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Can't post a question containing code?
Bioconductor
updated 7 days ago by
NATASHA
• 0 • written 3 months ago by
DS
▴ 10
3
votes
10
replies
436
views
Extremely small p-values using Limma for proteomic data
Proteomics
limma
updated 7 days ago by
James W. MacDonald
65k • written 10 days ago by
Abbey
• 0
0
votes
2
replies
1.5k
views
How to use spike-in information (sequences from another species) with DESeq2::DESeq()
DESeq2
SpikeIn
Normalization
updated 7 days ago by
maria.soler
• 0 • written 16 months ago by
kalavattam
▴ 10
0
votes
1
reply
158
views
Differential gene expression analysis results
DESeq2
DifferentialExpression
updated 7 days ago by
ATpoint
★ 4.1k • written 7 days ago by
sajadahmad41454
• 0
5
votes
3
replies
304
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 7 days ago by
Gordon Smyth
50k • written 29 days ago by
Shaimaa Gamal
• 0
1
vote
2
replies
254
views
Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq
duplicateCorrelation
limma
voom
8 days ago • updated 7 days ago
Dylan.Sheerin
• 0
0
votes
0
replies
67
views
Recommendations on deploying cytoviewer shiny.appobj to shinyapps.io?
cytoviewer
ShinyApps
8 days ago
neilzhao
▴ 30
0
votes
1
reply
1.3k
views
DSS CpG coverage threshold
DSS
WGBS
coverage
updated 8 days ago by
j.gilbert
• 0 • written 6.6 years ago by
floriandeckert
▴ 30
0
votes
1
reply
97
views
normalization using Deseq2
DESeq2
rnaseqGene
Normalization
updated 8 days ago by
ATpoint
★ 4.1k • written 8 days ago by
sajadahmad41454
• 0
2
votes
4
replies
1.7k
views
EGSEA usage with microarray data (with vooma)?
EGSEA
gene set testing
vooma
limma voom
gsea
updated 9 days ago by
Chris
▴ 10 • written 7.4 years ago by
Pekka Kohonen
▴ 190
3
votes
4
replies
505
views
Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it does not happen in Linux
GenomAutomorphism
updated 9 days ago by
Mike Smith
★ 6.5k • written 12 days ago by
robersy
• 0
1
vote
3
replies
302
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 9 days ago by
ATpoint
★ 4.1k • written 16 days ago by
angelathuynh5
• 0
1
vote
5
replies
1.5k
views
Cannot connect to ExperimentHub server
ExperimentHub
updated 9 days ago by
Jiayu
• 0 • written 5 months ago by
yanling
• 0
3
votes
5
replies
285
views
Help with running egsea()
EGSEA
11 days ago • updated 9 days ago
Chris
▴ 10
3
votes
1
reply
1.5k
views
Limma without eBayes, is it indistunguishable from Ordinary Least Square?
Limma
ebayes
bayesian
ls
updated 9 days ago by
Gordon Smyth
50k • written 5.6 years ago by
CantExitVIM
▴ 10
0
votes
0
replies
68
views
Treeio as.treedata function seq lenght error
treeio
9 days ago
nromerov
• 0
4
votes
9
replies
489
views
Memory errors using read.bismark?
dmrseq
bsseq
5 weeks ago • updated 10 days ago
Juan Higareda
• 0
2
votes
1
reply
160
views
minfi latest update for EPIC V2 chip
minfi
minfiDataEPIC
updated 10 days ago by
James W. MacDonald
65k • written 10 days ago by
e1271094
• 0
0
votes
1
reply
102
views
Recovering my account credentials on Bioconductor
Bioconductor
updated 10 days ago by
shepherl
3.9k • written 10 days ago by
cyril.dalmasso
• 0
0
votes
0
replies
85
views
need help with Diffbind multiple groups
DiffBind
ChIPSeqData
11 days ago
Dinesh
• 0
0
votes
3
replies
3.7k
views
[Mfuzz] Error in cmeans(exprs(eset)
Mfuzz
Mfuzz
updated 11 days ago by
Caio
• 0 • written 13.1 years ago by
boczniak767
▴ 720
0
votes
3
replies
220
views
Couldn't connect to server while using "pathways"
graphite
updated 11 days ago by
Michael Love
42k • written 11 days ago by
fduguchunhui
• 0
4
votes
2
replies
619
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea
edgeR
15 days ago • updated 11 days ago
gene_bioconductor
▴ 10
3
votes
1
reply
147
views
How to save the DEXSeq results
DEXSeq
updated 11 days ago by
Michael Love
42k • written 11 days ago by
Sara
• 0
2
votes
1
reply
141
views
Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 11 days ago by
Michael Love
42k • written 11 days ago by
mat149
▴ 70
1
vote
2
replies
211
views
Improving the design matrices vignette in RNAseq123
RNAseq123
25 days ago • updated 11 days ago
Lluís Revilla Sancho
▴ 730
2
votes
3
replies
261
views
package goseq seems to be not available on the latest version of R
goseq
updated 11 days ago by
Gordon Smyth
50k • written 14 days ago by
Patrycja
▴ 20
0
votes
5
replies
2.9k
views
DNAString: Standard checksum function?
Biostrings
FASTA
sequencing
8.2 years ago • updated 12 days ago
Henrik Bengtsson
★ 2.4k
2
votes
2
replies
223
views
fgsea significant result
fgsea
13 days ago • updated 12 days ago
Chris
▴ 10
1
vote
1
reply
184
views
Handling multiple differential expression comparisons
DESeq2
updated 12 days ago by
Michael Love
42k • written 14 days ago by
Zainab
▴ 10
2
votes
3
replies
253
views
Too many significant genes when integrating gtex and tcga
RNA-seq
DESeq2
updated 12 days ago by
ATpoint
★ 4.1k • written 14 days ago by
Reza
• 0
0
votes
6
replies
285
views
Once again a "Model matrix not full rank"
DESeq2
design
coldata
updated 13 days ago by
swbarnes2
★ 1.4k • written 15 days ago by
arfranco
▴ 130
1
vote
2
replies
396
views
limma Intercept vs No-intercept models completely changing DMR results?
limma
DMRcate
MethylationArray
EPICV2
updated 13 days ago by
Gordon Smyth
50k • written 14 days ago by
Kim
• 0
0
votes
0
replies
135
views
Empty table plot using plotGseaTable()
fgsea
16 days ago • updated 14 days ago
Chris
▴ 10
1
vote
2
replies
366
views
CombineArrays for EPIC and EPIC V2
EPICV1
Methylation
combineArrays
minifi
EPICv2manifest
6 weeks ago • updated 14 days ago
Kim
• 0
0
votes
0
replies
117
views
dba.plotProfile() plotting and interpretation
DiffBind
14 days ago
Henry
▴ 10
0
votes
2
replies
166
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
17 days ago • updated 14 days ago
Aurora
• 0
0
votes
0
replies
142
views
One error problem occurred caused by data type during using GDCprepare function of TCGAbiolinks to handle TCGAbiolinks BRCA data
GDCRNATools
TCGA
22 days ago • updated 14 days ago
glaciya2018
• 0
0
votes
2
replies
207
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
16 days ago • updated 14 days ago
kcarey
• 0
0
votes
1
reply
172
views
NEED FOR NESSASORY HELP
RNASeqData
edgeR
updated 15 days ago by
Gordon Smyth
50k • written 15 days ago by
z_bahari
• 0
0
votes
1
reply
154
views
Gene-by-sample covariates in limma
Metabolomics
limma
updated 15 days ago by
Gordon Smyth
50k • written 15 days ago by
c53aba27
• 0
0
votes
0
replies
95
views
flowStats for CyTOF
flowStats
15 days ago
tholmes
• 0
0
votes
2
replies
159
views
DESeq2 v1.35.0
DESeq2
updated 15 days ago by
Michael Love
42k • written 15 days ago by
Espresso
• 0
5
votes
6
replies
2.8k
views
Although I successfully installed the package "simpleaffy'' , I cannot library it. Why?
simpleaffy
updated 15 days ago by
James W. MacDonald
65k • written 2.3 years ago by
yanchangjian2019
• 0
0
votes
0
replies
89
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
15 days ago
yvonneh
• 0
0
votes
0
replies
83
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
15 days ago
Ian D.
▴ 70
0
votes
1
reply
129
views
Job:
Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 15 days ago by
4r-rtg
• 0
0
votes
3
replies
218
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 15 days ago by
ATpoint
★ 4.1k • written 16 days ago by
james.zhang20
• 0
0
votes
2
replies
190
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
written 25 days ago by
taur.vil
• 0
1
vote
2
replies
287
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation
SequenceAnnotation
MethylationArray
GenomicDistributionsData
16 days ago • updated 15 days ago
Yveto
• 0
45,667 results • Page
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Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
swbarnes2
★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Comment: DESeq2- Mysterious interaction suppresses DEGs
by
shaunpeterson
• 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Comment: STRINGdb : error with string_db$plot_network()
by
damian.szk
▴ 80
ok. Forcing non-secure protocol should not be needed anymore, due to changes in the underlying library. However, I will look at why "HTTP" …
Comment: STRINGdb : error with string_db$plot_network()
by
ninidea
• 0
> Does the vignette produce the same error? No. Anyway, I finally solved the problem. I don't know why, but I removed: protocol='http' fr…
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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