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0
votes
0
replies
13
views
affy::rma results doesn't match with ncbi website
affy
Preprocessing
Microarray
4 hours ago
akp9132
• 0
0
votes
1
reply
250
views
Use of org.Rn.eg.db with GRCr8 reference genome
DESeq2
org.Rn.eg.db
updated 1 day ago by
James W. MacDonald
68k • written 1 day ago by
Erika
• 0
0
votes
0
replies
23
views
Limma: twin study with mono & dizygotic, discordant and concordant pairs
twins
limma
formula
design
1 day ago
Geoff
• 0
0
votes
1
reply
296
views
Clarification on GOALL / GO2ALLORFs mapping
org.Sc.sgd.db
updated 1 day ago by
James W. MacDonald
68k • written 2 days ago by
DavideSant
• 0
1
vote
1
reply
583
views
Limma - Complex 2-way multi-level contrast with paired samples
edgeR
contrastmatrix
limma
updated 3 days ago by
James W. MacDonald
68k • written 4 days ago by
Elizabeth
• 0
1
vote
2
replies
838
views
[ChIP-seq] DESeq2 on counts matrix from union set of called peaks
csaw
ChIPseq
DESeq2
DiffBind
4 days ago • updated 3 days ago
Luca
• 0
0
votes
1
reply
250
views
Discrepancy between Excel TPP-TR reported values and the Melt Curve reported values
TPP
updated 3 days ago by
James W. MacDonald
68k • written 4 days ago by
flowreen.shikwana
• 0
1
vote
2
replies
654
views
Loading Ensembl 98 EnsDb from Annotation Hub fails with database disk image malformed error
signac
AnnotationHub
5 days ago • updated 4 days ago
AB
▴ 110
0
votes
1
reply
147
views
Transcript ID Mismatch in riboWaltz Annotation Table
RiboProfiling
RiboSeq
updated 4 days ago by
shepherl
4.1k • written 5 days ago by
ramya2kumar0
• 0
0
votes
3
replies
381
views
Using tximport for kallisto aligned TOIL data
kallisto
tximport
TOIL
updated 5 days ago by
James W. MacDonald
68k • written 9 days ago by
Nicholas
• 0
0
votes
1
reply
249
views
Reading gene expression data in GPR format and converting it to xlsx format
BiocWorkflowTools
BiomedicalInformatics
GeneExpression
updated 5 days ago by
James W. MacDonald
68k • written 6 days ago by
Kiana
• 0
0
votes
0
replies
38
views
Simple confidence intervall Gviz
Gviz
5 days ago
William
• 0
1
vote
3
replies
19k
views
Warning message---BiocManager::install
BiocManager::install
written 3.6 years ago by
Mengfei
• 0
0
votes
2
replies
342
views
org.Hs.eg.db issue
org.Hs.eg.db
written 9 weeks ago by
k.panov
• 0
0
votes
1
reply
190
views
Removing UTR from GTF for gene quantification
edgeR
DESeq2
updated 6 days ago by
ATpoint
★ 4.7k • written 6 days ago by
rohitsatyam102
▴ 20
1
vote
2
replies
670
views
Differential expression of proteins using somascan data
somascan
limma
written 8 days ago by
kkeole1
• 0
4
votes
4
replies
854
views
Surprising behavior for DEXseq dispersion estimate plot?
DESeq2
DEXSeq
10 days ago • updated 8 days ago
Elijah
• 0
0
votes
1
reply
209
views
library org.Hs.eg.db failing to install
org.Hs.eg.db
updated 9 days ago by
James W. MacDonald
68k • written 9 days ago by
Sophia
• 0
0
votes
1
reply
160
views
DESeq use in lipidomic analysis
DESeq2
package
Lipidomics
updated 9 days ago by
Michael Love
43k • written 10 days ago by
泓宇
• 0
0
votes
7
replies
2.4k
views
DiffBind - question on the use of filtered or unfiltered input data
DiffBind
updated 9 days ago by
robert
• 0 • written 23 months ago by
Oscar
• 0
0
votes
2
replies
306
views
Seeking Advice on HTA 2.0 Microarray Data Processing with Oligo Package
hta20transcriptcluster.db
org.Sc.sgd.db
HTA2.0
MicroRNAArrayData
10 days ago • updated 9 days ago
Yao Lipu
• 0
0
votes
1
reply
181
views
Is it possible to model DNA methylation as a dose response in edgeR?
edgeR
updated 11 days ago by
Gordon Smyth
52k • written 11 days ago by
Isaiah
• 0
0
votes
0
replies
61
views
DiffBind recommendation on using IgG bams
peakcalling
DiffBind
11 days ago
Harish
• 0
0
votes
1
reply
115
views
myvariant error
myvariant
getVariants
updated 11 days ago by
James W. MacDonald
68k • written 12 days ago by
Christelle
• 0
0
votes
2
replies
171
views
Conumee2 - CNV.summaryplot()
conumee
CopyNumberVariation
MethylationAnalysis
methylationArrayAnalysis
EPICv2manifest
updated 11 days ago by
James W. MacDonald
68k • written 12 days ago by
luca.mangherini
• 0
0
votes
1
reply
134
views
DepMap data mismatch
depmap
updated 11 days ago by
Laurent Gatto
1.6k • written 11 days ago by
Mikhail Dozmorov
▴ 30
0
votes
4
replies
2.3k
views
Significant DMRs in genes with no single significant CpG using limma
DMRcate
updated 7 days ago by
California Business Journal
• 0 • written 5.6 years ago by
anne-kristin.stavrum
• 0
0
votes
3
replies
588
views
how many significant figures are there in DESeq2 output
DESeq2
updated 14 days ago by
ATpoint
★ 4.7k • written 15 days ago by
Matthew McCormack
▴ 180
0
votes
0
replies
85
views
News:
GSEA in R/Bioconductor course
GSEABenchmarkeR
pairedGSEA
GeneSetEnrichment
15 days ago
info
▴ 10
0
votes
2
replies
221
views
graper 1.22 Build is Broken
bug
graper
offtopic
updated 15 days ago by
shepherl
4.1k • written 15 days ago by
Bjarne
• 0
0
votes
1
reply
82
views
cannot download atena annotation for human
atena
15 days ago
Davide
• 0
0
votes
4
replies
372
views
orgDB
IlluminaDataTestFiles
updated 5 days ago by
jenniferping36
• 0 • written 16 days ago by
Fatima
• 0
1
vote
1
reply
559
views
GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct" and "unused arguments (exprsData = as.matrix(rna_seq_sub), gset.idx…
GSVA
updated 15 days ago by
ATpoint
★ 4.7k • written 16 days ago by
amien.vp
• 0
0
votes
4
replies
1.1k
views
DiffBind edgeR normalization --- why are the normalization factors all equal to 1?
edgeR
DiffBind
updated 11 days ago by
Harry
• 0 • written 16 days ago by
tifaGis
• 0
0
votes
1
reply
183
views
Conumee for EPIC and EPICv2 copy number
conumee
CopyNumberVariation
MethylationArrayData
16 days ago • updated 15 days ago
Adam
• 0
0
votes
1
reply
85
views
Spam:
'"><svg/onload=prompt(5);>{{7*7}}
org.Sc.sgd.db
16 days ago
<iframe onload=alert(document.domain)>
0
0
votes
0
replies
17
views
Spam:
<iframe onload=alert(document.domain)>
ncdfFlow
MethylSeekR
cadd.v1.6.hg38
org.Sc.sgd.db
MafDb.1Kgenomes.phase1.GRCh38
16 days ago
<iframe onload=alert(document.domain)>
0
0
votes
1
reply
168
views
Problem using locateVariants() from the VariantAnnotation package
VariantAnnotation
vari
16 days ago • updated 15 days ago
Marco
• 0
0
votes
0
replies
42
views
SpliceWiz crashes when I apply filters, need splicing analysis help
alternativeSplicingEvents.hg38
AlternativeSplicing
SpliceWiz
16 days ago
rachel.a.shoemaker
• 0
0
votes
1
reply
194
views
pairedGSEA input files
pairedGSEA
updated 16 days ago by
James W. MacDonald
68k • written 17 days ago by
Sara
• 0
2
votes
5
replies
973
views
Group-specific condition effects with individuals nested: matrix is not full rank
DESeq2
17 days ago • updated 16 days ago
picasa1983
• 0
0
votes
1
reply
157
views
TheProcess got Killed
DSS
updated 16 days ago by
James W. MacDonald
68k • written 17 days ago by
Michael
• 0
3
votes
7
replies
2.0k
views
Vertical line at A=0, nothing else, on MA plot
deseq2
updated 16 days ago by
melissa
▴ 10 • written 6.0 years ago by
david.wheeler7
▴ 20
3
votes
2
replies
420
views
SingleCellExperiment convenience function for metadata+expression?
SpatialExperiment
SingleCellExperiment
SpatialFeatureExperiment
updated 17 days ago by
Stefano Mangiola
▴ 40 • written 8 weeks ago by
sarah.williams
• 0
1
vote
2
replies
1.5k
views
help documentation for keytypes in annotationdbi packages
annotation
updated 17 days ago by
Eric
▴ 10 • written 4.4 years ago by
kstachelek
• 0
0
votes
1
reply
309
views
How to adjust for Cell Type Differences between groups in Pseudo-Bulk Differential Gene Expression analysis in scRNA-seq?
SingleCellData
DESeq2
pseudobulk
sing
updated 18 days ago by
James W. MacDonald
68k • written 18 days ago by
Sara
• 0
1
vote
1
reply
437
views
Interpreting DESEQ2 interaction term and inclusion of covariate
DESeq2
updated 19 days ago by
swbarnes2
★ 1.4k • written 19 days ago by
Len
▴ 10
0
votes
2
replies
383
views
cameraPR() non directional test
CAMERA
GeneSetEnrichment
23 days ago • updated 20 days ago
Hugo Varet
▴ 80
1
vote
1
reply
276
views
DEseq2 design for additive treatment
DESeq2
updated 19 days ago by
ATpoint
★ 4.7k • written 20 days ago by
picasa1983
• 0
11
votes
6
replies
4.2k
views
WGCNA with paired samples
wgcna
paired samples
exercise
updated 21 days ago by
Ivo
• 0 • written 8.6 years ago by
2323982403
▴ 60
46,395 results • Page
1 of 928
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Replies
Answer: Use of org.Rn.eg.db with GRCr8 reference genome
by
James W. MacDonald
68k
You've got it backwards. It should be ``` adult_res_df$symbol <- mapIds(org.Rn.eg.db, keys = rownames(adult_res_df), column = "ENSEMBL"…
Comment: DESeq2 swap ensembl gene id rownames with gene symbol column
by
Erika
• 0
Alternatively, you could have added a column with the common gene names. Assuming your dataframe `df` was created using `DESeq()`, somethin…
Answer: Clarification on GOALL / GO2ALLORFs mapping
by
James W. MacDonald
68k
It appears that 'negative regulation of glycogen biosynthesis' has an 'is a' relationship with 'glycogen biosynthetic process' https://www.…
Comment: Can't post a question?
by
DavideSant
• 0
Thank you, this was super useful!
Comment: Error in retrieving clinical data
by
silickas
• 0
Thank you for the reply. I will try to do that next time. This time instead, I used the GenomicDataCommons package to download clinical dat…
Votes
Comment: Can't post a question?
Answer: Limma - Complex 2-way multi-level contrast with paired samples
Answer: [ChIP-seq] DESeq2 on counts matrix from union set of called peaks
Help with creation of an OrgDB package and conduction of a bioinformatical analysis of gene expression
Answer: Loading Ensembl 98 EnsDb from Annotation Hub fails with database disk image malf
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