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40
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minfi::read.metharray.exp
minfiData
minfi
updated 3 hours ago by
Basti
▴ 770 • written 19 hours ago by
clacarion
• 0
0
votes
0
replies
15
views
featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_get_next_read_BIN: Assertion `l_name < 256' failed. Aborted (core dumpe…
metaMSdata
7 hours ago
shuwangxinze1996
• 0
1
vote
2
replies
903
views
DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE, : NA/NaN/Inf in foreign function call (arg 1)"
DMRcate
Gviz
updated 8 hours ago by
Tim Peters
▴ 170 • written 13 months ago by
jose.ramirez1
▴ 10
0
votes
1
reply
64
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
updated 11 hours ago by
Gordon Smyth
50k • written 12 hours ago by
taur.vil
• 0
2
votes
2
replies
81
views
DESeq2 - dispersion estimation when there is none
DESeq2
19 hours ago • updated 3 hours ago
WardDeb
• 0
1
vote
4
replies
108
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
updated 18 hours ago by
James W. MacDonald
65k • written 4 days ago by
Mirella Aurora
• 0
0
votes
1
reply
68
views
FDR via q-value
qvalue
updated 21 hours ago by
James W. MacDonald
65k • written 3 days ago by
John
• 0
0
votes
2
replies
95
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb
AnnotationForge
1 day ago • updated 6 hours ago
Gayatri
• 0
0
votes
2
replies
131
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
3 days ago • updated 1 day ago
catv
• 0
0
votes
0
replies
32
views
Improving the design matrices vignette in RNAseq123
RNAseq123
1 day ago
Lluís Revilla Sancho
▴ 730
0
votes
3
replies
1.1k
views
News:
European Bioconductor Conference 2023 planning
Europe
Conference
EuroBioC
Events
News
updated 1 day ago by
lauryfriese932
• 0 • written 18 months ago by
Maria Doyle
▴ 70
6
votes
12
replies
4.6k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache
AnnotationHub
ExperimentHub
5 months ago • updated 21 hours ago
shepherl
3.8k
0
votes
2
replies
81
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
1 day ago • updated 10 hours ago
fernanda.backsouza
• 0
0
votes
0
replies
30
views
Unlocking Potential: NURS FPX Strategies and Insights
levi
NURSFPX
ragene20sttranscriptcluster.db
ssrch
2 days ago
vaxahey107
• 0
12
votes
12
replies
712
views
Why p value inconsistent when using different number of pathway score?
limma
updated 1 day ago by
Robert Castelo
★ 3.3k • written 2 days ago by
Chris
• 0
0
votes
0
replies
51
views
I am trying to detect alternative splicing.
ASpli
2 days ago
Sebashish
• 0
3
votes
2
replies
132
views
Cannabis and KEGGgraph
KEGGREST
GenomicDistributionsData
KEGGgraph
KEGG
updated 1 day ago by
Guido Hooiveld
★ 3.9k • written 3 days ago by
fernanda.backsouza
• 0
0
votes
6
replies
584
views
News:
List of Deprecated Packages for Bioc3.19
Release
Devel
ExperimentData
Software
7 weeks ago • updated 3 days ago
shepherl
3.8k
0
votes
3
replies
90
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 3 days ago by
James W. MacDonald
65k • written 3 days ago by
bas_work
▴ 30
2
votes
2
replies
126
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 3 days ago by
James W. MacDonald
65k • written 4 days ago by
sansan
• 0
1
vote
0
replies
177
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
bioconductor
Install
3 days ago
BioinfGuru
▴ 30
3
votes
6
replies
295
views
FilterByExpr low counts with small sample size
edgeR
5 days ago • updated 18 hours ago
Jonathan
▴ 10
0
votes
2
replies
81
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
4 days ago
prity6459
• 0
0
votes
3
replies
116
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 4 days ago by
Gordon Smyth
50k • written 4 days ago by
prity6459
• 0
0
votes
1
reply
100
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 4 days ago by
Gordon Smyth
50k • written 5 days ago by
Shaimaa Gamal
• 0
0
votes
4
replies
120
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
4 days ago
sropri
• 0
0
votes
1
reply
71
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 4 days ago by
Alejandro Reyes
★ 1.9k • written 5 days ago by
Alessia
• 0
0
votes
1
reply
109
views
Adding columns to DEXSeqResults object
DEXSeq
updated 4 days ago by
Alejandro Reyes
★ 1.9k • written 6 days ago by
Clyde
• 0
0
votes
0
replies
78
views
Warning while loading DEP package
DEP
updated 4 days ago by
shepherl
3.8k • written 4 days ago by
Namrata
• 0
0
votes
1
reply
78
views
rlog transformation
DESeq2
updated 4 days ago by
Michael Love
41k • written 5 days ago by
ishij9717
• 0
0
votes
1
reply
74
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 4 days ago by
Michael Love
41k • written 5 days ago by
09191919
• 0
0
votes
1
reply
86
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
updated 4 days ago by
Michael Love
41k • written 5 days ago by
ussarizona
• 0
0
votes
1
reply
100
views
covariate with negative and positive values
DESeq2
updated 4 days ago by
Michael Love
41k • written 6 days ago by
Brynn
• 0
0
votes
1
reply
107
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 4 days ago by
ATpoint
★ 4.0k • written 5 days ago by
quanah.hudson
• 0
1
vote
2
replies
175
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
5 days ago • updated 4 days ago
Le
• 0
1
vote
2
replies
118
views
Error in champ.load(): The following specified files do not exist
ChAMP
5 days ago • updated 4 days ago
Sherin
• 0
0
votes
1
reply
74
views
Input Question for deseq.r
RSeqAn
updated 4 days ago by
ATpoint
★ 4.0k • written 5 days ago by
Nina
• 0
0
votes
4
replies
179
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
5 days ago • updated 3 days ago
lonn
• 0
0
votes
7
replies
217
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
6 days ago • updated 2 hours ago
hortense96
• 0
0
votes
0
replies
56
views
News:
Services
flowBeads
6 days ago
creativepeptides2018
• 0
0
votes
0
replies
45
views
Enzyme Engineering
BioTIP
6 days ago
bocchemistry
• 0
0
votes
0
replies
56
views
News:
TIDES USA 2024
flowBeads
6 days ago
bocsci11
• 0
0
votes
0
replies
69
views
Syntaxt Error in IsorcorrectoR package with Molecule Info File
Syntaxerror
IsoCorrectoR
6 days ago
Maliha Tabassum
• 0
0
votes
4
replies
143
views
flowStats Search Error
flowStats
updated 6 days ago by
shepherl
3.8k • written 7 days ago by
tholmes
• 0
3
votes
18
replies
2.8k
views
News:
List of Deprecated Packages for Bioc3.18
Deprecation
devel
Bioconductor
Devel
10 months ago • updated 5 days ago
shepherl
3.8k
0
votes
1
reply
114
views
SNP locus package for mouse?
SNPlocs
packFinder
updated 6 days ago by
James W. MacDonald
65k • written 9 days ago by
tian.liu0720
• 0
1
vote
2
replies
104
views
geneList error in clusterprofiler
clusterProfiler
GeneSetEnrichment
6 days ago
Ana
• 0
0
votes
5
replies
1.6k
views
blockwiseModule crashes in the end and doesn't generate modules
WGCNA
written 12 months ago by
mauricio.microbiol
• 0
0
votes
1
reply
95
views
what is the sampleFiles
chipseq
updated 6 days ago by
James W. MacDonald
65k • written 7 days ago by
zhulin
• 0
1
vote
1
reply
150
views
Differentially expressed genes in monocle pseudotime
monocle
updated 7 days ago by
Gordon Smyth
50k • written 9 days ago by
kthapa
• 0
1,747 results • Page
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Recent ...
Replies
Comment: Methylation Analysis experiment design using Limma
by
hortense96
• 0
Thank you very much for your reply and your suggestion, as I'm having a bit of trouble finding information on how to manage this part of th…
Comment: Limma design with continuous and categorical covariates
by
hortense96
• 0
Hello, I'm trying to do a differential methylation analysis with the Limma package and was wondering if you had any suggestions on how to …
Answer: minfi::read.metharray.exp
by
Basti
▴ 770
Could you show `list.files("~/Users/clarachretienneau/Desktop/clock epigenetic/PJ1209132_ScanData")` ? There may be a problem related to th…
Comment: DESeq2 - dispersion estimation when there is none
by
WardDeb
• 0
Thank you for the pointers, I'll revert back again to the method section of the paper. As for the negative relationship of the estimated di…
Comment: Error for AnnotationForge makeOrgPackageFromNCBI function
by
Gayatri
• 0
Hello James, How to generate the db? By running the makeOrgPackageFromNCBI() command? I have tried doing that, first by just deleting the …
Votes
Answer: OrgDb for maize
Answer: DESeq2 - dispersion estimation when there is none
Comment: Cannabis and KEGGgraph
Comment: Cannabis and KEGGgraph
Answer: Cannabis and KEGGgraph
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