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9
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Reproducibility issue with scran together with lapply and BiocParallel
scran
BiocParallel
bluster
1 hour ago
ATpoint
★ 4.0k
0
votes
2
replies
26
views
Different Shrunk Log2FC according with reference
DESeq2
3 hours ago
andrebolerbarros
▴ 20
0
votes
0
replies
16
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
4 hours ago
winwater0928
• 0
1
vote
2
replies
46
views
get BM error
ensembldb
5 hours ago • updated 4 hours ago
Fara
• 0
0
votes
2
replies
55
views
How to retrieve gene ontology GO class from gene list?
GO.db
goTools
14 hours ago • updated 5 hours ago
bandconductor
• 0
1
vote
1
reply
47
views
Citation for edgeR user guide
edgeR
updated 13 hours ago by
Gordon Smyth
50k • written 16 hours ago by
k___
▴ 30
1
vote
1
reply
94
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 9 hours ago by
Michael Love
41k • written 17 hours ago by
i.sudbery
▴ 40
1
vote
1
reply
44
views
Cannabis OrgDb
KEGGgraph
org.Cs.eg.db
clusterProfiler
KEGG
AnnotationHubSoftware
updated 19 hours ago by
James W. MacDonald
65k • written 20 hours ago by
fernanda.backsouza
▴ 10
0
votes
3
replies
66
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 3 hours ago by
ATpoint
★ 4.0k • written 20 hours ago by
Aaliya
• 0
0
votes
0
replies
20
views
News:
Interested in the analysis of Spatial Omics data?
tidySpatialExperiment
SpatialExperiment
MoleculeExperiment
20 hours ago
info
▴ 10
0
votes
1
reply
43
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
updated 3 hours ago by
ATpoint
★ 4.0k • written 1 day ago by
shuwangxinze1996
• 0
0
votes
1
reply
79
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
updated 1 day ago by
Gordon Smyth
50k • written 1 day ago by
taur.vil
• 0
3
votes
3
replies
139
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 22 hours ago by
Michael Love
41k • written 1 day ago by
WardDeb
• 0
1
vote
4
replies
117
views
minfi::read.metharray.exp
minfiData
minfi
updated 4 hours ago by
Basti
▴ 780 • written 1 day ago by
clacarion
• 0
0
votes
0
replies
38
views
Improving the design matrices vignette in RNAseq123
RNAseq123
2 days ago
Lluís Revilla Sancho
▴ 730
0
votes
4
replies
162
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb
AnnotationForge
2 days ago • updated 3 hours ago
Gayatri
• 0
1
vote
12
replies
198
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
updated 2 hours ago by
Guido Hooiveld
★ 3.9k • written 2 days ago by
fernanda.backsouza
▴ 10
0
votes
0
replies
35
views
Unlocking Potential: NURS FPX Strategies and Insights
levi
NURSFPX
ragene20sttranscriptcluster.db
ssrch
3 days ago
vaxahey107
• 0
12
votes
12
replies
745
views
Why p value inconsistent when using different number of pathway score?
limma
updated 2 days ago by
Robert Castelo
★ 3.3k • written 3 days ago by
Chris
• 0
0
votes
0
replies
58
views
I am trying to detect alternative splicing.
ASpli
3 days ago
Sebashish
• 0
3
votes
2
replies
144
views
Cannabis and KEGGgraph
KEGGREST
GenomicDistributionsData
KEGGgraph
KEGG
updated 2 days ago by
Guido Hooiveld
★ 3.9k • written 4 days ago by
fernanda.backsouza
▴ 10
0
votes
1
reply
73
views
FDR via q-value
qvalue
updated 1 day ago by
James W. MacDonald
65k • written 4 days ago by
John
• 0
0
votes
2
replies
142
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
4 days ago • updated 2 days ago
catv
• 0
0
votes
3
replies
95
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
1
vote
0
replies
186
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
bioconductor
Install
4 days ago
BioinfGuru
▴ 30
0
votes
2
replies
85
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
5 days ago
prity6459
• 0
2
votes
2
replies
133
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 4 days ago by
James W. MacDonald
65k • written 5 days ago by
sansan
• 0
0
votes
4
replies
128
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
5 days ago
sropri
• 0
1
vote
4
replies
135
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
updated 1 day ago by
James W. MacDonald
65k • written 5 days ago by
Mirella Aurora
• 0
0
votes
3
replies
124
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 5 days ago by
Gordon Smyth
50k • written 5 days ago by
prity6459
• 0
0
votes
0
replies
84
views
Warning while loading DEP package
DEP
updated 5 days ago by
shepherl
3.8k • written 5 days ago by
Namrata
• 0
0
votes
1
reply
78
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 5 days ago by
Alejandro Reyes
★ 1.9k • written 6 days ago by
Alessia
• 0
0
votes
1
reply
84
views
rlog transformation
DESeq2
updated 5 days ago by
Michael Love
41k • written 6 days ago by
ishij9717
• 0
0
votes
1
reply
83
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 5 days ago by
Michael Love
41k • written 6 days ago by
09191919
• 0
0
votes
1
reply
105
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 5 days ago by
Gordon Smyth
50k • written 6 days ago by
Shaimaa Gamal
• 0
1
vote
2
replies
177
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
6 days ago • updated 5 days ago
Le
• 0
1
vote
2
replies
123
views
Error in champ.load(): The following specified files do not exist
ChAMP
6 days ago • updated 5 days ago
Sherin
• 0
0
votes
1
reply
77
views
Input Question for deseq.r
RSeqAn
updated 5 days ago by
ATpoint
★ 4.0k • written 6 days ago by
Nina
• 0
3
votes
6
replies
316
views
FilterByExpr low counts with small sample size
edgeR
6 days ago • updated 1 day ago
Jonathan
▴ 10
0
votes
4
replies
191
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
6 days ago • updated 4 days ago
lonn
• 0
0
votes
1
reply
94
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
updated 5 days ago by
Michael Love
41k • written 6 days ago by
ussarizona
• 0
0
votes
1
reply
109
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
0
votes
7
replies
236
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
7 days ago • updated 1 day ago
hortense96
• 0
0
votes
0
replies
60
views
News:
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flowBeads
7 days ago
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0
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Enzyme Engineering
BioTIP
7 days ago
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58
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News:
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flowBeads
7 days ago
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• 0
0
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1
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107
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covariate with negative and positive values
DESeq2
updated 5 days ago by
Michael Love
41k • written 7 days ago by
Brynn
• 0
0
votes
1
reply
113
views
Adding columns to DEXSeqResults object
DEXSeq
updated 5 days ago by
Alejandro Reyes
★ 1.9k • written 7 days ago by
Clyde
• 0
0
votes
0
replies
74
views
Syntaxt Error in IsorcorrectoR package with Molecule Info File
Syntaxerror
IsoCorrectoR
7 days ago
Maliha Tabassum
• 0
1
vote
2
replies
107
views
geneList error in clusterprofiler
clusterProfiler
GeneSetEnrichment
7 days ago
Ana
• 0
45,571 results • Page
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Comment: How to tell and visualize up/down regulation of pathways from clusterprofiler gs
by
Guangchuang Yu
★ 1.2k
an example is also presented in <https://pubmed.ncbi.nlm.nih.gov/34557778/>.
Comment: Trying to use enrichGO
by
Guido Hooiveld
★ 3.9k
Nothing would prevent you from using the `enrichGO` function (or any other function for over-representation analysis [ORA]) with only 14 ge…
Comment: Different Shrunk Log2FC according with reference
by
andrebolerbarros
▴ 20
Thanks @atpoint for your answer! The issue with that is then it severely hinders the possiblity of using `apeglm` shrinking approach, sinc…
Comment: featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_ge
by
ATpoint
★ 4.0k
The error that is relevant is `Aborted (core dumped)`. This line 2890 refers to the C source code that throws the error, it is not relevant…
Answer: Different Shrunk Log2FC according with reference
by
ATpoint
★ 4.0k
Please see: https://support.bioconductor.org/p/p134551/ I asked basically the same before. In short, reference level might have an influ…
Votes
C: SGSeq: moving toward diffex from SGSeq analysis
DEXSeq-Error in FUN(X[[i]], ...) : subscript out of bounds
Subset DEXSeqDataSet In DEXSeq
How to get all possible comparisons in DiffBind
Comment: get BM error
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