Post does not exist.
0
votes
2
replies
279
views
affy::rma results doesn't match with ncbi website
affy Preprocessing Microarray
updated 12 hours ago by 68k • written 1 day ago by • 0
0
votes
1
reply
79
views
Problem installing package TxDb.Mmusculus.UCSC.mm10.knownGene
TxDb.Mmusculus.UCSC.mm10.knownGene
updated 14 hours ago by 4.1k • written 16 hours ago by ▴ 140
0
votes
0
replies
37
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fgsea: ranking genes using log2FC and pvalues derived from spline model
fgsea GeneSetEnrichment splines RNASeq
1 day ago GT • 0
0
votes
1
reply
383
views
Use of org.Rn.eg.db with GRCr8 reference genome
DESeq2 org.Rn.eg.db
updated 3 days ago by 68k • written 3 days ago by • 0
0
votes
0
replies
29
views
Limma: twin study with mono & dizygotic, discordant and concordant pairs
twins limma formula design
3 days ago Geoff • 0
0
votes
1
reply
427
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Clarification on GOALL / GO2ALLORFs mapping
org.Sc.sgd.db
updated 3 days ago by 68k • written 4 days ago by • 0
2
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2
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836
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Limma - Complex 2-way multi-level contrast with paired samples
edgeR contrastmatrix limma
6 days ago • updated 17 hours ago Elizabeth • 0
1
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2
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994
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[ChIP-seq] DESeq2 on counts matrix from union set of called peaks
csaw ChIPseq DESeq2 DiffBind
6 days ago • updated 5 days ago Luca • 0
0
votes
1
reply
254
views
Discrepancy between Excel TPP-TR reported values and the Melt Curve reported values
TPP
updated 5 days ago by 68k • written 6 days ago by • 0
1
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2
replies
737
views
Loading Ensembl 98 EnsDb from Annotation Hub fails with database disk image malformed error
signac AnnotationHub
6 days ago AB ▴ 110
0
votes
1
reply
151
views
Transcript ID Mismatch in riboWaltz Annotation Table
RiboProfiling RiboSeq
updated 6 days ago by 4.1k • written 6 days ago by • 0
0
votes
4
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476
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Using tximport for kallisto aligned TOIL data
kallisto tximport TOIL
11 days ago • updated 11 hours ago Nicholas • 0
0
votes
1
reply
254
views
Reading gene expression data in GPR format and converting it to xlsx format
BiocWorkflowTools BiomedicalInformatics GeneExpression
updated 7 days ago by 68k • written 7 days ago by • 0
0
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0
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41
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Simple confidence intervall Gviz
Gviz
7 days ago William • 0
1
vote
3
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19k
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Warning message---BiocManager::install
BiocManager::install
written 3.6 years ago by • 0
0
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2
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345
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org.Hs.eg.db issue
org.Hs.eg.db
written 9 weeks ago by • 0
0
votes
2
replies
284
views
Removing UTR from GTF for gene quantification
edgeR DESeq2
updated 10 hours ago by 43k • written 8 days ago by ▴ 20
1
vote
2
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687
views
Differential expression of proteins using somascan data
somascan limma
written 10 days ago by • 0
4
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4
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863
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Surprising behavior for DEXseq dispersion estimate plot?
DESeq2 DEXSeq
12 days ago • updated 10 days ago Elijah • 0
0
votes
1
reply
212
views
library org.Hs.eg.db failing to install
org.Hs.eg.db
updated 11 days ago by 68k • written 11 days ago by • 0
0
votes
1
reply
163
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DESeq use in lipidomic analysis
DESeq2 package Lipidomics
updated 11 days ago by 43k • written 12 days ago by • 0
0
votes
7
replies
2.4k
views
DiffBind - question on the use of filtered or unfiltered input data
DiffBind
updated 11 days ago by • 0 • written 23 months ago by • 0
0
votes
2
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308
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Seeking Advice on HTA 2.0 Microarray Data Processing with Oligo Package
hta20transcriptcluster.db org.Sc.sgd.db HTA2.0 MicroRNAArrayData
11 days ago • updated 10 days ago Yao Lipu • 0
0
votes
1
reply
184
views
Is it possible to model DNA methylation as a dose response in edgeR?
edgeR
updated 13 days ago by 52k • written 13 days ago by • 0
0
votes
0
replies
63
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DiffBind recommendation on using IgG bams
peakcalling DiffBind
13 days ago Harish • 0
0
votes
1
reply
117
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myvariant error
myvariant getVariants
updated 13 days ago by 68k • written 14 days ago by • 0
0
votes
2
replies
171
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Conumee2 - CNV.summaryplot()
conumee CopyNumberVariation MethylationAnalysis methylationArrayAnalysis EPICv2manifest
updated 13 days ago by 68k • written 13 days ago by • 0
0
votes
1
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137
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DepMap data mismatch
depmap
updated 13 days ago by 1.6k • written 13 days ago by ▴ 30
0
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4
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2.3k
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Significant DMRs in genes with no single significant CpG using limma
DMRcate
updated 9 days ago by • 0 • written 5.6 years ago by • 0
0
votes
3
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590
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how many significant figures are there in DESeq2 output
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updated 15 days ago by ★ 4.7k • written 16 days ago by ▴ 180
0
votes
0
replies
87
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News: GSEA in R/Bioconductor course
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17 days ago info ▴ 10
0
votes
2
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223
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graper 1.22 Build is Broken
bug graper offtopic
updated 17 days ago by 4.1k • written 17 days ago by • 0
0
votes
1
reply
84
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cannot download atena annotation for human
atena
17 days ago Davide • 0
0
votes
4
replies
378
views
orgDB
IlluminaDataTestFiles
updated 6 days ago by • 0 • written 17 days ago by • 0
1
vote
1
reply
584
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 17 days ago by ★ 4.7k • written 17 days ago by • 0
0
votes
4
replies
1.1k
views
DiffBind edgeR normalization --- why are the normalization factors all equal to 1?
edgeR DiffBind
updated 12 days ago by • 0 • written 18 days ago by • 0
0
votes
1
reply
186
views
Conumee for EPIC and EPICv2 copy number
conumee CopyNumberVariation MethylationArrayData
17 days ago Adam • 0
0
votes
1
reply
85
views
Spam: '"><svg/onload=prompt(5);>{{7*7}}
org.Sc.sgd.db
18 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
18 days ago <iframe onload=alert(document.domain)> 0
0
votes
1
reply
172
views
Problem using locateVariants() from the VariantAnnotation package
VariantAnnotation vari
18 days ago • updated 17 days ago Marco • 0
0
votes
0
replies
44
views
SpliceWiz crashes when I apply filters, need splicing analysis help
alternativeSplicingEvents.hg38 AlternativeSplicing SpliceWiz
18 days ago rachel.a.shoemaker • 0
0
votes
1
reply
195
views
pairedGSEA input files
pairedGSEA
updated 18 days ago by 68k • written 19 days ago by • 0
2
votes
5
replies
975
views
Group-specific condition effects with individuals nested: matrix is not full rank
DESeq2
19 days ago • updated 18 days ago picasa1983 • 0
0
votes
1
reply
159
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TheProcess got Killed
DSS
updated 18 days ago by 68k • written 19 days ago by • 0
3
votes
7
replies
2.0k
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Vertical line at A=0, nothing else, on MA plot
deseq2
updated 18 days ago by ▴ 10 • written 6.0 years ago by ▴ 20
3
votes
2
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425
views
SingleCellExperiment convenience function for metadata+expression?
SpatialExperiment SingleCellExperiment SpatialFeatureExperiment
updated 18 days ago by ▴ 40 • written 8 weeks ago by • 0
1
vote
2
replies
1.5k
views
help documentation for keytypes in annotationdbi packages
annotation
updated 18 days ago by ▴ 10 • written 4.4 years ago by • 0
0
votes
1
reply
315
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How to adjust for Cell Type Differences between groups in Pseudo-Bulk Differential Gene Expression analysis in scRNA-seq?
SingleCellData DESeq2 pseudobulk sing
updated 20 days ago by 68k • written 20 days ago by • 0
1
vote
1
reply
444
views
Interpreting DESEQ2 interaction term and inclusion of covariate
DESeq2
updated 21 days ago by ★ 1.4k • written 21 days ago by ▴ 10
0
votes
2
replies
388
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cameraPR() non directional test
CAMERA GeneSetEnrichment
24 days ago • updated 21 days ago Hugo Varet ▴ 80
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Comment: Complex contrasts for between and within subject comparisons by wuwenhui2 • 0
@gordonsmyth Dear Dr. Smyth, in this design, I am interested to extract genes that have different expression profile at any of the time poi…
Comment: edgeR design between and within subjects by wuwenhui2 • 0
@luna Hi Aaron, Your explanation is very helpful. If having three time points instead of three cell types measured for each patient, usin…
Comment: Issue when attempting to use output from DECIPHER IDtaxa (pr2 V5) with dada2/phy by Daniel • 0
Two things: - PR2 version 5.0 and above have 9 levels and not 8 (up to version 4.14). So the code should be: > ranks.pr2 <- c("domain",…
Comment: Removing UTR from GTF for gene quantification by Michael Love 43k
Yes, we need to discourage tagging software packages arbitrarily on Bioconductor support site. This sends emails to the package maintainers…
Comment: Using tximport for kallisto aligned TOIL data by Nicholas • 0
Great, thanks. I have the transcriptome version and the corresponding GTF file for the ENSEMBL transcriptome version. Is there a way to do …
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Comment: Identifying potentially associated gene set to drug response using GSVA
Answer: Limma - Complex 2-way multi-level contrast with paired samples
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
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