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15
votes
22
replies
1.8k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
27 days ago • updated 5 days ago
Chris
• 0
12
votes
12
replies
781
views
Why p value inconsistent when using different number of pathway score?
limma
updated 4 days ago by
Robert Castelo
★ 3.3k • written 5 days ago by
Chris
• 0
11
votes
5
replies
7.3k
views
Theoretical WGCNA Question
WGCNA
Theory
Scale-Free Topology
updated 7 days ago by
Garrett
• 0 • written 9.1 years ago by
brohawndg
▴ 150
9
votes
12
replies
7.8k
views
Multi factor design edgeR/Deseq2
deseq2
edgeR
rna-seq
updated 7 days ago by
Elizabeth
• 0 • written 8.8 years ago by
gthm
▴ 30
8
votes
23
replies
853
views
Convert Seurat Object to Summarised Experiment or ExpressionSet
SummarizedExperiment
ExpressionSet
updated 14 days ago by
Robert Castelo
★ 3.3k • written 15 days ago by
Bine
▴ 40
7
votes
36
replies
5.5k
views
Ensembl plants at annotationHub?
ensembl
ensembldb
plant
arabidopsis thaliana
annotationhub
updated 21 days ago by
Shiva
• 0 • written 5.4 years ago by
Guido Hooiveld
★ 3.9k
6
votes
16
replies
2.3k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 2 days ago by
Michael Love
41k • written 4.6 years ago by
hsbio
▴ 10
6
votes
5
replies
398
views
Estimating Cell Counts for EPIC V2 array data
FlowSorted.Blood.EPIC
minifi
written 8 weeks ago by
Kim
• 0
6
votes
10
replies
2.2k
views
overlapsAny for elements in GRangesList
granges
grangeslist
overlapsAny
updated 12 days ago by
Samuel Ahuno
• 0 • written 8.0 years ago by
maltethodberg
▴ 170
6
votes
12
replies
4.7k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache
AnnotationHub
ExperimentHub
6 months ago • updated 3 days ago
shepherl
3.8k
6
votes
10
replies
1.6k
views
Which input file is used for DGEList in EgdeR?
salmon
edgeR
tximport
nf-core
gene_counts
updated 6 days ago by
i.atanasoai
• 0 • written 14 months ago by
mohammedtoufiq91
▴ 10
5
votes
7
replies
430
views
DEG Filtering
MicroarrayData
limma
Genefiltering
updated 29 days ago by
Gordon Smyth
50k • written 5 weeks ago by
Amit
• 0
5
votes
9
replies
860
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
15 days ago • updated 7 days ago
Chris
• 0
5
votes
25
replies
825
views
limma models out of memory issue on Slurm HPC
Regression
limma
STATISITICS
HPC
updated 21 days ago by
Gordon Smyth
50k • written 4 weeks ago by
Jitendra
▴ 10
5
votes
3
replies
688
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR
DifferentialExpression
updated 29 days ago by
Gordon Smyth
50k • written 5 weeks ago by
Jack S.
▴ 50
5
votes
6
replies
399
views
Not fully paired differential gene expression analysis
edgeR
DifferentialExpression
updated 13 days ago by
ATpoint
★ 4.0k • written 16 days ago by
nhaus
▴ 30
5
votes
9
replies
1.2k
views
Batch correction and repeated measures
RUVSeq
sva
limma
updated 8 days ago by
Gordon Smyth
50k • written 7 months ago by
Jonathan
▴ 10
5
votes
8
replies
8.8k
views
Limma design with continuous and categorical covariates
limma
batch effect
covariates
microarray
updated 3 days ago by
hortense96
• 0 • written 7.7 years ago by
dmcleanuk
▴ 30
4
votes
8
replies
348
views
Memory errors using read.bismark?
dmrseq
bsseq
updated 7 days ago by
Peter Hickey
▴ 740 • written 14 days ago by
Juan Higareda
• 0
4
votes
6
replies
334
views
FilterByExpr low counts with small sample size
edgeR
8 days ago • updated 3 days ago
Jonathan
▴ 10
3
votes
3
replies
13k
views
How to fix 'long vectors not supported yet' error in R
r
updated 22 days ago by
Amruta
• 0 • written 5.2 years ago by
r.tor
• 0
3
votes
1
reply
120
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 7 days ago by
Gordon Smyth
50k • written 8 days ago by
Shaimaa Gamal
• 0
3
votes
3
replies
290
views
permutation test in edgeR
rna-seq
edgeR
updated 5 days ago by
Gordon Smyth
50k • written 18 days ago by
Netanel
• 0
3
votes
3
replies
171
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 2 days ago by
Michael Love
41k • written 3 days ago by
WardDeb
• 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
3
votes
3
replies
173
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
13 days ago • updated 8 days ago
jacques.imbert
• 0
3
votes
1
reply
214
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 2 days ago by
Michael Love
41k • written 2 days ago by
i.sudbery
▴ 40
3
votes
18
replies
2.9k
views
News:
List of Deprecated Packages for Bioc3.18
Deprecation
devel
Bioconductor
Devel
10 months ago • updated 8 days ago
shepherl
3.8k
3
votes
5
replies
340
views
Differing results from plotMDS and PCAtools
edgeR
PCAtools
updated 26 days ago by
Gordon Smyth
50k • written 28 days ago by
Fabian
• 0
3
votes
6
replies
236
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq
sva
14 days ago
nhaus
▴ 30
3
votes
2
replies
164
views
Cannabis and KEGGgraph
KEGGREST
GenomicDistributionsData
KEGGgraph
KEGG
updated 3 days ago by
Guido Hooiveld
★ 3.9k • written 6 days ago by
fernanda.backsouza
▴ 10
3
votes
1
reply
745
views
News:
[Pre-print] Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex
biorxiv
spatialLIBD
News
written 4.2 years ago by
Leonardo Collado Torres
★ 1.0k
2
votes
8
replies
497
views
Microarray Limma Model fitting and DEG
limma
DGEanalysis
updated 29 days ago by
Gordon Smyth
50k • written 4 weeks ago by
Amit
• 0
2
votes
2
replies
1.6k
views
Running featureCounts() in 'IntersectionStrict' mode
rsubread
featurecounts
summarizeoverlaps
updated 25 days ago by
isaac.vock
• 0 • written 7.9 years ago by
Jon Manning
▴ 90
2
votes
3
replies
295
views
ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with variable number of continuous columns
ComplexHeatmap
11 days ago • updated 10 days ago
daniel.carbajo
• 0
2
votes
2
replies
359
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
14 days ago • updated 13 days ago
Henry
▴ 10
2
votes
5
replies
700
views
DESeq2 setting significant p-value
DESeq2
updated 6 days ago by
Michael Love
41k • written 5.0 years ago by
Merlin
▴ 10
2
votes
3
replies
329
views
PCA of different bacterial species
DESeq2
updated 29 days ago by
Michael Love
41k • written 4 weeks ago by
Laura
▴ 10
2
votes
2
replies
142
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 6 days ago by
James W. MacDonald
65k • written 7 days ago by
sansan
• 0
2
votes
9
replies
238
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 13 hours ago by
James W. MacDonald
65k • written 21 hours ago by
Alexandre
• 0
2
votes
2
replies
148
views
ComplexHeatmap: change the names of a HeatmapAnnotation object
ComplexHeatmap
13 days ago • updated 11 days ago
daniel.carbajo
• 0
2
votes
2
replies
149
views
[DiffBind] Obtaining normalization factors
DiffBind
13 days ago • updated 10 days ago
Henry
▴ 10
2
votes
2
replies
170
views
Bluster and Varieties of Louvain Clulstering
bluster
updated 20 days ago by
ATpoint
★ 4.0k • written 21 days ago by
Dario Strbenac
★ 1.5k
2
votes
6
replies
352
views
How to make boxplot with pairwise and overall p value from Limma
t.test
boxplot
limma
anova
17 days ago
Chris
• 0
2
votes
6
replies
1.3k
views
How to get DMR for Infinium methylation EPIC v2
ChAMP
DMRcate
minfi
updated 23 days ago by
Tim Peters
▴ 170 • written 5 months ago by
rae.alshammari
▴ 10
2
votes
5
replies
1.1k
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 8 days ago by
Ashley
• 0 • written 10 months ago by
zxc741xb
• 0
2
votes
5
replies
1.0k
views
STRINGdb R package reference class instantiation with v12.0
STRINGdb
updated 21 days ago by
damian.szk
▴ 80 • written 5 months ago by
Abhishek
• 0
2
votes
5
replies
144
views
How to retrieve gene ontology GO class from gene list?
GO.db
goTools
updated 17 hours ago by
James W. MacDonald
65k • written 2 days ago by
bandconductor
• 0
2
votes
5
replies
147
views
get BM error
ensembldb
updated 1 day ago by
James W. MacDonald
65k • written 2 days ago by
Fara
• 0
2
votes
2
replies
169
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways
clusterProfiler
gseKEGG
KEGG
13 days ago
julia_mcdonough
• 0
202 results • Page
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Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
ATpoint
★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Answer: Improving the design matrices vignette in RNAseq123
by
Gordon Smyth
50k
Thanks to Shian Su, we have confirmed that the problem in the design matrices vignette html is caused by a bug in knitr 1.44 (to do with sp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
winwater0928
• 0
Thank you for your comment! I'll review my code from top to bottom.
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
James W. MacDonald
65k
So basically you are using HTML markup to set your subscripts and whatnot, and then `element_markdown` does the rest.
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
James W. MacDonald
65k
Oh snap. Foiled again. Here it is with spaces & ge ; and & lt ;
Votes
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Answer: Cross-species analysis - how to compute the mid parent value?
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
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