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8
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DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 7 days ago by
swbarnes2
★ 1.3k • written 9 days ago by
Aaliya
• 0
0
votes
1
reply
129
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 7 days ago by
Michael Love
41k • written 7 days ago by
kcarey
• 0
1
vote
13
replies
368
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
11 days ago • updated 7 days ago
fernanda.backsouza
▴ 10
2
votes
5
replies
237
views
get BM error
ensembldb
updated 8 days ago by
James W. MacDonald
65k • written 8 days ago by
Fara
• 0
0
votes
5
replies
284
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb
AnnotationForge
updated 8 days ago by
James W. MacDonald
65k • written 10 days ago by
Gayatri
• 0
0
votes
0
replies
72
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
8 days ago
Dario Strbenac
★ 1.5k
1
vote
3
replies
200
views
Different Shrunk Log2FC according with reference
DESeq2
updated 8 days ago by
Michael Love
41k • written 8 days ago by
andrebolerbarros
▴ 20
1
vote
3
replies
845
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler
RNASeq
updated 8 days ago by
Guangchuang Yu
★ 1.2k • written 14 months ago by
ruiqi.li
▴ 10
1
vote
4
replies
193
views
minfi::read.metharray.exp
minfiData
minfi
updated 8 days ago by
Basti
▴ 780 • written 10 days ago by
clacarion
• 0
3
votes
1
reply
294
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 8 days ago by
Michael Love
41k • written 8 days ago by
i.sudbery
▴ 40
1
vote
1
reply
160
views
Citation for edgeR user guide
edgeR
updated 8 days ago by
Gordon Smyth
50k • written 8 days ago by
k___
▴ 30
0
votes
7
replies
682
views
News:
List of Deprecated Packages for Bioc3.19
Release
Devel
ExperimentData
Software
8 weeks ago • updated 8 days ago
shepherl
3.8k
1
vote
1
reply
102
views
Cannabis OrgDb
KEGGgraph
org.Cs.eg.db
clusterProfiler
KEGG
AnnotationHubSoftware
updated 9 days ago by
James W. MacDonald
65k • written 9 days ago by
fernanda.backsouza
▴ 10
0
votes
0
replies
64
views
News:
Interested in the analysis of Spatial Omics data?
tidySpatialExperiment
SpatialExperiment
MoleculeExperiment
9 days ago
info
▴ 10
3
votes
3
replies
212
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 9 days ago by
Michael Love
41k • written 10 days ago by
WardDeb
• 0
0
votes
7
replies
288
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
15 days ago • updated 9 days ago
hortense96
• 0
5
votes
8
replies
8.8k
views
Limma design with continuous and categorical covariates
limma
batch effect
covariates
microarray
updated 9 days ago by
hortense96
• 0 • written 7.7 years ago by
dmcleanuk
▴ 30
1
vote
2
replies
980
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 9 days ago by
Tim Peters
▴ 170 • written 14 months ago by
jose.ramirez1
▴ 10
1
vote
4
replies
212
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
updated 10 days ago by
James W. MacDonald
65k • written 13 days ago by
Mirella Aurora
• 0
4
votes
6
replies
399
views
FilterByExpr low counts with small sample size
edgeR
15 days ago • updated 10 days ago
Jonathan
▴ 10
0
votes
1
reply
118
views
FDR via q-value
qvalue
updated 10 days ago by
James W. MacDonald
65k • written 12 days ago by
John
• 0
6
votes
12
replies
4.8k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache
AnnotationHub
ExperimentHub
6 months ago • updated 10 days ago
shepherl
3.8k
3
votes
2
replies
201
views
Cannabis and KEGGgraph
KEGGREST
GenomicDistributionsData
KEGGgraph
KEGG
updated 10 days ago by
Guido Hooiveld
★ 3.9k • written 12 days ago by
fernanda.backsouza
▴ 10
0
votes
2
replies
192
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
13 days ago • updated 10 days ago
catv
• 0
0
votes
3
replies
1.2k
views
News:
European Bioconductor Conference 2023 planning
Europe
Conference
EuroBioC
Events
News
updated 10 days ago by
lauryfriese932
• 0 • written 18 months ago by
Maria Doyle
▴ 70
0
votes
0
replies
75
views
Unlocking Potential: NURS FPX Strategies and Insights
levi
NURSFPX
ragene20sttranscriptcluster.db
ssrch
11 days ago
vaxahey107
• 0
3
votes
3
replies
316
views
permutation test in edgeR
rna-seq
edgeR
updated 11 days ago by
Gordon Smyth
50k • written 24 days ago by
Netanel
• 0
0
votes
18
replies
2.5k
views
problem installing ENmix package
ENmix
Bioconductor
rtracklayer
written 3.2 years ago by
lea
• 0
0
votes
0
replies
89
views
I am trying to detect alternative splicing.
ASpli
12 days ago
Sebashish
• 0
3
votes
1
reply
1.5k
views
Job:
Post Doctoral position in AI (Deep learning / Machine learning) approaches for Cancer Research, MRC Cancer Unit, University of Cambridge, UK
job
Job
machine learning
deep learning
computational biology
written 6.3 years ago by
Shamith.Samarajiwa
▴ 180
0
votes
2
replies
781
views
Job:
Bioinformatics Laboratory Head in AI or machine learning (WEHI, Australia)
bioconductor
artificialintelligence
JobPosting
machinelearning
written 8 months ago by
Gordon Smyth
50k
0
votes
4
replies
228
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
15 days ago • updated 12 days ago
lonn
• 0
1
vote
2
replies
237
views
How to retrieve detailed regression results from deseq2
DESeq2
21 days ago • updated 12 days ago
Weiqian
▴ 10
1
vote
0
replies
257
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
bioconductor
Install
13 days ago • updated 12 days ago
BioinfGuru
▴ 30
0
votes
7
replies
402
views
DESeq filtering specific to contrasts
DESeq2
updated 13 days ago by
Michael Love
41k • written 10 weeks ago by
Emma
• 0
0
votes
2
replies
251
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
4 weeks ago • updated 13 days ago
isaac.vock
• 0
0
votes
3
replies
133
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 13 days ago by
James W. MacDonald
65k • written 13 days ago by
bas_work
▴ 30
2
votes
5
replies
733
views
DESeq2 setting significant p-value
DESeq2
updated 13 days ago by
Michael Love
41k • written 5.0 years ago by
Merlin
▴ 10
2
votes
2
replies
177
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 13 days ago by
James W. MacDonald
65k • written 13 days ago by
sansan
• 0
6
votes
10
replies
1.6k
views
Which input file is used for DGEList in EgdeR?
salmon
edgeR
tximport
nf-core
gene_counts
updated 13 days ago by
i.atanasoai
• 0 • written 14 months ago by
mohammedtoufiq91
▴ 10
0
votes
4
replies
260
views
DEG with low counts
DESeq2
updated 13 days ago by
Michael Love
41k • written 17 days ago by
Rajat
• 0
6
votes
5
replies
418
views
Estimating Cell Counts for EPIC V2 array data
FlowSorted.Blood.EPIC
minifi
written 8 weeks ago by
Kim
• 0
0
votes
3
replies
176
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 13 days ago by
Gordon Smyth
50k • written 14 days ago by
prity6459
• 0
0
votes
2
replies
121
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
13 days ago
prity6459
• 0
3
votes
1
reply
159
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 13 days ago by
Gordon Smyth
50k • written 14 days ago by
Shaimaa Gamal
• 0
0
votes
2
replies
915
views
Problem for loading Bioconductor package in R
Bioconductor
written 4.2 years ago by
araaaju
• 0
4
votes
8
replies
382
views
Memory errors using read.bismark?
dmrseq
bsseq
updated 13 days ago by
Peter Hickey
▴ 740 • written 21 days ago by
Juan Higareda
• 0
11
votes
5
replies
7.4k
views
Theoretical WGCNA Question
WGCNA
Theory
Scale-Free Topology
updated 13 days ago by
Garrett
• 0 • written 9.1 years ago by
brohawndg
▴ 150
0
votes
4
replies
182
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
13 days ago
sropri
• 0
1
vote
2
replies
206
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
14 days ago • updated 13 days ago
Le
• 0
1,000 results • Page
2 of 20
Recent ...
Replies
Answer: DESeq2 v1.35.0
by
Michael Love
41k
That is not a release (odd 'y' digit). See Bioconductor help pages: https://contributions.bioconductor.org/description.html#description-ver…
Comment: Although I successfully installed the package "simpleaffy'' , I cannot library i
by
James W. MacDonald
65k
Please don't piggyback on posts from 2.3 years ago. If you have a question, post as a new question.
Answer: DESeq2 v1.35.0
by
James W. MacDonald
65k
Odd release versions indicate a devel version, which upon release is incremented to the next even version, so you won't be able to find tha…
Comment: Although I successfully installed the package "simpleaffy'' , I cannot library i
by
fatinataly
• 0
I tried also with oligo does not work, any other suggestion?
Comment: More regions in union when increasing DBA$config$mergeOverlap
by
Ian D.
▴ 70
Hello. Thanks for the reply. Sorry about this. My testing is telling me that 1 is the default (a gap), not -1 (1bp overlap). Negative …
Votes
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
SPIA plotP giving error
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