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Cannabis and KEGGgraph
KEGGREST
GenomicDistributionsData
KEGGgraph
KEGG
1 hour ago
fernanda.backsouza
• 0
0
votes
0
replies
16
views
FDR via q-value
qvalue
5 hours ago
John
• 0
0
votes
6
replies
556
views
News:
List of Deprecated Packages for Bioc3.19
Release
Devel
ExperimentData
Software
7 weeks ago • updated 5 hours ago
shepherl
3.8k
0
votes
0
replies
16
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
7 hours ago
catv
• 0
0
votes
3
replies
43
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 7 hours ago by
James W. MacDonald
65k • written 8 hours ago by
bas_work
▴ 30
1
vote
2
replies
62
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 9 hours ago by
James W. MacDonald
65k • written 1 day ago by
sansan
• 0
1
vote
0
replies
55
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
bioconductor
Install
10 hours ago • updated 5 hours ago
BioinfGuru
▴ 30
0
votes
4
replies
179
views
FilterByExpr low counts with small sample size
edgeR
2 days ago • updated 6 hours ago
Jonathan
▴ 10
0
votes
2
replies
50
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
14 hours ago • updated 13 hours ago
prity6459
• 0
0
votes
3
replies
74
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 12 hours ago by
Gordon Smyth
50k • written 1 day ago by
prity6459
• 0
0
votes
1
reply
62
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 13 hours ago by
Gordon Smyth
50k • written 1 day ago by
Shaimaa Gamal
• 0
0
votes
4
replies
77
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
1 day ago
sropri
• 0
0
votes
0
replies
26
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
1 day ago
Mirella Aurora
• 0
0
votes
1
reply
44
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 1 day ago by
Alejandro Reyes
★ 1.9k • written 1 day ago by
Alessia
• 0
0
votes
1
reply
77
views
Adding columns to DEXSeqResults object
DEXSeq
updated 1 day ago by
Alejandro Reyes
★ 1.9k • written 3 days ago by
Clyde
• 0
0
votes
0
replies
39
views
Warning while loading DEP package
DEP
updated 1 day ago by
shepherl
3.8k • written 1 day ago by
Namrata
• 0
0
votes
1
reply
53
views
rlog transformation
DESeq2
updated 1 day ago by
Michael Love
41k • written 1 day ago by
ishij9717
• 0
0
votes
1
reply
49
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 1 day ago by
Michael Love
41k • written 1 day ago by
09191919
• 0
0
votes
1
reply
58
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
updated 1 day ago by
Michael Love
41k • written 2 days ago by
ussarizona
• 0
0
votes
1
reply
76
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covariate with negative and positive values
DESeq2
updated 1 day ago by
Michael Love
41k • written 3 days ago by
Brynn
• 0
0
votes
1
reply
77
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DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 1 day ago by
ATpoint
★ 4.0k • written 2 days ago by
quanah.hudson
• 0
1
vote
2
replies
138
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
1 day ago
Le
• 0
1
vote
2
replies
87
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Error in champ.load(): The following specified files do not exist
ChAMP
2 days ago • updated 1 day ago
Sherin
• 0
0
votes
1
reply
53
views
Input Question for deseq.r
RSeqAn
updated 1 day ago by
ATpoint
★ 4.0k • written 2 days ago by
Nina
• 0
0
votes
3
replies
108
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
updated 14 hours ago by
ATpoint
★ 4.0k • written 2 days ago by
lonn
• 0
0
votes
6
replies
155
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
updated 1 day ago by
Gordon Smyth
50k • written 2 days ago by
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• 0
0
votes
0
replies
38
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2 days ago
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2 days ago
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0
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0
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48
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Syntaxt Error in IsorcorrectoR package with Molecule Info File
Syntaxerror
IsoCorrectoR
3 days ago
Maliha Tabassum
• 0
0
votes
4
replies
117
views
flowStats Search Error
flowStats
updated 3 days ago by
shepherl
3.8k • written 3 days ago by
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3
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18
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2.8k
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News:
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Deprecation
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Devel
9 months ago • updated 2 days ago
shepherl
3.8k
0
votes
1
reply
95
views
SNP locus package for mouse?
SNPlocs
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updated 3 days ago by
James W. MacDonald
65k • written 6 days ago by
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• 0
1
vote
2
replies
79
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geneList error in clusterprofiler
clusterProfiler
GeneSetEnrichment
3 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
74
views
what is the sampleFiles
chipseq
updated 3 days ago by
James W. MacDonald
65k • written 3 days ago by
zhulin
• 0
0
votes
1
reply
114
views
Differentially expressed genes in monocle pseudotime
monocle
updated 3 days ago by
Gordon Smyth
50k • written 5 days ago by
kthapa
• 0
4
votes
8
replies
300
views
Memory errors using read.bismark?
dmrseq
bsseq
updated 22 hours ago by
Peter Hickey
▴ 740 • written 8 days ago by
Juan Higareda
• 0
3
votes
3
replies
137
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
7 days ago • updated 1 day ago
jacques.imbert
• 0
0
votes
1
reply
107
views
The issue with SGSeq_analyzeFeatures() returns errors on BAM files
SGSeq
updated 3 days ago by
kamryncole1963
• 0 • written 8 days ago by
Sara
• 0
0
votes
3
replies
142
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 3 days ago by
Michael Love
41k • written 4 days ago by
andrebolerbarros
▴ 20
0
votes
0
replies
59
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
4 days ago
Virangika
• 0
0
votes
0
replies
44
views
[ChIPseeker] Unable to perform gene ontology analysis
ChIPseeker
4 days ago
Henry
▴ 10
1
vote
2
replies
181
views
How to retrieve detailed regression results from deseq2
DESeq2
8 days ago • updated 3 hours ago
Weiqian
▴ 10
0
votes
4
replies
198
views
DEG with low counts
DESeq2
updated 11 hours ago by
Michael Love
41k • written 5 days ago by
Rajat
• 0
1
vote
2
replies
229
views
GSVA error
GSVA
5 days ago • updated 4 days ago
Alex
• 0
2
votes
3
replies
255
views
ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with variable number of continuous columns
ComplexHeatmap
4 days ago • updated 3 days ago
daniel.carbajo
• 0
3
votes
3
replies
261
views
permutation test in edgeR
rna-seq
edgeR
updated 4 days ago by
Gordon Smyth
50k • written 11 days ago by
Netanel
• 0
1
vote
3
replies
307
views
Why is my gene not significantly differentially expressed?
limmaGUI
edgeR
limma
updated 4 days ago by
Gordon Smyth
50k • written 9 days ago by
Simran
• 0
0
votes
1
reply
94
views
Deseq2 Rlog transformation
DESeq2
updated 4 days ago by
ATpoint
★ 4.0k • written 5 days ago by
Sahar
• 0
45,551 results • Page
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Comment: DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, param
by
russ.bainer
▴ 10
Hi, I'm hitting this too. As far as I can tell my DataTrack is fine, but perhaps I am missing something. Notably the same code works on o…
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions
by
Chris
• 0
Hi Robert, If I don't want to use all pathway in c2 gene set but only a few pathways of interested, how can I do that? So we try to get a …
Comment: How to retrieve detailed regression results from deseq2
by
Weiqian
▴ 10
Hi Michael, thanks for the answer! I'll have a look : )
Comment: DESeq filtering specific to contrasts
by
Michael Love
41k
It will likely not filter it out, but really the per-dataset details would affect the results.
Comment: DESeq filtering specific to contrasts
by
Carlin95
• 0
Thanks for clarifying. Could I ask maybe one more thing for my sanity? Let's say you had a multi-factor experiment with contrasts including…
Votes
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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