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votes
2
replies
44
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DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
12 hours ago • updated 31 minutes ago
Aaliya
• 0
1
vote
1
reply
48
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 1 hour ago by
Michael Love
41k • written 9 hours ago by
i.sudbery
▴ 40
1
vote
1
reply
37
views
Citation for edgeR user guide
edgeR
updated 5 hours ago by
Gordon Smyth
50k • written 8 hours ago by
k___
▴ 30
0
votes
1
reply
34
views
How to retrieve gene ontology GO class?
GO.db
goTools
6 hours ago • updated 5 hours ago
bandconductor
• 0
1
vote
3
replies
103
views
minfi::read.metharray.exp
minfiData
minfi
1 day ago • updated 8 hours ago
clacarion
• 0
0
votes
7
replies
603
views
News:
List of Deprecated Packages for Bioc3.19
Release
Devel
ExperimentData
Software
7 weeks ago • updated 10 hours ago
shepherl
3.8k
1
vote
11
replies
173
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
2 days ago • updated 10 hours ago
fernanda.backsouza
▴ 10
1
vote
1
reply
37
views
Cannabis OrgDb
KEGGgraph
org.Cs.eg.db
clusterProfiler
KEGG
AnnotationHubSoftware
updated 11 hours ago by
James W. MacDonald
65k • written 12 hours ago by
fernanda.backsouza
▴ 10
0
votes
0
replies
19
views
News:
Interested in the analysis of Spatial Omics data?
tidySpatialExperiment
SpatialExperiment
MoleculeExperiment
12 hours ago
info
▴ 10
6
votes
16
replies
2.2k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 13 hours ago by
Michael Love
41k • written 4.6 years ago by
hsbio
▴ 10
3
votes
3
replies
134
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 14 hours ago by
Michael Love
41k • written 1 day ago by
WardDeb
• 0
0
votes
3
replies
142
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb
AnnotationForge
updated 14 hours ago by
James W. MacDonald
65k • written 2 days ago by
Gayatri
• 0
0
votes
7
replies
233
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
6 days ago • updated 18 hours ago
hortense96
• 0
5
votes
8
replies
8.7k
views
Limma design with continuous and categorical covariates
limma
batch effect
covariates
microarray
updated 19 hours ago by
hortense96
• 0 • written 7.7 years ago by
dmcleanuk
▴ 30
0
votes
0
replies
26
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
23 hours ago
shuwangxinze1996
• 0
1
vote
2
replies
912
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 1 day ago by
Tim Peters
▴ 170 • written 13 months ago by
jose.ramirez1
▴ 10
0
votes
1
reply
75
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
1
vote
4
replies
126
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
3
votes
6
replies
309
views
FilterByExpr low counts with small sample size
edgeR
6 days ago • updated 1 day ago
Jonathan
▴ 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
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
3
votes
2
replies
140
views
Cannabis and KEGGgraph
KEGGREST
GenomicDistributionsData
KEGGgraph
KEGG
updated 1 day ago by
Guido Hooiveld
★ 3.9k • written 4 days ago by
fernanda.backsouza
▴ 10
0
votes
2
replies
140
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
4 days ago • updated 1 day ago
catv
• 0
0
votes
0
replies
37
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 2 days ago by
lauryfriese932
• 0 • written 18 months ago by
Maria Doyle
▴ 70
12
votes
12
replies
741
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
34
views
Unlocking Potential: NURS FPX Strategies and Insights
levi
NURSFPX
ragene20sttranscriptcluster.db
ssrch
2 days ago
vaxahey107
• 0
3
votes
3
replies
280
views
permutation test in edgeR
rna-seq
edgeR
updated 2 days ago by
Gordon Smyth
50k • written 15 days ago by
Netanel
• 0
0
votes
18
replies
2.4k
views
problem installing ENmix package
ENmix
Bioconductor
rtracklayer
written 3.1 years ago by
lea
• 0
15
votes
22
replies
1.8k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
25 days ago • updated 3 days ago
Chris
• 0
0
votes
0
replies
57
views
I am trying to detect alternative splicing.
ASpli
3 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
763
views
Job:
Bioinformatics Laboratory Head in AI or machine learning (WEHI, Australia)
bioconductor
artificialintelligence
JobPosting
machinelearning
written 7 months ago by
Gordon Smyth
50k
0
votes
4
replies
185
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
1
vote
2
replies
215
views
How to retrieve detailed regression results from deseq2
DESeq2
13 days ago • updated 4 days ago
Weiqian
▴ 10
1
vote
0
replies
184
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
bioconductor
Install
4 days ago
BioinfGuru
▴ 30
0
votes
7
replies
383
views
DESeq filtering specific to contrasts
DESeq2
updated 4 days ago by
Michael Love
41k • written 9 weeks ago by
Emma
• 0
0
votes
2
replies
233
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
23 days ago • updated 4 days ago
isaac.vock
• 0
0
votes
3
replies
93
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
5
replies
692
views
DESeq2 setting significant p-value
DESeq2
updated 4 days ago by
Michael Love
41k • written 5.0 years ago by
Merlin
▴ 10
2
votes
2
replies
130
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
6
votes
10
replies
1.5k
views
Which input file is used for DGEList in EgdeR?
salmon
edgeR
tximport
nf-core
gene_counts
updated 4 days ago by
i.atanasoai
• 0 • written 14 months ago by
mohammedtoufiq91
▴ 10
0
votes
4
replies
227
views
DEG with low counts
DESeq2
updated 4 days ago by
Michael Love
41k • written 9 days ago by
Rajat
• 0
6
votes
5
replies
392
views
Estimating Cell Counts for EPIC V2 array data
FlowSorted.Blood.EPIC
minifi
written 7 weeks ago by
Kim
• 0
0
votes
3
replies
121
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 4 days ago by
Gordon Smyth
50k • written 5 days ago by
prity6459
• 0
0
votes
2
replies
84
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
4 days ago
prity6459
• 0
0
votes
1
reply
105
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
2
replies
894
views
Problem for loading Bioconductor package in R
Bioconductor
written 4.2 years ago by
araaaju
• 0
4
votes
8
replies
332
views
Memory errors using read.bismark?
dmrseq
bsseq
updated 5 days ago by
Peter Hickey
▴ 740 • written 12 days ago by
Juan Higareda
• 0
11
votes
5
replies
7.3k
views
Theoretical WGCNA Question
WGCNA
Theory
Scale-Free Topology
updated 5 days ago by
Garrett
• 0 • written 9.1 years ago by
brohawndg
▴ 150
1,000 results • Page
1 of 20
Recent ...
Replies
Comment: DESeq2 output used for PCA plot on R studio
by
Aaliya
• 0
How am i making the data? I am using the DESeq2 output data which I had generated
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
by
Michael Love
41k
Sounds reasonable. For ranking genes, you could choose those with low decay rate but removing thoses where it is indistinguishable from …
Answer: Citation for edgeR user guide
by
Gordon Smyth
50k
Thanks for thinking about how to cite edgeR. Citations are indeed the main way by which the edgeR authors get credit for their work. The Us…
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
You are just making up data? What is the point of this exercise?
Comment: How to retrieve gene ontology GO class?
by
James W. MacDonald
65k
What do you mean by 'the information'? Do you have things in particular that you want?
Votes
Answer: Citation for edgeR user guide
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
Answer: How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
Answer: minfi::read.metharray.exp
Comment: Trying to use enrichGO
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