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News:
Interested in the analysis of Spatial Omics data?
tidySpatialExperiment
SpatialExperiment
MoleculeExperiment
26 days ago
info
▴ 10
3
votes
3
replies
253
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 26 days ago by
Michael Love
42k • written 27 days ago by
WardDeb
• 0
0
votes
7
replies
365
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
4 weeks ago • updated 26 days ago
hortense96
• 0
5
votes
8
replies
8.9k
views
Limma design with continuous and categorical covariates
limma
batch effect
covariates
microarray
updated 26 days ago by
hortense96
• 0 • written 7.8 years ago by
dmcleanuk
▴ 30
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 26 days ago by
Tim Peters
▴ 180 • written 14 months ago by
jose.ramirez1
▴ 10
2
votes
4
replies
286
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
updated 27 days ago by
James W. MacDonald
65k • written 4 weeks ago by
Mirella Aurora
• 0
4
votes
6
replies
474
views
FilterByExpr low counts with small sample size
edgeR
4 weeks ago • updated 27 days ago
Jonathan
▴ 10
0
votes
1
reply
137
views
FDR via q-value
qvalue
updated 27 days ago by
James W. MacDonald
65k • written 4 weeks ago by
John
• 0
6
votes
12
replies
5.1k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache
AnnotationHub
ExperimentHub
6 months ago • updated 27 days ago
shepherl
3.9k
3
votes
2
replies
234
views
Cannabis and KEGGgraph
KEGGREST
GenomicDistributionsData
KEGGgraph
KEGG
updated 27 days ago by
Guido Hooiveld
★ 4.0k • written 29 days ago by
fernanda.backsouza
▴ 10
0
votes
2
replies
241
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
4 weeks ago • updated 27 days ago
catv
• 0
0
votes
0
replies
95
views
Unlocking Potential: NURS FPX Strategies and Insights
levi
NURSFPX
ragene20sttranscriptcluster.db
ssrch
28 days ago
vaxahey107
• 0
3
votes
3
replies
368
views
permutation test in edgeR
rna-seq
edgeR
updated 28 days ago by
Gordon Smyth
50k • written 5 weeks ago by
Netanel
• 0
0
votes
18
replies
2.6k
views
problem installing ENmix package
ENmix
Bioconductor
rtracklayer
written 3.2 years ago by
lea
• 0
0
votes
0
replies
106
views
I am trying to detect alternative splicing.
ASpli
29 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 6.4 years ago by
Shamith.Samarajiwa
▴ 180
0
votes
2
replies
819
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
269
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
4 weeks ago • updated 29 days ago
lonn
• 0
1
vote
2
replies
265
views
How to retrieve detailed regression results from deseq2
DESeq2
5 weeks ago • updated 4 weeks ago
Weiqian
▴ 10
1
vote
0
replies
354
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
bioconductor
Install
4 weeks ago
BioinfGuru
▴ 30
0
votes
7
replies
452
views
DESeq filtering specific to contrasts
DESeq2
updated 4 weeks ago by
Michael Love
42k • written 3 months ago by
Emma
• 0
0
votes
2
replies
285
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
7 weeks ago • updated 4 weeks ago
isaac.vock
• 0
0
votes
3
replies
178
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 4 weeks ago by
James W. MacDonald
65k • written 4 weeks ago by
bas_work
▴ 30
2
votes
5
replies
794
views
DESeq2 setting significant p-value
DESeq2
updated 4 weeks ago by
Michael Love
42k • written 5.0 years ago by
Merlin
▴ 10
2
votes
2
replies
221
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 4 weeks ago by
James W. MacDonald
65k • written 4 weeks ago by
sansan
• 0
6
votes
10
replies
1.7k
views
Which input file is used for DGEList in EgdeR?
salmon
edgeR
tximport
nf-core
gene_counts
updated 4 weeks ago by
i.atanasoai
• 0 • written 15 months ago by
mohammedtoufiq91
▴ 10
0
votes
4
replies
292
views
DEG with low counts
DESeq2
updated 4 weeks ago by
Michael Love
42k • written 5 weeks ago by
Rajat
• 0
6
votes
5
replies
478
views
Estimating Cell Counts for EPIC V2 array data
FlowSorted.Blood.EPIC
minifi
written 11 weeks ago by
Kim
• 0
0
votes
3
replies
217
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 4 weeks ago by
Gordon Smyth
50k • written 4 weeks ago by
prity6459
• 0
0
votes
2
replies
150
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
4 weeks ago
prity6459
• 0
0
votes
2
replies
930
views
Problem for loading Bioconductor package in R
Bioconductor
written 4.3 years ago by
araaaju
• 0
11
votes
5
replies
7.4k
views
Theoretical WGCNA Question
WGCNA
Theory
Scale-Free Topology
updated 4 weeks ago by
Garrett
• 0 • written 9.2 years ago by
brohawndg
▴ 150
0
votes
4
replies
224
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
4 weeks ago
sropri
• 0
1
vote
2
replies
241
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
4 weeks ago
Le
• 0
0
votes
3
replies
287
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 4 weeks ago by
W. Evan Johnson
▴ 850 • written 5 weeks ago by
schlumbohm
• 0
0
votes
0
replies
134
views
Warning while loading DEP package
DEP
updated 4 weeks ago by
shepherl
3.9k • written 4 weeks ago by
Namrata
• 0
0
votes
1
reply
167
views
Adding columns to DEXSeqResults object
DEXSeq
updated 4 weeks ago by
Alejandro Reyes
★ 1.9k • written 4 weeks ago by
Clyde
• 0
0
votes
1
reply
158
views
rlog transformation
DESeq2
updated 4 weeks ago by
Michael Love
42k • written 4 weeks ago by
ishij9717
• 0
0
votes
1
reply
128
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 4 weeks ago by
Michael Love
42k • written 4 weeks ago by
09191919
• 0
0
votes
1
reply
149
views
covariate with negative and positive values
DESeq2
updated 4 weeks ago by
Michael Love
42k • written 4 weeks ago by
Brynn
• 0
1
vote
2
replies
180
views
Error in champ.load(): The following specified files do not exist
ChAMP
4 weeks ago
Sherin
• 0
9
votes
12
replies
7.9k
views
Multi factor design edgeR/Deseq2
deseq2
edgeR
rna-seq
updated 4 weeks ago by
Elizabeth
• 0 • written 8.9 years ago by
gthm
▴ 30
5
votes
9
replies
976
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
5 weeks ago • updated 4 weeks ago
Chris
▴ 10
0
votes
1
reply
112
views
Input Question for deseq.r
RSeqAn
updated 4 weeks ago by
ATpoint
★ 4.1k • written 4 weeks ago by
Nina
• 0
0
votes
1
reply
168
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 4 weeks ago by
ATpoint
★ 4.1k • written 4 weeks ago by
quanah.hudson
• 0
3
votes
3
replies
246
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
5 weeks ago • updated 4 weeks ago
jacques.imbert
• 0
5
votes
9
replies
1.3k
views
Batch correction and repeated measures
RUVSeq
sva
limma
updated 4 weeks ago by
Gordon Smyth
50k • written 7 months ago by
Jonathan
▴ 10
3
votes
18
replies
3.0k
views
News:
List of Deprecated Packages for Bioc3.18
Deprecation
devel
Bioconductor
Devel
10 months ago • updated 4 weeks ago
shepherl
3.9k
0
votes
2
replies
954
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell
RNASeq
RNASeqData
scRNAseq
updated 4 weeks ago by
wichaidi
• 0 • written 18 months ago by
irvin.ng
• 0
1
vote
7
replies
1.9k
views
Error using champ.import
ChAMP
EPICv2
updated 4 weeks ago by
shilpa
• 0 • written 10 months ago by
medha.suman
• 0
1,739 results • Page
4 of 35
Recent ...
Replies
Comment: all variables in design formula must be columns in colData (Deseq2) error
by
Galina
• 0
thank you!
Comment: all variables in design formula must be columns in colData (Deseq2) error
by
ATpoint
★ 4.1k
coldata_rat <- data.frame(conditions=..., batch=...)
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
by
robersy
• 0
Thank you all for your comments. I will follow your suggestions.
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
Ken C
• 0
Hi Michael, thanks a lot for your prompt reply! Not sure if this is appropriate or if you are the right person to ask -- is there anything…
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
Ken C
• 0
Well, if I look at genes with baseMean>50, then the relative absolute difference in log2FoldChange (say over the absolute log2FoldChange of…
Votes
biomaRt not working - lazy table error
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
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euge.eugenio
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Dario Strbenac
★ 1.5k
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to
Vincent J. Carey, Jr.
6.7k
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Koen Van den Berge
▴ 180
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shepherl
3.9k
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