▴ 10
4
votes
5
replies
1.7k
views
Bioconductor code browser time out
Bioconductor
updated 6 months ago by
Mike Smith
★ 6.6k • written 23 months ago by
Marek Gierlinski
▴ 30
4
votes
9
replies
2.5k
views
RNAseq paired-sample differantial expression analysis with many samples
DESeq2
edgeR
23 months ago
Luca
• 0
1
vote
2
replies
1.2k
views
Access genes associated with GO terms for a topGO object created with gene2GO
topGO
23 months ago
Dan
• 0
0
votes
0
replies
559
views
annotatr rn7?
annotatr
23 months ago
chuanjiao6
• 0
0
votes
1
reply
843
views
DESeq Design for Time-Series Analysis
RNASeq
DESeq2
timecourse
23 months ago
WS
• 0
0
votes
3
replies
2.8k
views
DESeq2 design with multiple factors
DESeq2
written 23 months ago by
KW
• 0
0
votes
1
reply
1.0k
views
Mismatch between MAST DE results and expression dot plot
MAST
mastR
23 months ago
Simon
• 0
0
votes
0
replies
955
views
Job:
Openings for Doctoral Researchers at the University of Helsinki
easyreporting
MolecularMedicine
LifeSciences
bioinformatics
23 months ago
rubina.tabassum
• 0
1
vote
1
reply
1.1k
views
DESeq2 Normalization for QC Samples
DESeq2
Normalization
updated 23 months ago by
Michael Love
43k • written 24 months ago by
phmai1148
• 0
0
votes
1
reply
633
views
download problem
edgeR
updated 23 months ago by
Gordon Smyth
53k • written 23 months ago by
theokirkland3
• 0
1
vote
3
replies
1.3k
views
Read Count Normalisation and validation of analysis
DifferentialExpression
DESeq2
written 2.0 years ago by
Dinesh
• 0
0
votes
0
replies
1.0k
views
Job:
Postdoc for computational biology on cancer omics data analysis at Liang lab of Wistar Institute, Philadelphia, US
omics
cancerdata
Pathways
23 months ago
omicsresearch
• 0
4
votes
14
replies
5.4k
views
Data input for aracne2regulon function in viper package
viper
updated 24 months ago by
YNPAN910
• 0 • written 6.4 years ago by
maya.kappil
▴ 30
2
votes
2
replies
3.8k
views
DESeq2 median of ratios normalization instead of VST or rlog for ordinations?
DESeq2
medianofratiostransformation
StatisticalMethod
Normalization
dispersion
24 months ago • updated 23 months ago
Linton
• 0
0
votes
5
replies
2.0k
views
Can SVs identified from sva be used for removeBatchEffect() in DESeq2
sva
DESeq2
BatchEffect
limma
updated 24 months ago by
ATpoint
★ 5.0k • written 24 months ago by
Xiao
• 0
1
vote
1
reply
716
views
Going back to default settings in RCy3
Cytoscape
RCy3
RCy
updated 24 months ago by
alex.pico
▴ 30 • written 2.0 years ago by
David R
▴ 90
1
vote
1
reply
1.5k
views
How to select subnetworks, or regions, with a certain number of nodes or edges with RCy3
Network
RCy3
updated 24 months ago by
alex.pico
▴ 30 • written 2.0 years ago by
David R
▴ 90
0
votes
1
reply
1.0k
views
DESeq2 interaction term + sva
sva
DESeq2
updated 24 months ago by
Michael Love
43k • written 2.0 years ago by
marinaw
▴ 20
0
votes
0
replies
15
views
Spam:
What happens after 99999 in chrome dinosaur game?
Experimental
24 months ago
larsenlola06
0
0
votes
3
replies
5.2k
views
extract rsids of SNPs using their genomic positions
rsids
SNPlocs.Hsapiens.dbSNP150.GRCh38
written 2.5 years ago by
olgadolgova
• 0
3
votes
1
reply
769
views
News:
Bioconductor.org has a new look!
Bioconductor
Website
written 24 months ago by
shepherl
4.2k
0
votes
3
replies
1.2k
views
Group comparison with one sample
rnaseqcomp
updated 23 months ago by
Gordon Smyth
53k • written 24 months ago by
kay2023
• 0
9
votes
18
replies
4.8k
views
Generation of QSEA TCGA 450K Human Methylation Calibration Dataset
illimina 450k methylation
qsea
MEDIPS
TCGA
updated 24 months ago by
Matthias Lienhard
▴ 280 • written 8.7 years ago by
justinburgener
▴ 20
1
vote
1
reply
1.3k
views
Cytohubba in RCY3
RCy3
Cytohubba
updated 24 months ago by
alex.pico
▴ 30 • written 2.0 years ago by
jzhan067
▴ 10
0
votes
0
replies
813
views
Differential Binding of CUT&Tag peaks with normalization using scaling factor
DiffBind
CUT&Tag
24 months ago
Hai
• 0
0
votes
5
replies
1.4k
views
Help with model for differential expression analysis
DifferentialExpression
edgeR
24 months ago • updated 23 months ago
Lucy
▴ 60
0
votes
2
replies
1.1k
views
MIcrosynteny block information - Syntenet
syntenet
microsynteny
blocks
synteny
written 2.4 years ago by
Alexandros
• 0
0
votes
0
replies
690
views
ATACseq- Counts around TSS plot
DiffBind
ATACSeq
24 months ago
inna.gur
• 0
2
votes
2
replies
2.0k
views
DiffBind; Error: No sites have activity greater than filter value
DiffBind
updated 8 months ago by
etiennedanis
• 0 • written 2.3 years ago by
Mark
▴ 10
0
votes
3
replies
1.2k
views
DESeq with multiple condition
MoleculeExperiment
DifferentialExpression
DESeq2
updated 24 months ago by
ATpoint
★ 5.0k • written 24 months ago by
michelafrancesconi8
• 0
1
vote
1
reply
990
views
Deseq2 -Model matrix not full rank error: A complex case
RNASeqData
DifferentialExpression
DESeq2
updated 2.0 years ago by
ATpoint
★ 5.0k • written 2.0 years ago by
kubracelikbas4
• 0
0
votes
1
reply
1.1k
views
Syntenet application to bacterial genome and file processing
syntenet
Bacteria
synteny
updated 2.0 years ago by
Fabricio Almeida-Silva
▴ 40 • written 2.2 years ago by
kluongni
• 0
0
votes
2
replies
1.7k
views
Trouble generating a dendrogram with colored gene modules using WGCNA for large RNA-seq experiment
WGCNA
written 2.0 years ago by
aehall26
• 0
0
votes
2
replies
1.3k
views
Problem with loading ensembl version 105.
biomaRt
2.0 years ago
RC
• 0
2
votes
3
replies
3.8k
views
Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR
tximport
RNASeq
DESeq2
updated 2.0 years ago by
swbarnes2
★ 1.4k • written 2.0 years ago by
Bo
• 0
0
votes
6
replies
1.5k
views
Deseq2 Coefficients from resultsNames() not reflecting all coefficient possibilities.
DESeq2
2.0 years ago • updated 22 months ago
JalapenoCornbread
• 0
2
votes
3
replies
1.5k
views
lfcSE always positive. Does this make sense?
DESeq2
updated 24 months ago by
Sean Davis
21k • written 2.0 years ago by
JalapenoCornbread
• 0
1
vote
2
replies
1.3k
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod
FoldChange
edgeR
RNASeq
2.0 years ago
Sabiha
▴ 20
0
votes
1
reply
1.4k
views
Job:
Postdoc and Bioinformatician position in metagenomic data analysis available
Metagenomics
curatedMetagenomicData
bugsigdbr
updated 17 months ago by
nika.daskova
• 0 • written 2.0 years ago by
Levi Waldron
★ 1.1k
0
votes
3
replies
892
views
DESeq2: Difference in DEG numbers when switching reference condition (numerator, denominator) using contrast
DESeq2
updated 2.0 years ago by
Michael Love
43k • written 2.0 years ago by
Suvrat
• 0
0
votes
2
replies
1.8k
views
DESeq2 collinearity, adjusting for covariates, and the ground truth
DESeq2
updated 2.0 years ago by
Michael Love
43k • written 2.0 years ago by
Anonymous Genetics Gnome
• 0
0
votes
0
replies
718
views
RN to EC Mapping Not Working for Some Nodes
RStudio
ggkegg
updated 2.0 years ago by
James W. MacDonald
68k • written 2.0 years ago by
Ramirj49
• 0
1
vote
3
replies
1.1k
views
DESeq2: the model matrix is not full rank issue
DESeq2
updated 2.0 years ago by
malliardtee
• 0 • written 2.0 years ago by
Guangsheng
• 0
0
votes
0
replies
1.1k
views
News:
Online course - FLOW CYTOMETRY DATA ANALYSIS WITH R/BIOCONDUCTOR
Bioconductor
FlowCytometryData
FlowCytometry
2.0 years ago
info
▴ 10
1
vote
3
replies
2.3k
views
Difference between vst() and varianceStabilizingTransform()
DESeq2
written 2.0 years ago by
chiwut.wong
• 0
0
votes
3
replies
754
views
Statistical test
NewWave
written 2.0 years ago by
mario
• 0
46,700 results • Page
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Fun, dramatic, and incredibly addictive [Poor Bunny][1] will make you laugh, scream, and keep you glued to the screen. Can you help the poo…
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Answer: Limma-voom sample weights and impact on DEG numbers
by
Gordon Smyth
53k
I recommend that you always use voomLmFit() instead of the earlier voom() or voomWithQualityWeights() functions. Personally, I would use sa…
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Limma-voom sample weights and impact on DEG numbers
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Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
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