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0
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0
replies
99
views
how to do Differential splicing from SGSeq analysis
DEXSeq
SGSeq
23 days ago • updated 18 days ago
Sara
• 0
2
votes
5
replies
303
views
get BM error
ensembldb
updated 23 days ago by
James W. MacDonald
65k • written 23 days ago by
Fara
• 0
2
votes
5
replies
258
views
How to retrieve gene ontology GO class from gene list?
GO.db
goTools
updated 22 days ago by
James W. MacDonald
65k • written 23 days ago by
bandconductor
• 0
0
votes
0
replies
97
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
23 days ago
Dario Strbenac
★ 1.5k
1
vote
3
replies
235
views
Different Shrunk Log2FC according with reference
DESeq2
updated 23 days ago by
Michael Love
42k • written 23 days ago by
andrebolerbarros
▴ 20
1
vote
4
replies
355
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
23 days ago • updated 21 days ago
winwater0928
• 0
3
votes
1
reply
328
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 23 days ago by
Michael Love
42k • written 24 days ago by
i.sudbery
▴ 40
1
vote
2
replies
202
views
Citation for edgeR user guide
edgeR
written 24 days ago by
k___
▴ 30
0
votes
7
replies
746
views
News:
List of Deprecated Packages for Bioc3.19
Release
Devel
ExperimentData
Software
11 weeks ago • updated 24 days ago
shepherl
3.9k
1
vote
1
reply
131
views
Cannabis OrgDb
KEGGgraph
org.Cs.eg.db
clusterProfiler
KEGG
AnnotationHubSoftware
updated 24 days ago by
James W. MacDonald
65k • written 24 days ago by
fernanda.backsouza
▴ 10
0
votes
8
replies
381
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 22 days ago by
swbarnes2
★ 1.4k • written 24 days ago by
Aaliya
• 0
0
votes
0
replies
81
views
News:
Interested in the analysis of Spatial Omics data?
tidySpatialExperiment
SpatialExperiment
MoleculeExperiment
24 days ago
info
▴ 10
1
vote
4
replies
228
views
minfi::read.metharray.exp
minfiData
minfi
updated 23 days ago by
Basti
▴ 780 • written 25 days ago by
clacarion
• 0
0
votes
2
replies
264
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
24 days ago • updated 22 days ago
shuwangxinze1996
• 0
1
vote
2
replies
1.0k
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 24 days ago by
Tim Peters
▴ 180 • written 14 months ago by
jose.ramirez1
▴ 10
0
votes
2
replies
190
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
written 24 days ago by
taur.vil
• 0
3
votes
3
replies
250
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 24 days ago by
Michael Love
42k • written 25 days ago by
WardDeb
• 0
2
votes
4
replies
279
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
updated 25 days ago by
James W. MacDonald
65k • written 29 days ago by
Mirella Aurora
• 0
0
votes
1
reply
136
views
FDR via q-value
qvalue
updated 25 days ago by
James W. MacDonald
65k • written 28 days ago by
John
• 0
0
votes
5
replies
324
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb
AnnotationForge
updated 23 days ago by
James W. MacDonald
65k • written 26 days ago by
Gayatri
• 0
0
votes
2
replies
237
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
28 days ago • updated 25 days ago
catv
• 0
0
votes
4
replies
1.2k
views
News:
European Bioconductor Conference 2023 planning
Europe
Conference
EuroBioC
Events
News
updated 12 hours ago by
angelaesper43
• 0 • written 19 months ago by
Maria Doyle
▴ 70
6
votes
12
replies
5.1k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache
AnnotationHub
ExperimentHub
6 months ago • updated 25 days ago
shepherl
3.9k
2
votes
13
replies
476
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
26 days ago • updated 23 days ago
fernanda.backsouza
▴ 10
0
votes
0
replies
94
views
Unlocking Potential: NURS FPX Strategies and Insights
levi
NURSFPX
ragene20sttranscriptcluster.db
ssrch
26 days ago
vaxahey107
• 0
15
votes
17
replies
1.3k
views
Why p value inconsistent when using different number of pathway score?
limma
27 days ago • updated 16 days ago
Chris
▴ 10
0
votes
0
replies
105
views
I am trying to detect alternative splicing.
ASpli
27 days ago
Sebashish
• 0
3
votes
2
replies
229
views
Cannabis and KEGGgraph
KEGGREST
GenomicDistributionsData
KEGGgraph
KEGG
updated 25 days ago by
Guido Hooiveld
★ 4.0k • written 27 days ago by
fernanda.backsouza
▴ 10
0
votes
3
replies
173
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 28 days ago by
James W. MacDonald
65k • written 28 days ago by
bas_work
▴ 30
2
votes
2
replies
211
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 28 days ago by
James W. MacDonald
65k • written 28 days ago by
sansan
• 0
1
vote
0
replies
346
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
bioconductor
Install
28 days ago
BioinfGuru
▴ 30
4
votes
6
replies
465
views
FilterByExpr low counts with small sample size
edgeR
4 weeks ago • updated 25 days ago
Jonathan
▴ 10
0
votes
2
replies
147
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
28 days ago
prity6459
• 0
0
votes
3
replies
209
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 28 days ago by
Gordon Smyth
50k • written 29 days ago by
prity6459
• 0
5
votes
3
replies
304
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 7 days ago by
Gordon Smyth
50k • written 29 days ago by
Shaimaa Gamal
• 0
0
votes
4
replies
216
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
29 days ago
sropri
• 0
0
votes
3
replies
187
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 17 days ago by
Alejandro Reyes
★ 1.9k • written 29 days ago by
Alessia
• 0
0
votes
1
reply
165
views
Adding columns to DEXSeqResults object
DEXSeq
updated 29 days ago by
Alejandro Reyes
★ 1.9k • written 4 weeks ago by
Clyde
• 0
0
votes
0
replies
132
views
Warning while loading DEP package
DEP
updated 29 days ago by
shepherl
3.9k • written 29 days ago by
Namrata
• 0
0
votes
1
reply
155
views
rlog transformation
DESeq2
updated 29 days ago by
Michael Love
42k • written 29 days ago by
ishij9717
• 0
0
votes
1
reply
124
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 29 days ago by
Michael Love
42k • written 29 days ago by
09191919
• 0
1
vote
2
replies
738
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
4 weeks ago • updated 21 days ago
Patadù
▴ 10
0
votes
1
reply
149
views
covariate with negative and positive values
DESeq2
updated 29 days ago by
Michael Love
42k • written 4 weeks ago by
Brynn
• 0
0
votes
1
reply
165
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 29 days ago by
ATpoint
★ 4.1k • written 4 weeks ago by
quanah.hudson
• 0
1
vote
2
replies
233
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
29 days ago
Le
• 0
1
vote
2
replies
176
views
Error in champ.load(): The following specified files do not exist
ChAMP
4 weeks ago • updated 29 days ago
Sherin
• 0
0
votes
1
reply
110
views
Input Question for deseq.r
RSeqAn
updated 29 days ago by
ATpoint
★ 4.1k • written 4 weeks ago by
Nina
• 0
0
votes
4
replies
263
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
4 weeks ago • updated 27 days ago
lonn
• 0
0
votes
7
replies
360
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
4 weeks ago • updated 24 days ago
hortense96
• 0
0
votes
0
replies
95
views
News:
Services
flowBeads
4 weeks ago
creativepeptides2018
• 0
1,000 results • Page
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Comment: DESeq2- Mysterious interaction suppresses DEGs
by
shaunpeterson
• 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Comment: STRINGdb : error with string_db$plot_network()
by
damian.szk
▴ 80
ok. Forcing non-secure protocol should not be needed anymore, due to changes in the underlying library. However, I will look at why "HTTP" …
Comment: STRINGdb : error with string_db$plot_network()
by
ninidea
• 0
> Does the vignette produce the same error? No. Anyway, I finally solved the problem. I don't know why, but I removed: protocol='http' fr…
Comment: maSigPro genes from clusters
by
anne-laure
• 0
Hello It is a litlle bit late but I do not get how to extract the genes from each cluster identified by see.genes(sigs$sig.genes$Day4vs…
Comment: STRINGdb : error with string_db$plot_network()
by
damian.szk
▴ 80
Your code seems ok. Does the vignette produce the same error? [link to STRINGdb R script vignette][1] [1]: https://www.bioconductor.or…
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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