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News:
Last Call: Nominations for Bioconductor Awards 2024! Deadline May 15
Recognition
Awards
Bioconductor
Bioc204
8 weeks ago • updated 6 days ago
shepherl
3.9k
0
votes
2
replies
110
views
Problem finding certain variables when importing a public database GSE73103
GSEABase
GenomicDistributionsData
7 days ago • updated 6 days ago
Yveto
• 0
0
votes
1
reply
104
views
normalization across different species for DESeq2 analysis
DESeq2
normalization
Normalization
acrossspecies
updated 6 days ago by
Michael Love
42k • written 7 days ago by
piemmea
• 0
0
votes
44
replies
3.2k
views
How to use bootRanges to bootstrap small RNA loci (nullranges package)
bootRanges
nullranges
updated 6 days ago by
Michael Love
42k • written 15 months ago by
Poonam
• 0
1
vote
0
replies
69
views
News:
Ensembl 112 has been released.
ensembldb
biomaRt
ensemblrelease
6 days ago
Aleena
▴ 30
0
votes
3
replies
192
views
ChAMP installation issue
Cha
ChAMP
7 days ago • updated 6 days ago
e1271094
• 0
0
votes
0
replies
61
views
QSEA- Extraction of Normalized methylation across the samples
qsea
ngsReports
correlation
6 days ago
Researcher
• 0
3
votes
4
replies
293
views
Store output of matchPWM()
biostrings
Biostrings
19 days ago • updated 7 days ago
mat149
▴ 70
2
votes
3
replies
1.8k
views
ChipQC 'names' attribute [9] must be the same length as the vector [2]'
chipqc
updated 7 days ago by
bandconductor
• 0 • written 3.6 years ago by
ZheFrench
▴ 60
0
votes
1
reply
155
views
Gene set enrichment analysis
clusterProfiler
GeneSetEnrichment
updated 7 days ago by
Guido Hooiveld
★ 4.0k • written 8 days ago by
aogunbaw
• 0
2
votes
2
replies
286
views
error in limma , contrast.matrix Number of rows of contrast matrix must match number of coefficients in fit
limma
13 days ago • updated 7 days ago
zzrammal
• 0
0
votes
4
replies
379
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
updated 9 days ago by
Ziliang
• 0 • written 19 days ago by
Ian D.
▴ 70
0
votes
3
replies
9.3k
views
SingleR Label.Ont
SingleR
updated 9 days ago by
Denis
• 0 • written 8 months ago by
saeed.khalili
• 0
2
votes
7
replies
417
views
deseq2 results
DESeq2
DifferentialExpression
rnaseqGene
DifferentialRegulation
12 days ago • updated 9 days ago
sajadahmad41454
• 0
1
vote
5
replies
527
views
Can't post a question containing code?
Bioconductor
updated 10 days ago by
NATASHA
• 0 • written 3 months ago by
DS
▴ 10
3
votes
10
replies
488
views
Extremely small p-values using Limma for proteomic data
Proteomics
limma
updated 10 days ago by
James W. MacDonald
65k • written 13 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 10 days ago by
maria.soler
• 0 • written 16 months ago by
kalavattam
▴ 10
0
votes
1
reply
185
views
Differential gene expression analysis results
DESeq2
DifferentialExpression
updated 10 days ago by
ATpoint
★ 4.1k • written 10 days ago by
sajadahmad41454
• 0
5
votes
3
replies
319
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 10 days ago by
Gordon Smyth
50k • written 4 weeks ago by
Shaimaa Gamal
• 0
1
vote
2
replies
286
views
Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq
duplicateCorrelation
limma
voom
11 days ago • updated 10 days ago
Dylan.Sheerin
• 0
0
votes
0
replies
87
views
Recommendations on deploying cytoviewer shiny.appobj to shinyapps.io?
cytoviewer
ShinyApps
11 days ago
neilzhao
▴ 30
0
votes
1
reply
1.3k
views
DSS CpG coverage threshold
DSS
WGBS
coverage
updated 11 days ago by
j.gilbert
• 0 • written 6.6 years ago by
floriandeckert
▴ 30
0
votes
1
reply
115
views
normalization using Deseq2
DESeq2
rnaseqGene
Normalization
updated 11 days ago by
ATpoint
★ 4.1k • written 11 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 12 days ago by
Chris
▴ 10 • written 7.4 years ago by
Pekka Kohonen
▴ 190
1
vote
3
replies
306
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 12 days ago by
ATpoint
★ 4.1k • written 19 days ago by
angelathuynh5
• 0
1
vote
5
replies
1.5k
views
Cannot connect to ExperimentHub server
ExperimentHub
updated 12 days ago by
Jiayu
• 0 • written 5 months ago by
yanling
• 0
3
votes
5
replies
305
views
Help with running egsea()
EGSEA
14 days ago • updated 12 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 12 days ago by
Gordon Smyth
50k • written 5.6 years ago by
CantExitVIM
▴ 10
0
votes
0
replies
78
views
Treeio as.treedata function seq lenght error
treeio
12 days ago
nromerov
• 0
4
votes
9
replies
494
views
Memory errors using read.bismark?
dmrseq
bsseq
5 weeks ago • updated 13 days ago
Juan Higareda
• 0
2
votes
1
reply
186
views
minfi latest update for EPIC V2 chip
minfi
minfiDataEPIC
updated 13 days ago by
James W. MacDonald
65k • written 13 days ago by
e1271094
• 0
0
votes
1
reply
119
views
Recovering my account credentials on Bioconductor
Bioconductor
updated 13 days ago by
shepherl
3.9k • written 13 days ago by
cyril.dalmasso
• 0
0
votes
0
replies
100
views
need help with Diffbind multiple groups
DiffBind
ChIPSeqData
14 days ago
Dinesh
• 0
0
votes
3
replies
3.7k
views
[Mfuzz] Error in cmeans(exprs(eset)
Mfuzz
Mfuzz
updated 14 days ago by
Caio
• 0 • written 13.1 years ago by
boczniak767
▴ 720
0
votes
3
replies
234
views
Couldn't connect to server while using "pathways"
graphite
updated 14 days ago by
Michael Love
42k • written 14 days ago by
fduguchunhui
• 0
4
votes
2
replies
634
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea
edgeR
18 days ago • updated 14 days ago
gene_bioconductor
▴ 10
3
votes
1
reply
153
views
How to save the DEXSeq results
DEXSeq
updated 14 days ago by
Michael Love
42k • written 14 days ago by
Sara
• 0
2
votes
1
reply
148
views
Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 14 days ago by
Michael Love
42k • written 14 days ago by
mat149
▴ 70
1
vote
2
replies
217
views
Improving the design matrices vignette in RNAseq123
RNAseq123
28 days ago • updated 14 days ago
Lluís Revilla Sancho
▴ 730
2
votes
3
replies
279
views
package goseq seems to be not available on the latest version of R
goseq
updated 14 days ago by
Gordon Smyth
50k • written 17 days ago by
Patrycja
▴ 20
0
votes
5
replies
2.9k
views
DNAString: Standard checksum function?
Biostrings
FASTA
sequencing
8.2 years ago • updated 15 days ago
Henrik Bengtsson
★ 2.4k
2
votes
2
replies
233
views
fgsea significant result
fgsea
16 days ago • updated 15 days ago
Chris
▴ 10
1
vote
1
reply
193
views
Handling multiple differential expression comparisons
DESeq2
updated 15 days ago by
Michael Love
42k • written 17 days ago by
Zainab
▴ 10
2
votes
3
replies
258
views
Too many significant genes when integrating gtex and tcga
RNA-seq
DESeq2
updated 15 days ago by
ATpoint
★ 4.1k • written 17 days ago by
Reza
• 0
0
votes
6
replies
306
views
Once again a "Model matrix not full rank"
DESeq2
design
coldata
updated 16 days ago by
swbarnes2
★ 1.4k • written 18 days ago by
arfranco
▴ 130
1
vote
2
replies
409
views
limma Intercept vs No-intercept models completely changing DMR results?
limma
DMRcate
MethylationArray
EPICV2
updated 16 days ago by
Gordon Smyth
50k • written 17 days ago by
Kim
• 0
0
votes
0
replies
142
views
Empty table plot using plotGseaTable()
fgsea
19 days ago • updated 17 days ago
Chris
▴ 10
1
vote
2
replies
380
views
CombineArrays for EPIC and EPIC V2
EPICV1
Methylation
combineArrays
minifi
EPICv2manifest
6 weeks ago • updated 17 days ago
Kim
• 0
0
votes
0
replies
124
views
dba.plotProfile() plotting and interpretation
DiffBind
17 days ago
Henry
▴ 10
0
votes
2
replies
170
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
20 days ago • updated 17 days ago
Aurora
• 0
45,679 results • Page
2 of 914
Recent ...
Replies
Answer: Errors in chromosome annotation-biomaRt
by
James W. MacDonald
65k
If you are just using HGNC symbols for the lookup, and you are trying to get NCBI IDs, then I wouldn't use `biomaRt` because it's based on …
Comment: Help with ENmix readidat
by
James W. MacDonald
65k
Please don't add to posts from two years ago. Instead make a new post. Also, please read the help page for `readidat`. The only reason to …
Comment: LRT, more than two conditions and pairwise comparisons
by
James W. MacDonald
65k
In that case, probably easiest to subset to the groups being compared.
Comment: Help with ENmix readidat
by
minardsmitha
▴ 10
Did you figure this out? I have the same issue.
Comment: LRT, more than two conditions and pairwise comparisons
by
boczniak767
▴ 720
Thank you for response, apparently I still don't know much about statistics. In fact I want to campare time-profiles [and the LRT has been …
Votes
Comment: DESeq2- Mysterious interaction suppresses DEGs
Answer: DESeq2- Mysterious interaction suppresses DEGs
Answer: Subsetting RNAseq data | voomaByGroup()
biomaRt not working - lazy table error
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
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