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3
votes
2
replies
1.4k
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Unable to convert Uniprot ID to Gene IDs using Biomart
biomaRt
3.5 years ago
rohitsatyam102
▴ 20
0
votes
0
replies
1.1k
views
Plot of variable importance
Metabolomics
3.5 years ago
Eddie
• 0
0
votes
0
replies
668
views
gscreend: Multiple T0 replicates
gscreend
3.5 years ago
pk_labrador
• 0
0
votes
2
replies
1.5k
views
DESeq2 analysis has not been run for this contrast
R
DiffBind
3.5 years ago
Wang
• 0
0
votes
0
replies
1.3k
views
intron coordination and annotation
ChIPSeq
updated 3.5 years ago by
ATpoint
★ 5.0k • written 3.5 years ago by
mehdi
• 0
0
votes
1
reply
1.8k
views
WGCNA Export Eigengene Adjacency/Correlation values export
WGCNA
updated 3.5 years ago by
Cannabis Equipment Financing
• 0 • written 3.5 years ago by
803ebee7
• 0
0
votes
1
reply
4.2k
views
Annotation in pheatmap
pheatmap
updated 3.5 years ago by
Guido Hooiveld
★ 4.1k • written 3.5 years ago by
Rob
• 0
0
votes
0
replies
1.0k
views
CytoML: gatingset_to_flowjo() "Could not find files for the given pattern(s)" error
CytoML
3.5 years ago
nmchavez
• 0
1
vote
6
replies
2.0k
views
Iterating over a column within colData@listData
DESeq2
iterating
SummarizedExperiment
3.5 years ago
BioInfoBeginnerrr
• 0
0
votes
0
replies
1.3k
views
Job:
Computational Biology Contractor - Chinook Therapeutics
Patient_stratification
Multi-omics
RNA-seq
Kidney_Disease
3.5 years ago
eolson
• 0
1
vote
3
replies
1.6k
views
LFC shrinkage setting negative LFC svalues to zero
DESeq2
DifferentialExpression
apeglm
updated 3.5 years ago by
Michael Love
43k • written 3.5 years ago by
81das_col
• 0
1
vote
7
replies
3.0k
views
DESeqDataSetFromMatrix error
BiocGenerics
DESeq2
DEGreport
RNASeqData
DEG
updated 3.5 years ago by
James W. MacDonald
68k • written 3.5 years ago by
Diya
• 0
0
votes
9
replies
2.9k
views
Questions about the false positives indicated by DESeq2 and QQ plot
pre-filterin
DESeq2
updated 2.3 years ago by
yujin
▴ 10 • written 3.5 years ago by
Weiqian
▴ 10
2
votes
7
replies
3.0k
views
biomaRt error during getBM
biomaRt
updated 3.5 years ago by
Mike Smith
★ 6.6k • written 3.5 years ago by
Shoma Tsubota
• 0
1
vote
3
replies
2.8k
views
ColData and ERROR: rows did not converge in beta, labelled in mcols(object)$betaConv. Use larger maxit argument with nbinomWaldTest
DESeq2
updated 14 months ago by
Michael Love
43k • written 3.5 years ago by
LorManj
• 0
2
votes
2
replies
1.8k
views
How to deal with stronger effect by donor than treatment
MDS
RNA-Seq
updated 3.5 years ago by
Gordon Smyth
53k • written 3.5 years ago by
Pei
• 0
0
votes
1
reply
1.1k
views
how to identify the unwanted variables independent of phenotypes
RUVSeq
svaseq
3.5 years ago
Tongjun
• 0
1
vote
0
replies
1.1k
views
Why does surrogate variable confound with variable given in mod?
sva
3.5 years ago
shdam
▴ 10
1
vote
0
replies
1.3k
views
News:
Ensembl 107 has been released
ensembldb
3.5 years ago
Aleena_Ensembl
▴ 30
2
votes
5
replies
1.9k
views
MafH5.gnomAD.v3.1.2.GRCh38 omitted indels
GenomicScores
updated 3.3 years ago by
Robert Castelo
★ 3.4k • written 3.5 years ago by
Robert
• 0
0
votes
1
reply
5.4k
views
gff3 file for featureCounts
gtf/gff3
subread
featureCounts
updated 3.5 years ago by
Gordon Smyth
53k • written 3.5 years ago by
selmanurkeskin
• 0
1
vote
0
replies
1.0k
views
Error while running Case study n. 3: Integration of methylation and expression for ACC
geneexpression
methylation
3.5 years ago
hlee
▴ 10
1
vote
1
reply
1.1k
views
Weight Array Quality before of after applying variance filtering?
limma
arrays
genefilter
updated 3.5 years ago by
James W. MacDonald
68k • written 3.5 years ago by
jacorvar
▴ 40
0
votes
0
replies
1.2k
views
News:
Introduction to genomic data analysis with R and Bioconductor in Heidelberg, 12-13 September 2022
Workshop
3.5 years ago
Laurent Gatto
1.6k
0
votes
1
reply
940
views
DESeq2 LRT not returning genes
LRT
linearmodels
DESeq2
updated 3.5 years ago by
Michael Love
43k • written 3.5 years ago by
meeta.mistry
▴ 30
1
vote
2
replies
3.3k
views
DEseq2 anlysis - LfcThreshold and Lfcshrink options
lfcshrink
DESeq2
RNASeq
lfcthreshold
3.5 years ago
ClaudiaE
• 0
1
vote
12
replies
4.7k
views
How to use "p-value" instead of "p-adj value" in DESeq2
DESeq2
updated 2.3 years ago by
Assa Yeroslaviz
★ 1.5k • written 3.5 years ago by
Maryam.sed1400
• 0
1
vote
1
reply
681
views
Error message : DESeq2
DESeq2
updated 3.5 years ago by
Michael Love
43k • written 3.5 years ago by
Md. Faridul
• 0
2
votes
2
replies
1.2k
views
should smooth quantile normalization be used with limma-voom?
limma-voom
smooth-quantile-normalization
quantro
3.5 years ago
raf4
▴ 30
0
votes
1
reply
3.0k
views
setReadable function missing information in clusterProfiler
clusterProfiler
updated 3.5 years ago by
James W. MacDonald
68k • written 3.5 years ago by
ltb47
• 0
2
votes
1
reply
10k
views
using biomaRt to look up human gene symbols and map them to human ensembl ENSG IDs
biomaRt
updated 3.5 years ago by
James W. MacDonald
68k • written 3.5 years ago by
colantuonicarlo
• 0
0
votes
1
reply
1.3k
views
DiffBind: dba.plotPCA() ellipse
PrincipalComponent
DiffBind
updated 3.5 years ago by
swbarnes2
★ 1.4k • written 3.5 years ago by
Lisa
• 0
1
vote
1
reply
982
views
result does not change after relevel
DESeq2
updated 3.5 years ago by
Michael Love
43k • written 3.5 years ago by
JaneDoe
• 0
0
votes
0
replies
717
views
how to obtain the download number of a bioconductor package
badges
3.5 years ago
zhilongjia
• 0
0
votes
0
replies
1.1k
views
ARACNe Sample Size
grndata
GRN
ARACNE
WGCNA
3.5 years ago
Harrsha
• 0
0
votes
0
replies
1.7k
views
how to calculate similarity between each cluster in scRNA and bulk RNA-seq
SingleR
scRNAseq
3.5 years ago
Guandong Shang
▴ 40
0
votes
14
replies
6.5k
views
GenomeInfoDbData had non-zero exit status
DESeq2
RStudio
GenomeInfoDbData
hadnon-zeroexitstatus
updated 3.3 years ago by
wshao9
• 0 • written 3.5 years ago by
JoseR
• 0
0
votes
0
replies
1.3k
views
Cannot Install genefilter
genefilter
3.5 years ago
Francis
• 0
1
vote
0
replies
965
views
Which algorithm would you use for the cell-cell communication analysis of bulk RNA seq datasets?
RNASeq
3.5 years ago
curiousmind007
▴ 10
2
votes
5
replies
3.1k
views
proteomics analysis
Proteomics
analysis
updated 3.5 years ago by
jeroen.gilis
▴ 100 • written 3.5 years ago by
Shakiba
• 0
0
votes
1
reply
928
views
suggested additional study
curatedMetagenomicData
updated 3.5 years ago by
Lucas Schiffer
▴ 240 • written 3.5 years ago by
zachary.flamholz
• 0
2
votes
2
replies
1.2k
views
Inconsistent Dirichlet-multinominal coefficient and Beta-Binominal coefficient for a transcript in DTU analysis.
rnaseqDTU
DRIMSeq
3.5 years ago
wangziwei0010
▴ 10
0
votes
1
reply
2.1k
views
Error with ropls when using oplsda: Error in svd(wwMN) : infinite or missing values in 'x'
ropls
3.5 years ago
g0079
• 0
0
votes
0
replies
1.1k
views
biomaRt has encountered an unknown server error
biomaRt
3.5 years ago
Grace_H
• 0
0
votes
0
replies
876
views
Enrichment in genomic regions
Enrichment
clusterPro
WGCNA
3.5 years ago
María José
• 0
0
votes
4
replies
4.8k
views
How to get significant genes annotated to go term using TopGO?
topGO
updated 3.5 years ago by
Lluís Revilla Sancho
▴ 760 • written 3.5 years ago by
Lucía
▴ 30
0
votes
0
replies
1.2k
views
How to get the chrominfo from ENSEMBL? (biomaRt and customProDB)
biomaRt
customProDB
3.5 years ago
04.marshal-decibel
• 0
1
vote
1
reply
2.7k
views
enrichGO results
clusterProfiler
enrichGO
3.5 years ago
Shakiba
• 0
2
votes
2
replies
950
views
DESeq2 question
DESeq2
3.5 years ago
Yu
• 0
0
votes
4
replies
1.5k
views
Multi-factorial Time-based design in DEseq2: defining full and reduced model
DESeq2
updated 3.5 years ago by
Michael Love
43k • written 3.5 years ago by
Alex
• 0
46,730 results • Page
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Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2
by
chp265
• 0
Confirming my understanding after executing the code provided: this is similar to a design formula of `~0+mouse+group+group:allele`, except…
Comment: Combining two proteomics datasets with limpa
by
Andrew Pattison
• 0
Thanks heaps Gordon. I went with option 1 and no normalisation and all seems to have worked well. Cheers, Andrew
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry
by
Gordon Smyth
53k
Flagging protein groups as likely contaminants in this way will be fine for a limpa analysis. The `Cont_` proteins can optionally stay in f…
Answer: Making a Full Rank Model for Allele-Specific Expression with DESeq2
by
Gordon Smyth
53k
Aaron Lun was a PhD student in my Lab back in 2015, when he posted the answers about allele-specific expression that you and Mike Love have…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2
by
Michael Love
43k
You just need the mouse identifier (controls baseline) and the group specific allelic effect.
Votes
A: DESeq2: Is it possible to convert read counts to expression values via TPM and r
A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen
Comment: limpa analysis advice
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
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