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3
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6
replies
283
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq
sva
28 days ago
nhaus
▴ 30
0
votes
1
reply
178
views
DESeq2 gives an error and R crashes
DESeq2
28 days ago • updated 27 days ago
Shefali
• 0
0
votes
0
replies
140
views
LearnTaxa with custom Silva
DECIPHER
LearnTaxa
29 days ago
Eryn
• 0
0
votes
0
replies
87
views
queryDGIdb lexical error for some genes
lexicalerror
rDGIdb
DGIdb
json
29 days ago
Dennis
• 0
0
votes
1
reply
164
views
compareCluster dotplot: how to modify the genesets order
DOSE
enrichplot
clusterProfiler
updated 25 days ago by
Guido Hooiveld
★ 3.9k • written 29 days ago by
Lucie
• 0
8
votes
23
replies
972
views
Convert Seurat Object to Summarised Experiment or ExpressionSet
SummarizedExperiment
ExpressionSet
updated 28 days ago by
Robert Castelo
★ 3.3k • written 29 days ago by
Bine
▴ 40
0
votes
1
reply
143
views
Can you find the correct transcript in scRNA seq data
scRNAseq
RNAseq
updated 29 days ago by
ATpoint
★ 4.1k • written 4 weeks ago by
Merav
• 0
0
votes
2
replies
225
views
Interaction term vs grouping variable design considerations
DESeq2
DifferentialExpression
updated 29 days ago by
Michael Love
42k • written 4 weeks ago by
nhaus
▴ 30
0
votes
1
reply
172
views
IgG control in RIP-seq with Deseq2
DESeq2
RIP-seq
updated 29 days ago by
Michael Love
42k • written 4 weeks ago by
Adelaide
• 0
0
votes
2
replies
249
views
Regressing out batch effects
DESeq2
updated 29 days ago by
Michael Love
42k • written 5 weeks ago by
kys91240
• 0
5
votes
6
replies
435
views
Not fully paired differential gene expression analysis
edgeR
DifferentialExpression
updated 26 days ago by
ATpoint
★ 4.1k • written 4 weeks ago by
nhaus
▴ 30
1
vote
6
replies
500
views
GSVA on separate healthy and disease datasets
GSVA
updated 29 days ago by
James W. MacDonald
65k • written 4 weeks ago by
Lucy
▴ 60
0
votes
0
replies
115
views
ggtree tip label position (depth)
ggtree
4 weeks ago • updated 29 days ago
Roope
• 0
1
vote
2
replies
322
views
CombineArrays for EPIC and EPIC V2
EPICV1
Methylation
combineArrays
minifi
EPICv2manifest
5 weeks ago • updated 6 days ago
Kim
• 0
0
votes
6
replies
344
views
unable to access Annotationhub latest record
DNAMethylation
AnnotationHub
EPICv2manifest
annotation
updated 28 days ago by
Tim Peters
▴ 180 • written 5 weeks ago by
s.malik
• 0
0
votes
2
replies
260
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
5 weeks ago • updated 20 days ago
isaac.vock
• 0
15
votes
23
replies
2.0k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
5 weeks ago • updated 9 days ago
Chris
• 0
0
votes
4
replies
252
views
Minfi - estimatecellscount
min
minfi
updated 10 days ago by
James W. MacDonald
65k • written 5 weeks ago by
clacarion
• 0
6
votes
5
replies
452
views
Estimating Cell Counts for EPIC V2 array data
FlowSorted.Blood.EPIC
minifi
written 10 weeks ago by
Kim
• 0
1
vote
4
replies
489
views
DEseq2 coefficient
DESeq2
coefficient
10 weeks ago • updated 8 days ago
JKim
• 0
0
votes
7
replies
430
views
DESeq filtering specific to contrasts
DESeq2
updated 20 days ago by
Michael Love
42k • written 12 weeks ago by
Emma
• 0
1
vote
5
replies
1.5k
views
Cannot connect to ExperimentHub server
ExperimentHub
updated 1 day ago by
Jiayu
• 0 • written 5 months ago by
yanling
• 0
0
votes
2
replies
800
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
606
views
How to correct for known and surrogate variables in DESeq2?
DESeq2
BatchEffect
sva
limma
updated 23 days ago by
Michael Love
42k • written 6 months ago by
Crystal571
• 0
0
votes
1
reply
348
views
Gene names from Matrix
BioCor
StarBioTrek
MatrixGenerics
updated 29 days ago by
Lluís Revilla Sancho
▴ 730 • written 7 months ago by
karmasstark
• 0
5
votes
9
replies
1.3k
views
Batch correction and repeated measures
RUVSeq
sva
limma
updated 21 days ago by
Gordon Smyth
50k • written 7 months ago by
Jonathan
▴ 10
0
votes
4
replies
6.8k
views
SingleR Label.Ont
SingleR
updated 24 days ago by
lisia
• 0 • written 7 months ago by
saeed.khalili
• 0
0
votes
18
replies
2.5k
views
problem installing ENmix package
ENmix
Bioconductor
rtracklayer
written 3.2 years ago by
lea
• 0
1
vote
7
replies
1.8k
views
Error using champ.import
ChAMP
EPICv2
updated 22 days ago by
shilpa
• 0 • written 10 months ago by
medha.suman
• 0
2
votes
5
replies
1.2k
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 22 days ago by
Ashley
• 0 • written 11 months ago by
zxc741xb
• 0
1
vote
3
replies
872
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler
RNASeq
updated 15 days ago by
Guangchuang Yu
★ 1.2k • written 14 months ago by
ruiqi.li
▴ 10
0
votes
1
reply
1.3k
views
Tutorial:
Online workshop "Working with ChatGPT in R" 2023-03-09
chatgpt
programming
updated 26 days ago by
gptnederlands.nl
• 0 • written 14 months ago by
Wolfgang Huber
★ 13k
6
votes
10
replies
1.7k
views
Which input file is used for DGEList in EgdeR?
salmon
edgeR
tximport
nf-core
gene_counts
updated 20 days ago by
i.atanasoai
• 0 • written 15 months ago by
mohammedtoufiq91
▴ 10
0
votes
2
replies
928
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell
RNASeq
RNASeqData
scRNAseq
updated 22 days ago by
wichaidi
• 0 • written 17 months ago by
irvin.ng
• 0
5
votes
6
replies
2.8k
views
Although I successfully installed the package "simpleaffy'' , I cannot library it. Why?
simpleaffy
updated 7 days ago by
James W. MacDonald
65k • written 2.3 years ago by
yanchangjian2019
• 0
3
votes
1
reply
756
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
0
votes
2
replies
921
views
Problem for loading Bioconductor package in R
Bioconductor
written 4.2 years ago by
araaaju
• 0
6
votes
19
replies
2.5k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 9 days ago by
Sey R.
• 0 • written 4.6 years ago by
hsbio
▴ 10
2
votes
5
replies
766
views
DESeq2 setting significant p-value
DESeq2
updated 20 days ago by
Michael Love
42k • written 5.0 years ago by
Merlin
▴ 10
3
votes
1
reply
1.5k
views
Limma without eBayes, is it indistunguishable from Ordinary Least Square?
Limma
ebayes
bayesian
ls
updated 1 day ago by
Gordon Smyth
50k • written 5.6 years ago by
CantExitVIM
▴ 10
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
1
reply
1.3k
views
DSS CpG coverage threshold
DSS
WGBS
coverage
updated 7 hours ago by
j.gilbert
• 0 • written 6.6 years ago by
floriandeckert
▴ 30
2
votes
4
replies
1.7k
views
EGSEA usage with microarray data (with vooma)?
EGSEA
gene set testing
vooma
limma voom
gsea
updated 23 hours ago by
Chris
• 0 • written 7.4 years ago by
Pekka Kohonen
▴ 190
5
votes
8
replies
8.8k
views
Limma design with continuous and categorical covariates
limma
batch effect
covariates
microarray
updated 16 days ago by
hortense96
• 0 • written 7.7 years ago by
dmcleanuk
▴ 30
2
votes
2
replies
1.1k
views
limma for gene expression analysis with big and unbalanced sample size
limma
microarray
statistics
updated 9 days ago by
XW
• 0 • written 7.9 years ago by
tati6406
• 0
6
votes
10
replies
2.2k
views
overlapsAny for elements in GRangesList
granges
grangeslist
overlapsAny
updated 25 days ago by
Samuel Ahuno
• 0 • written 8.0 years ago by
maltethodberg
▴ 180
0
votes
5
replies
2.9k
views
DNAString: Standard checksum function?
Biostrings
FASTA
sequencing
8.2 years ago • updated 4 days ago
Henrik Bengtsson
★ 2.4k
9
votes
12
replies
7.8k
views
Multi factor design edgeR/Deseq2
deseq2
edgeR
rna-seq
updated 21 days ago by
Elizabeth
• 0 • written 8.8 years ago by
gthm
▴ 30
11
votes
5
replies
7.4k
views
Theoretical WGCNA Question
WGCNA
Theory
Scale-Free Topology
updated 21 days ago by
Garrett
• 0 • written 9.1 years ago by
brohawndg
▴ 150
0
votes
3
replies
1.5k
views
Limma, eBayes different sample size of groups and adjustment
limma
limma
updated 9 days ago by
XW
• 0 • written 13.0 years ago by
Babara Mueller
▴ 10
201 results • Page
4 of 5
Recent ...
Replies
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
That ll be helpful. Thank you.
Comment: Log-cpm values from limma
by
Shaimaa Gamal
• 0
I have performed RUVg correction and extracted W, factors of unwanted variation. According to limma guide, > In the limma approach to RNA…
Comment: DSS CpG coverage threshold
by
j.gilbert
• 0
Might be a bit late for the original poster :') but in case anyone else is wondering, the DSS user guide says: *Q: Do I need to filter out…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
42k
Segmentation is of the whole genome, I'll write some code for doing this later today.
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
42k
I'll take a look later. For next time, I've edited your post by enclosing the code in triple backticks (on their own link). This properly …
Votes
Bioconductor 3.19 is Released!
A: Volcanoplot with limma - RAW P-values or Adj.P-Values
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: minfi latest update for EPIC V2 chip
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