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15
votes
23
replies
2.0k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
6 weeks ago • updated 16 days ago
Chris
▴ 10
2
votes
5
replies
172
views
Error while installing BiocManager::install("org.Vdahliae.eg.db")
org.vdahlaie.eg.db
Bioconductor
1 day ago • updated 2 hours ago
Patadù
▴ 10
3
votes
1
reply
1.5k
views
Limma without eBayes, is it indistunguishable from Ordinary Least Square?
Limma
ebayes
bayesian
ls
updated 9 days ago by
Gordon Smyth
50k • written 5.6 years ago by
CantExitVIM
▴ 10
0
votes
1
reply
101
views
Recovering my account credentials on Bioconductor
Bioconductor
updated 9 days ago by
shepherl
3.9k • written 10 days ago by
cyril.dalmasso
• 0
5
votes
3
replies
304
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 7 days ago by
Gordon Smyth
50k • written 29 days ago by
Shaimaa Gamal
• 0
0
votes
1
reply
154
views
Differential gene expression analysis results
DESeq2
DifferentialExpression
updated 7 days ago by
ATpoint
★ 4.1k • written 7 days ago by
sajadahmad41454
• 0
1
vote
4
replies
226
views
minfi::read.metharray.exp
minfiData
minfi
updated 23 days ago by
Basti
▴ 780 • written 24 days ago by
clacarion
• 0
3
votes
1
reply
144
views
How to save the DEXSeq results
DEXSeq
updated 10 days ago by
Michael Love
42k • written 10 days ago by
Sara
• 0
2
votes
9
replies
425
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 21 days ago by
James W. MacDonald
65k • written 21 days ago by
Alexandre
• 0
4
votes
9
replies
3.1k
views
Create protein sequences including variants from a VCF file
VariantAnnotation
customProDB
updated 1 day ago by
Yun
• 0 • written 5.2 years ago by
daniel.magnus.bader
▴ 50
0
votes
4
replies
360
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
updated 5 days ago by
Ziliang
• 0 • written 16 days ago by
Ian D.
▴ 70
1
vote
1
reply
152
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 20 days ago by
Leo Lahti
▴ 40 • written 20 days ago by
Dario Strbenac
★ 1.5k
3
votes
3
replies
244
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
4 weeks ago • updated 29 days ago
jacques.imbert
• 0
1
vote
2
replies
284
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation
SequenceAnnotation
MethylationArray
GenomicDistributionsData
16 days ago • updated 15 days ago
Yveto
• 0
1
vote
3
replies
234
views
Different Shrunk Log2FC according with reference
DESeq2
updated 22 days ago by
Michael Love
42k • written 23 days ago by
andrebolerbarros
▴ 20
4
votes
2
replies
618
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea
edgeR
14 days ago • updated 10 days ago
gene_bioconductor
▴ 10
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 24 days ago by
Tim Peters
▴ 180 • written 14 months ago by
jose.ramirez1
▴ 10
0
votes
2
replies
1.5k
views
How to use spike-in information (sequences from another species) with DESeq2::DESeq()
DESeq2
SpikeIn
Normalization
updated 7 days ago by
maria.soler
• 0 • written 15 months ago by
kalavattam
▴ 10
3
votes
1
reply
328
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 23 days ago by
Michael Love
42k • written 23 days ago by
i.sudbery
▴ 40
0
votes
1
reply
153
views
Gene-by-sample covariates in limma
Metabolomics
limma
updated 14 days ago by
Gordon Smyth
50k • written 14 days ago by
c53aba27
• 0
0
votes
2
replies
165
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
17 days ago • updated 14 days ago
Aurora
• 0
0
votes
2
replies
949
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell
RNASeq
RNASeqData
scRNAseq
updated 29 days ago by
wichaidi
• 0 • written 18 months ago by
irvin.ng
• 0
2
votes
5
replies
1.2k
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 29 days ago by
Ashley
• 0 • written 11 months ago by
zxc741xb
• 0
1
vote
3
replies
218
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression
TimeCourse
timeOmics
edgeR
RNAseq
updated 2 days ago by
Gordon Smyth
50k • written 3 days ago by
Ashley
• 0
0
votes
3
replies
220
views
Couldn't connect to server while using "pathways"
graphite
updated 10 days ago by
Michael Love
42k • written 11 days ago by
fduguchunhui
• 0
0
votes
1
reply
120
views
Version 3.15 S4Vectors packages are missing
S4Vectors
updated 16 days ago by
shepherl
3.9k • written 17 days ago by
bounlu
• 0
2
votes
1
reply
159
views
minfi latest update for EPIC V2 chip
minfi
minfiDataEPIC
updated 9 days ago by
James W. MacDonald
65k • written 10 days ago by
e1271094
• 0
1
vote
4
replies
522
views
DEseq2 coefficient
DESeq2
coefficient
11 weeks ago • updated 15 days ago
JKim
• 0
1
vote
5
replies
1.5k
views
Cannot connect to ExperimentHub server
ExperimentHub
updated 9 days ago by
Jiayu
• 0 • written 5 months ago by
yanling
• 0
2
votes
3
replies
104
views
How to correctly adjust for gender in edgeR
design
glm
edgeR
updated 1 day ago by
Gordon Smyth
50k • written 1 day ago by
Guillermo
• 0
0
votes
1
reply
154
views
rlog transformation
DESeq2
updated 28 days ago by
Michael Love
42k • written 29 days ago by
ishij9717
• 0
0
votes
2
replies
82
views
DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set
DECIPHER
19 hours ago • updated 16 hours ago
makala
• 0
0
votes
3
replies
3.7k
views
[Mfuzz] Error in cmeans(exprs(eset)
Mfuzz
Mfuzz
updated 10 days ago by
Caio
• 0 • written 13.1 years ago by
boczniak767
▴ 720
2
votes
1
reply
141
views
Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 10 days ago by
Michael Love
42k • written 10 days ago by
mat149
▴ 70
0
votes
1
reply
136
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 16 days ago by
Michael Love
42k • written 17 days ago by
Agung
• 0
2
votes
1
reply
57
views
How to design DEXSeq formula for multiple variables
DEXSeq
updated 1 day ago by
Alejandro Reyes
★ 1.9k • written 3 days ago by
Sara
• 0
2
votes
2
replies
270
views
Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(paste("networks", net.suid, "tables", tbl, sep = "/"), : object 're…
RCy3
5 days ago • updated 18 hours ago
Matthew Thornton
▴ 360
4
votes
9
replies
215
views
Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2
timecoursedata
GeneExpression
updated 23 hours ago by
ATpoint
★ 4.1k • written 2 days ago by
pangtaihin
• 0
0
votes
2
replies
146
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
28 days ago
prity6459
• 0
5
votes
9
replies
1.3k
views
Batch correction and repeated measures
RUVSeq
sva
limma
updated 29 days ago by
Gordon Smyth
50k • written 7 months ago by
Jonathan
▴ 10
1
vote
1
reply
184
views
Handling multiple differential expression comparisons
DESeq2
updated 12 days ago by
Michael Love
42k • written 13 days ago by
Zainab
▴ 10
0
votes
1
reply
108
views
Gene set enrichment analysis
clusterProfiler
GeneSetEnrichment
updated 4 days ago by
Guido Hooiveld
★ 4.0k • written 4 days ago by
aogunbaw
• 0
2
votes
5
replies
258
views
How to retrieve gene ontology GO class from gene list?
GO.db
goTools
updated 21 days ago by
James W. MacDonald
65k • written 23 days ago by
bandconductor
• 0
0
votes
4
replies
262
views
Minfi - estimatecellscount
min
minfi
updated 17 days ago by
James W. MacDonald
65k • written 6 weeks ago by
clacarion
• 0
0
votes
2
replies
206
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
15 days ago • updated 14 days ago
kcarey
• 0
0
votes
1
reply
168
views
ATACseq merge peaks
DiffBind
updated 20 days ago by
ATpoint
★ 4.1k • written 22 days ago by
Shloka
• 0
0
votes
2
replies
816
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
1
reply
96
views
normalization using Deseq2
DESeq2
rnaseqGene
Normalization
updated 8 days ago by
ATpoint
★ 4.1k • written 8 days ago by
sajadahmad41454
• 0
0
votes
8
replies
465
views
Can I trust the differential expression analysis when the two groups overlap on the PCA?
DESeq2
pcaExplorer
updated 2 days ago by
BioinfGuru
▴ 30 • written 3 days ago by
Eric Katagirya
• 0
0
votes
7
replies
444
views
DESeq filtering specific to contrasts
DESeq2
updated 27 days ago by
Michael Love
42k • written 3 months ago by
Emma
• 0
193 results • Page
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Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db")
by
Patadù
▴ 10
Hi @marcelramos Thanks for the clarification. Yes, I have installed `org.Vdahlaie.eg.db` using the code you and Guido suggested and now i…
Comment: European Bioconductor Conference 2023 planning
by
angelaesper43
• 0
@Maria Doyle[sexdolltech][1]Hosting EuroBioC provides an excellent opportunity to showcase Bioconductor and computational biology research …
Comment: Ensembl plants at annotationHub?
by
Johannes Rainer
★ 2.0k
Dear Daniele, for which Ensembl release would you need the data? the most recent is 112, but if you used a different version before it wou…
Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Dear Johannes, Would it be possible to create the EnsDb for Triticum aestivum (IWGSC)? Thank you very much, Daniele
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
by
BioinfGuru
▴ 30
Figured it out with ?eigencorplot, thanks Michael. I was trying to pass 10 PCs when I only had 8, and I was including metadata columns that…
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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★ 4.0k
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