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0
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2
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659
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Problem finding certain variables when importing a public database GSE73103
GSEABase
GenomicDistributionsData
19 months ago
Yveto
• 0
0
votes
1
reply
1.4k
views
Gene set enrichment analysis
clusterProfiler
GeneSetEnrichment
updated 19 months ago by
Guido Hooiveld
★ 4.1k • written 19 months ago by
aogunbaw
• 0
0
votes
7
replies
2.1k
views
ChAMP installation issue
Cha
ChAMP
updated 18 months ago by
James W. MacDonald
68k • written 19 months ago by
e1271094
• 0
0
votes
1
reply
628
views
Differential gene expression analysis results
DESeq2
DifferentialExpression
updated 19 months ago by
ATpoint
★ 5.0k • written 19 months ago by
sajadahmad41454
• 0
1
vote
2
replies
1.1k
views
Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq
duplicateCorrelation
limma
voom
19 months ago
Dylan.Sheerin
• 0
0
votes
0
replies
354
views
Recommendations on deploying cytoviewer shiny.appobj to shinyapps.io?
cytoviewer
ShinyApps
19 months ago
neilzhao
▴ 30
0
votes
1
reply
723
views
normalization using Deseq2
DESeq2
rnaseqGene
Normalization
updated 19 months ago by
ATpoint
★ 5.0k • written 19 months ago by
sajadahmad41454
• 0
2
votes
7
replies
2.0k
views
deseq2 results
DESeq2
DifferentialExpression
rnaseqGene
DifferentialRegulation
19 months ago
sajadahmad41454
• 0
0
votes
0
replies
370
views
Treeio as.treedata function seq lenght error
treeio
19 months ago
nromerov
• 0
2
votes
2
replies
1.3k
views
error in limma , contrast.matrix Number of rows of contrast matrix must match number of coefficients in fit
limma
19 months ago
user_bioinfo
• 0
3
votes
10
replies
2.0k
views
Extremely small p-values using Limma for proteomic data
Proteomics
limma
updated 19 months ago by
James W. MacDonald
68k • written 19 months ago by
Abbey
• 0
2
votes
4
replies
3.3k
views
minfi latest update for EPIC V2 chip
minfi
minfiDataEPIC
updated 5 months ago by
UlyssesHenson
• 0 • written 19 months ago by
e1271094
• 0
0
votes
1
reply
444
views
Recovering my account credentials on Bioconductor
Bioconductor
updated 19 months ago by
shepherl
4.2k • written 19 months ago by
cyril.dalmasso
• 0
0
votes
0
replies
523
views
need help with Diffbind multiple groups
DiffBind
ChIPSeqData
19 months ago
Dinesh
• 0
3
votes
5
replies
1.1k
views
Help with running egsea()
EGSEA
19 months ago
Chris
▴ 20
3
votes
1
reply
874
views
How to save the DEXSeq results
DEXSeq
updated 19 months ago by
Michael Love
43k • written 19 months ago by
Sara
• 0
4
votes
5
replies
2.0k
views
Method to find pathways different between 2 groups
fgsea
GSVA
CAMERA
19 months ago • updated 18 months ago
Chris
▴ 20
0
votes
3
replies
815
views
Couldn't connect to server while using "pathways"
graphite
updated 19 months ago by
Michael Love
43k • written 19 months ago by
fduguchunhui
• 0
2
votes
1
reply
628
views
Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 19 months ago by
Michael Love
43k • written 19 months ago by
mat149
▴ 80
2
votes
1
reply
838
views
Handling multiple differential expression comparisons
DESeq2
19 months ago • updated 18 months ago
Zainab
▴ 20
2
votes
2
replies
1.6k
views
fgsea significant result
fgsea
19 months ago
Chris
▴ 20
0
votes
44
replies
6.2k
views
How to use bootRanges to bootstrap small RNA loci (nullranges package)
bootRanges
nullranges
updated 19 months ago by
Michael Love
43k • written 2.8 years ago by
Poonam
• 0
0
votes
6
replies
1.2k
views
Once again a "Model matrix not full rank"
DESeq2
design
coldata
updated 19 months ago by
swbarnes2
★ 1.4k • written 19 months ago by
arfranco
▴ 130
3
votes
2
replies
1.1k
views
limma Intercept vs No-intercept models completely changing DMR results?
limma
DMRcate
MethylationArray
EPICV2
updated 18 months ago by
Gordon Smyth
53k • written 19 months ago by
Kim
• 0
2
votes
3
replies
1.3k
views
package goseq seems to be not available on the latest version of R
goseq
updated 19 months ago by
Gordon Smyth
53k • written 19 months ago by
Patrycja
▴ 20
2
votes
6
replies
2.3k
views
Too many significant genes when integrating gtex and tcga
RNA-seq
DESeq2
updated 9 months ago by
Jane
• 0 • written 19 months ago by
Reza
• 0
0
votes
1
reply
1.1k
views
dba.plotProfile() plotting and interpretation
DiffBind
updated 13 months ago by
B.N
• 0 • written 19 months ago by
Henry
▴ 10
0
votes
1
reply
652
views
NEED FOR NESSASORY HELP
RNASeqData
edgeR
updated 19 months ago by
Gordon Smyth
53k • written 19 months ago by
z_bahari
• 0
0
votes
1
reply
731
views
Gene-by-sample covariates in limma
Metabolomics
limma
updated 19 months ago by
Gordon Smyth
53k • written 19 months ago by
c53aba27
• 0
4
votes
2
replies
1.8k
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea
edgeR
19 months ago
gene_bioconductor
▴ 10
0
votes
0
replies
405
views
flowStats for CyTOF
flowStats
19 months ago
tholmes
• 0
0
votes
2
replies
526
views
DESeq2 v1.35.0
DESeq2
updated 19 months ago by
Michael Love
43k • written 19 months ago by
Espresso
• 0
0
votes
0
replies
814
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
19 months ago
yvonneh
• 0
0
votes
0
replies
471
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
19 months ago
Ian D.
▴ 70
0
votes
1
reply
824
views
Job:
Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 19 months ago by
4r-rtg
• 0
0
votes
9
replies
1.9k
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
19 months ago • updated 13 months ago
Ian D.
▴ 70
0
votes
2
replies
905
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
19 months ago
kcarey
• 0
0
votes
3
replies
1.4k
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 19 months ago by
ATpoint
★ 5.0k • written 19 months ago by
james.zhang20
• 0
1
vote
3
replies
3.3k
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 19 months ago by
ATpoint
★ 5.0k • written 19 months ago by
angelathuynh5
• 0
4
votes
0
replies
1.6k
views
News:
Bioconductor 3.19 is Released!
Release
Bioconductor
Packages
Software
19 months ago
shepherl
4.2k
0
votes
0
replies
539
views
Empty table plot using plotGseaTable()
fgsea
19 months ago
Chris
▴ 20
0
votes
3
replies
720
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 19 months ago by
Michael Love
43k • written 19 months ago by
HAK
• 0
1
vote
2
replies
2.5k
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation
SequenceAnnotation
MethylationArray
GenomicDistributionsData
19 months ago
Yveto
• 0
0
votes
1
reply
918
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots
HMMcopy
CopyNumberVariation
updated 19 months ago by
James W. MacDonald
68k • written 19 months ago by
SSSJec
• 0
3
votes
4
replies
1.0k
views
Help with error using camera() in limma
CAMERA
limma
19 months ago
Chris
▴ 20
3
votes
1
reply
889
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 19 months ago by
Michael Love
43k • written 19 months ago by
marcusn
▴ 10
0
votes
2
replies
990
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
19 months ago
Aurora
• 0
0
votes
1
reply
574
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 19 months ago by
Michael Love
43k • written 19 months ago by
Agung
• 0
0
votes
0
replies
566
views
News:
BioC2024 deadlines approaching
BioC2024
Bioconductor
Community
19 months ago
Maria Doyle
▴ 110
0
votes
1
reply
543
views
Version 3.15 S4Vectors packages are missing
S4Vectors
updated 19 months ago by
shepherl
4.2k • written 19 months ago by
bounlu
• 0
46,691 results • Page
24 of 934
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Replies
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment
by
Michael Love
43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment
by
Michael Love
43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA
by
Gordon Smyth
53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR
by
James W. MacDonald
68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Answer: Question about DESeq2 Design for Paired Treatment Study
by
ATpoint
★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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