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8
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Recommendations on deploying cytoviewer shiny.appobj to shinyapps.io?
cytoviewer
ShinyApps
42 minutes ago
neilzhao
▴ 30
1
vote
0
replies
257
views
News:
Nominations for Bioconductor Awards 2024! Deadline May 15
Recognition
Awards
Bioconductor
Bioc204
6 weeks ago • updated 9 hours ago
shepherl
3.9k
0
votes
1
reply
38
views
normalization using Deseq2
DESeq2
rnaseqGene
Normalization
updated 13 hours ago by
ATpoint
★ 4.1k • written 14 hours ago by
sajadahmad41454
• 0
0
votes
0
replies
41
views
Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq
duplicateCorrelation
limma
voom
20 hours ago
Dylan.Sheerin
• 0
3
votes
4
replies
429
views
Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it does not happen in Linux
GenomAutomorphism
updated 1 day ago by
Mike Smith
★ 6.5k • written 4 days ago by
robersy
• 0
0
votes
3
replies
113
views
deseq2 results
DESeq2
DifferentialExpression
rnaseqGene
DifferentialRegulation
1 day ago • updated 11 hours ago
sajadahmad41454
• 0
0
votes
0
replies
26
views
Treeio as.treedata function seq lenght error
treeio
1 day ago
nromerov
• 0
1
vote
1
reply
104
views
error in limma , contrast.matrix Number of rows of contrast matrix must match number of coefficients in fit
limma
updated 2 days ago by
James W. MacDonald
65k • written 2 days ago by
zzrammal
• 0
2
votes
8
replies
187
views
Extremely small p-values using Limma for proteomic data
Proteomics
limma
updated 1 minute ago by
James W. MacDonald
65k • written 2 days ago by
Abbey
• 0
1
vote
1
reply
95
views
minfi latest update for EPIC V2 chip
minfi
minfiDataEPIC
updated 2 days ago by
James W. MacDonald
65k • written 2 days ago by
e1271094
• 0
0
votes
1
reply
56
views
Recovering my account credentials on Bioconductor
Bioconductor
updated 2 days ago by
shepherl
3.9k • written 2 days ago by
cyril.dalmasso
• 0
0
votes
0
replies
41
views
need help with Diffbind multiple groups
DiffBind
ChIPSeqData
3 days ago
Dinesh
• 0
3
votes
5
replies
202
views
Help with running egsea()
EGSEA
3 days ago • updated 1 day ago
Chris
• 0
3
votes
1
reply
100
views
How to save the DEXSeq results
DEXSeq
updated 3 days ago by
Michael Love
42k • written 3 days ago by
Sara
• 0
3
votes
4
replies
216
views
Method to find pathways different between 2 groups
fgsea
GSVA
CAMERA
updated 1 day ago by
Gordon Smyth
50k • written 3 days ago by
Chris
• 0
0
votes
3
replies
132
views
Couldn't connect to server while using "pathways"
graphite
updated 3 days ago by
Michael Love
42k • written 3 days ago by
fduguchunhui
• 0
1
vote
1
reply
93
views
Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 3 days ago by
Michael Love
42k • written 3 days ago by
mat149
▴ 70
1
vote
1
reply
136
views
Handling multiple differential expression comparisons
DESeq2
updated 4 days ago by
Michael Love
42k • written 6 days ago by
Zainab
▴ 10
2
votes
2
replies
176
views
fgsea significant result
fgsea
5 days ago • updated 4 days ago
Chris
• 0
0
votes
39
replies
2.8k
views
How to use bootRanges to bootstrap small RNA loci (nullranges package)
bootRanges
nullranges
15 months ago • updated 6 hours ago
Poonam
• 0
0
votes
6
replies
239
views
Once again a "Model matrix not full rank"
DESeq2
design
coldata
updated 5 days ago by
swbarnes2
★ 1.3k • written 7 days ago by
arfranco
▴ 130
1
vote
2
replies
353
views
limma Intercept vs No-intercept models completely changing DMR results?
limma
DMRcate
MethylationArray
EPICV2
updated 5 days ago by
Gordon Smyth
50k • written 6 days ago by
Kim
• 0
2
votes
3
replies
191
views
package goseq seems to be not available on the latest version of R
goseq
updated 3 days ago by
Gordon Smyth
50k • written 6 days ago by
Patrycja
▴ 20
2
votes
3
replies
199
views
Too many significant genes when integrating gtex and tcga
RNA-seq
DESeq2
updated 4 days ago by
ATpoint
★ 4.1k • written 6 days ago by
Reza
• 0
0
votes
0
replies
84
views
dba.plotProfile() plotting and interpretation
DiffBind
6 days ago
Henry
▴ 10
0
votes
1
reply
136
views
NEED FOR NESSASORY HELP
RNASeqData
edgeR
updated 6 days ago by
Gordon Smyth
50k • written 7 days ago by
z_bahari
• 0
0
votes
1
reply
119
views
Gene-by-sample covariates in limma
Metabolomics
limma
updated 7 days ago by
Gordon Smyth
50k • written 7 days ago by
c53aba27
• 0
4
votes
2
replies
568
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea
edgeR
7 days ago • updated 3 days ago
gene_bioconductor
▴ 10
0
votes
0
replies
65
views
flowStats for CyTOF
flowStats
7 days ago
tholmes
• 0
0
votes
2
replies
123
views
DESeq2 v1.35.0
DESeq2
updated 7 days ago by
Michael Love
42k • written 7 days ago by
Espresso
• 0
0
votes
0
replies
59
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
7 days ago
yvonneh
• 0
0
votes
0
replies
55
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
7 days ago
Ian D.
▴ 70
0
votes
1
reply
90
views
Job:
Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 7 days ago by
4r-rtg
• 0
0
votes
3
replies
190
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
8 days ago • updated 1 day ago
Ian D.
▴ 70
0
votes
2
replies
159
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
8 days ago • updated 6 days ago
kcarey
• 0
0
votes
3
replies
166
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 7 days ago by
ATpoint
★ 4.1k • written 8 days ago by
james.zhang20
• 0
1
vote
3
replies
255
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 1 day ago by
ATpoint
★ 4.1k • written 8 days ago by
angelathuynh5
• 0
4
votes
0
replies
98
views
News:
Bioconductor 3.19 is Released!
Release
Bioconductor
Packages
Software
8 days ago
shepherl
3.9k
0
votes
0
replies
107
views
Empty table plot using plotGseaTable()
fgsea
8 days ago • updated 6 days ago
Chris
• 0
0
votes
3
replies
179
views
Store output of matchPWM()
biostrings
Biostrings
updated 8 days ago by
James W. MacDonald
65k • written 8 days ago by
mat149
▴ 70
0
votes
3
replies
265
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 8 days ago by
Michael Love
42k • written 9 days ago by
HAK
• 0
1
vote
2
replies
249
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation
SequenceAnnotation
MethylationArray
GenomicDistributionsData
8 days ago • updated 7 days ago
Yveto
• 0
8
votes
7
replies
1.8k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq
rnaseq
updated 3 days ago by
Sara
• 0 • written 6.7 years ago by
Sylvain Foisy
▴ 80
0
votes
1
reply
238
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots
HMMcopy
CopyNumberVariation
updated 9 days ago by
James W. MacDonald
65k • written 9 days ago by
SSSJec
• 0
3
votes
4
replies
233
views
Help with error using camera() in limma
CAMERA
limma
9 days ago
Chris
• 0
1
vote
1
reply
130
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 9 days ago by
Michael Love
42k • written 9 days ago by
marcusn
• 0
0
votes
2
replies
139
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
9 days ago • updated 6 days ago
Aurora
• 0
0
votes
1
reply
119
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 9 days ago by
Michael Love
42k • written 10 days ago by
Agung
• 0
0
votes
0
replies
78
views
News:
BioC2024 deadlines approaching
BioC2024
Bioconductor
Community
9 days ago
Maria Doyle
▴ 70
0
votes
1
reply
104
views
Version 3.15 S4Vectors packages are missing
S4Vectors
updated 9 days ago by
shepherl
3.9k • written 9 days ago by
bounlu
• 0
45,633 results • Page
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Comment: Extremely small p-values using Limma for proteomic data
by
Abbey
• 0
Thank you James! This worked to fix the p-values. However, the plot still looks one-sided... any idea what's going on with the left side?…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
That ll be helpful. Thank you.
Comment: Log-cpm values from limma
by
Shaimaa Gamal
• 0
I have performed RUVg correction and extracted W, factors of unwanted variation. According to limma guide, > In the limma approach to RNA…
Comment: DSS CpG coverage threshold
by
j.gilbert
• 0
Might be a bit late for the original poster :') but in case anyone else is wondering, the DSS user guide says: *Q: Do I need to filter out…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
42k
Segmentation is of the whole genome, I'll write some code for doing this later today.
Votes
Answer: Extremely small p-values using Limma for proteomic data
Bioconductor 3.19 is Released!
A: Volcanoplot with limma - RAW P-values or Adj.P-Values
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
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