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vote
5
replies
2.0k
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batch effect
TargetScoreData
batchelor
written 3.5 years ago by
Syed Zaheer
▴ 10
0
votes
1
reply
1.4k
views
Problem with annotations using annotatr
annotatr
3.5 years ago
eric.rhoncalderon
• 0
1
vote
1
reply
2.0k
views
From KEGG ID's (Kxxxxx) to Uniprot IDs
KEGG
UniProt.ws
updated 3.5 years ago by
James W. MacDonald
68k • written 3.5 years ago by
Recep
▴ 20
0
votes
2
replies
1.5k
views
Rsubread align --R session aborts
RNA
Alignment
Rsubread
3.5 years ago • updated 3.4 years ago
sreekalasn
• 0
0
votes
1
reply
1.3k
views
Job:
BioConductor Tutor $50-$100/Hr
JobPosting
updated 3.3 years ago by
Ibra
• 0 • written 3.5 years ago by
Andrew
• 0
1
vote
5
replies
3.4k
views
DESeq2 outlier options and LFC Shrinkage
DESeq2
RNASeq
RnaSeqSampleSize
apeglm
updated 3.5 years ago by
Michael Love
43k • written 3.5 years ago by
Riley
• 0
1
vote
3
replies
1.7k
views
Swish: contrasts and interactions
fishpond
DESeq2
updated 2.7 years ago by
Michael Love
43k • written 3.5 years ago by
alexyz
• 0
3
votes
4
replies
1.5k
views
edgeR processAmplicons not recognizing hairpin sequences
edgeR
updated 3.5 years ago by
Gordon Smyth
53k • written 3.5 years ago by
Claire.Prince
▴ 10
0
votes
1
reply
1.5k
views
Building model matrix to correct for batch effect with biological and technical replicates: Problem with linear correlations
MassSpectrometryData
BatchEffect
r
limma
updated 3.5 years ago by
Gordon Smyth
53k • written 3.5 years ago by
mfaleevs
• 0
0
votes
7
replies
3.0k
views
CHIPQC error regarding BiocParallel
CHIPQC
Diffbind
chipseq
rory stark
Thomas Carroll
updated 3.4 years ago by
arisarkar88
▴ 40 • written 5.7 years ago by
bioinfouser2
▴ 10
1
vote
2
replies
1.6k
views
Could it be possible to get an older version of ChIPQC?
ChIPQC
ChIP-seq
DiffBind
Rory_Stark
3.5 years ago • updated 3.4 years ago
etiennedanis
• 0
1
vote
3
replies
2.2k
views
Extract specific portion of a string and paste to a new column in R
Rscript
tidyr
dataframe
tidyverse
offtopic
updated 3.4 years ago by
Marcel Ramos
700 • written 3.5 years ago by
Nikhil
• 0
2
votes
2
replies
1.1k
views
Contradictory results in smallRNA differential expression analysis using DESeq2
SmallRNA
DESeq2
3.5 years ago
jucosie
• 0
0
votes
8
replies
2.2k
views
Swish log2FC NA output
swish
fishpond
DifferentialExpression
3.5 years ago
jvandinter
• 0
1
vote
1
reply
1.4k
views
Dispersion estimates with DESeq2
dispersionestimates
dispersion
DESeq2
estimates
deseq2
updated 3.5 years ago by
Michael Love
43k • written 3.5 years ago by
Julia
▴ 10
0
votes
6
replies
2.4k
views
Is DESeq2 generating false postives when changing different pre-filtering thresholds?
RNASeq
DEG
DESeq2
3.5 years ago • updated 3.4 years ago
Weiqian
▴ 10
0
votes
1
reply
1.1k
views
DESeq2 - Batch effect correction in 2 conditions + 2 genotypes + interaction term design
DESeq2
updated 3.5 years ago by
Michael Love
43k • written 3.5 years ago by
barbara.mariotti
• 0
1
vote
1
reply
1.4k
views
CQN to DESeq2
cqn
DESeq2
updated 3.5 years ago by
Michael Love
43k • written 3.5 years ago by
bioinfo
• 0
0
votes
0
replies
634
views
Can I loosely say that a gene is expressed by simply look at the gene count from RNA-Seq?
RNASeqData
RNASeq
3.5 years ago
Pang
• 0
0
votes
1
reply
2.0k
views
Error in running: classifySingleR from SingleR package
SingleR
SingleCell
updated 3.5 years ago by
ATpoint
★ 5.0k • written 3.5 years ago by
amit.korngut
• 0
0
votes
2
replies
1.4k
views
MBD-seq non model species
MethylSeq
ramwas
MEDIPS
qsea
updated 3.4 years ago by
Simon Pearce
• 0 • written 3.5 years ago by
Marianna
▴ 20
1
vote
1
reply
1.4k
views
Filtering Orthologus Genes Before or After TMM normalization?
RNASeq
Normalization
TMM
edgeR
updated 3.5 years ago by
Gordon Smyth
53k • written 3.5 years ago by
e.g.w.miller
▴ 10
1
vote
5
replies
1.5k
views
what should be our references when 2 samples which I compare are treated and there is not any control?
DESeq2
updated 3.5 years ago by
Michael Love
43k • written 3.5 years ago by
Maryam.sed1400
• 0
4
votes
5
replies
9.1k
views
Convert an R data.frame to a bed file in R
rtracklayer
R
bed
updated 3.0 years ago by
Walters
• 0 • written 3.5 years ago by
L
▴ 50
0
votes
3
replies
2.7k
views
Differences in ENSEMBL => ENTREZID mapping coverage between org.Hs.eg.db and AnnotationHub resources
AnnotationHub
org.Hs.eg.db
ensembldb
3.5 years ago • updated 3.4 years ago
sandmann.t
▴ 70
1
vote
0
replies
1.2k
views
Job:
Bioinformatics Analyst (non-PhD level) in medical science
JobPosting
3.5 years ago
zhen-fu
▴ 10
0
votes
2
replies
710
views
MAAPER
MAAPER
updated 3.5 years ago by
ATpoint
★ 5.0k • written 3.5 years ago by
Sasha
• 0
0
votes
1
reply
1.1k
views
I have a query regarding differential gene expression using limma-voom.
RNASeqData
DESeq2
updated 3.5 years ago by
Gordon Smyth
53k • written 3.5 years ago by
btadfaramin
• 0
1
vote
4
replies
2.2k
views
xcmsRaw not reading data files in: invalid class “xcmsFileSource” object
xcms
updated 3.5 years ago by
jiahui
• 0 • written 5.2 years ago by
garfield320
▴ 30
9
votes
21
replies
17k
views
ah <- AnnotationHub() Error in UseMethod("filter_"): no applicable method for 'filter_' applied to an object of class "c('tbl_SQLiteConnection', 'tb…
AnnotationHub
dplyr
updated 3.5 years ago by
SmallChess
▴ 10 • written 5.2 years ago by
georgia.katsoula
▴ 40
0
votes
0
replies
1.5k
views
Job:
Scientific Programmer | Altos Labs | San Diego
SpatialData
scRNAseq
JobPosting
3.5 years ago
peter.kharchenko
▴ 30
0
votes
1
reply
803
views
End User Agreement License
licensing
updated 3.5 years ago by
sandmann.t
▴ 70 • written 3.5 years ago by
mgardner
• 0
0
votes
1
reply
869
views
APAanalyzer
APAlyzer
3.5 years ago
Sasha
• 0
0
votes
3
replies
1.2k
views
Can I create my own, private ExperimentHub instance?
ExperimentHub
3.5 years ago • updated 3.4 years ago
sandmann.t
▴ 70
0
votes
0
replies
1.7k
views
Boxplot annotation per cluster and column using ComplexHeatmap
ComplexHeatmap
3.5 years ago
gdeniz
• 0
0
votes
2
replies
2.0k
views
Gviz: Filtering AlignmentsTrack by read names
Gvi
Gviz
updated 3.5 years ago by
James W. MacDonald
68k • written 3.5 years ago by
anikajohn
• 0
2
votes
1
reply
1.1k
views
Subsetting a DESeq object - gene-wise dispersions
DESeq2
updated 3.5 years ago by
ATpoint
★ 5.0k • written 3.5 years ago by
andrebolerbarros
▴ 20
0
votes
1
reply
1.5k
views
DMRfinder findDMRs.r Error - Argument is of length zero
DSS
DMRcaller
updated 2.7 years ago by
Noelia
• 0 • written 3.5 years ago by
Claire
• 0
0
votes
0
replies
608
views
multiple widths using motifmatchr
motifmatchr
3.5 years ago
ltb47
• 0
1
vote
0
replies
1.3k
views
Job:
Lecturer in Statistics - School of Mathematics and Statistics - University of St Andrews
computational
teaching
statistics
research
3.5 years ago
Andy Lynch
▴ 120
1
vote
0
replies
1.3k
views
Job:
Research Fellow in Prostate Cancer Proteomics (Bioinformatics/Stats/Data Analysis) - University of St Andrews
Multiomics
Proteomics
Cancer
Statistics
Bioinformatics
3.5 years ago
Andy Lynch
▴ 120
0
votes
0
replies
849
views
MM-GS plot doesn't show any negative correlation
wgcna
3.5 years ago
shubhankar.pawar
• 0
0
votes
1
reply
1.0k
views
DESeq2 Interaction Term Error Occurred
interaction
DESeq2
updated 3.5 years ago by
swbarnes2
★ 1.4k • written 3.5 years ago by
Tait
• 0
2
votes
7
replies
26k
views
Install DESeq2
DESeq2
3.5 years ago
Chris
▴ 20
13
votes
20
replies
5.4k
views
cellCounts() function floating point error
Rsubread
3.7 years ago • updated 3.5 years ago
J-E
• 0
0
votes
2
replies
1.5k
views
IsoformSwitchAnalyzeR package on mouse data
rnaseq
IsoformSwitchAnalyzeR
updated 3.4 years ago by
k.vitting.seerup
▴ 120 • written 3.5 years ago by
Ryan
• 0
0
votes
6
replies
1.7k
views
Option to override removal of duplicate reads - GUIDEseq
GUIDEseq
updated 3.5 years ago by
Julie Zhu
★ 4.3k • written 3.5 years ago by
sharvari gujja
▴ 40
0
votes
1
reply
905
views
Can I force flowStats::quadrantGate to pick a separation point on the upper side of a signal distribution?
flowStats
quadrantGate
3.5 years ago
Christopher
• 0
0
votes
2
replies
1.5k
views
How do we get genes involved in all immune system pathways?
keggorthology
KEGG
updated 3.5 years ago by
sandmann.t
▴ 70 • written 3.5 years ago by
Recep
▴ 20
0
votes
0
replies
1.4k
views
About normalization of the datasets from Harmonized TCGA data
TCGAbiolinks
Proteomics
GENOMICS
bioinformatics
3.5 years ago
qiz218591
• 0
46,724 results • Page
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Answer: When to use edgeR or limma
by
Gordon Smyth
53k
The short answer is that we generally prefer edgeR for applications with lots of small counts and limma for complex designs with random eff…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry
by
Gordon Smyth
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I updated the above answer today.
Answer: When to use edgeR or limma
by
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68k
I would use edgeR's quasi-likelihood model for any analysis with a smaller number of observations (like 3 vs 3 or similar), but if you have…
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by
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53k
The short answer is that limpa reads standard feature-level intensities from Spectronaut or other quantifications tools. limpa is designed …
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by
mohammedtoufiq91
▴ 10
@gordonsmyth Noted, thank you very much.
Votes
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
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