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News:
Interested in the analysis of Spatial Omics data?
tidySpatialExperiment
SpatialExperiment
MoleculeExperiment
16 minutes ago
info
▴ 10
0
votes
1
reply
43
views
minfi::read.metharray.exp
minfiData
minfi
updated 7 hours ago by
Basti
▴ 770 • written 23 hours ago by
clacarion
• 0
0
votes
0
replies
19
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
10 hours ago
shuwangxinze1996
• 0
1
vote
2
replies
904
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 12 hours ago by
Tim Peters
▴ 170 • written 13 months ago by
jose.ramirez1
▴ 10
0
votes
1
reply
65
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
updated 15 hours ago by
Gordon Smyth
50k • written 16 hours ago by
taur.vil
• 0
3
votes
3
replies
98
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 1 hour ago by
Michael Love
41k • written 22 hours ago by
WardDeb
• 0
1
vote
4
replies
110
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
updated 22 hours ago by
James W. MacDonald
65k • written 4 days ago by
Mirella Aurora
• 0
0
votes
1
reply
70
views
FDR via q-value
qvalue
updated 1 day ago by
James W. MacDonald
65k • written 3 days ago by
John
• 0
0
votes
3
replies
123
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb
AnnotationForge
updated 2 hours ago by
James W. MacDonald
65k • written 1 day ago by
Gayatri
• 0
0
votes
2
replies
137
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
4 days ago • updated 1 day ago
catv
• 0
0
votes
0
replies
34
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
6 months ago • updated 1 day ago
shepherl
3.8k
0
votes
2
replies
83
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
1 day ago • updated 14 hours ago
fernanda.backsouza
• 0
0
votes
0
replies
32
views
Unlocking Potential: NURS FPX Strategies and Insights
levi
NURSFPX
ragene20sttranscriptcluster.db
ssrch
2 days ago
vaxahey107
• 0
12
votes
12
replies
719
views
Why p value inconsistent when using different number of pathway score?
limma
updated 1 day ago by
Robert Castelo
★ 3.3k • written 3 days ago by
Chris
• 0
0
votes
0
replies
52
views
I am trying to detect alternative splicing.
ASpli
3 days ago
Sebashish
• 0
3
votes
2
replies
135
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
91
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 4 days ago by
James W. MacDonald
65k • written 4 days ago by
bas_work
▴ 30
2
votes
2
replies
128
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 4 days ago by
James W. MacDonald
65k • written 4 days ago by
sansan
• 0
1
vote
0
replies
179
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
bioconductor
Install
4 days ago • updated 3 days ago
BioinfGuru
▴ 30
3
votes
6
replies
297
views
FilterByExpr low counts with small sample size
edgeR
5 days ago • updated 22 hours ago
Jonathan
▴ 10
0
votes
2
replies
82
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
4 days ago
prity6459
• 0
0
votes
3
replies
117
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
103
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
122
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
4 days ago
sropri
• 0
0
votes
1
reply
72
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
79
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
80
views
rlog transformation
DESeq2
updated 4 days ago by
Michael Love
41k • written 5 days ago by
ishij9717
• 0
0
votes
1
reply
78
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 6 days ago by
ussarizona
• 0
0
votes
1
reply
102
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 5 days ago by
ATpoint
★ 4.0k • written 6 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
Sherin
• 0
0
votes
1
reply
75
views
Input Question for deseq.r
RSeqAn
updated 5 days ago by
ATpoint
★ 4.0k • written 5 days ago by
Nina
• 0
0
votes
4
replies
180
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
6 days ago • updated 3 days ago
lonn
• 0
0
votes
7
replies
225
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
6 days ago • updated 6 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
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• 0
0
votes
0
replies
56
views
News:
TIDES USA 2024
flowBeads
6 days ago
bocsci11
• 0
0
votes
0
replies
70
views
Syntaxt Error in IsorcorrectoR package with Molecule Info File
Syntaxerror
IsoCorrectoR
6 days ago
Maliha Tabassum
• 0
0
votes
4
replies
144
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
7 days ago • updated 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 7 days ago by
James W. MacDonald
65k • written 7 days ago by
zhulin
• 0
45,562 results • Page
1 of 912
Recent ...
Replies
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa
by
Michael Love
41k
I don't really have any additional suggestion here.
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa
by
Seyram M.
• 0
Dear Michael, I tried all three ways (the orIginal, increasing the number of required samples,and subsetting (the countdata and metadata be…
Comment: DESeq2 - dispersion estimation when there is none
by
Michael Love
41k
The red line does assume that shape but the fact the black points show that pattern is discussed in the 2014 paper. > Some caution is warr…
Comment: Error for AnnotationForge makeOrgPackageFromNCBI function
by
James W. MacDonald
65k
I don't really follow what you are saying. All you have to do is delete the NCBI.sqlite db and *re-run the script exactly as you did above.…
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…
Votes
DESeq2: How to find out how well the model fits the data?
Comment: DESeq2 - dispersion estimation when there is none
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa
Answer: OrgDb for maize
Answer: DESeq2 - dispersion estimation when there is none
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