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0
votes
4
replies
230
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Storing directories inside an ExperimentHub package?
ExperimentHub
29 days ago • updated 28 days ago
Tim Barry
• 0
0
votes
0
replies
106
views
News:
Course Manipulation of NGS Data for Genomic and Population Genetics Analyses
sequencing
Sequencing
SequencingData
29 days ago
communication
• 0
3
votes
6
replies
285
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq
sva
29 days ago • updated 28 days ago
nhaus
▴ 30
0
votes
1
reply
180
views
DESeq2 gives an error and R crashes
DESeq2
29 days ago • updated 28 days ago
Shefali
• 0
0
votes
0
replies
141
views
LearnTaxa with custom Silva
DECIPHER
LearnTaxa
29 days ago
Eryn
• 0
0
votes
0
replies
88
views
queryDGIdb lexical error for some genes
lexicalerror
rDGIdb
DGIdb
json
29 days ago
Dennis
• 0
0
votes
1
reply
165
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
973
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
5
votes
6
replies
436
views
Not fully paired differential gene expression analysis
edgeR
DifferentialExpression
updated 27 days ago by
ATpoint
★ 4.1k • written 4 weeks ago by
nhaus
▴ 30
1
vote
6
replies
502
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
1
vote
2
replies
329
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 29 days ago by
Tim Peters
▴ 180 • written 5 weeks ago by
s.malik
• 0
0
votes
2
replies
265
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
255
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
455
views
Estimating Cell Counts for EPIC V2 array data
FlowSorted.Blood.EPIC
minifi
written 10 weeks ago by
Kim
• 0
1
vote
4
replies
493
views
DEseq2 coefficient
DESeq2
coefficient
10 weeks ago • updated 8 days ago
JKim
• 0
0
votes
7
replies
432
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 2 days ago by
Jiayu
• 0 • written 5 months ago by
yanling
• 0
0
votes
2
replies
805
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
608
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
5
votes
9
replies
1.3k
views
Batch correction and repeated measures
RUVSeq
sva
limma
updated 22 days ago by
Gordon Smyth
50k • written 7 months ago by
Jonathan
▴ 10
0
votes
4
replies
7.0k
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 23 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 16 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 27 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 21 days ago by
i.atanasoai
• 0 • written 15 months ago by
mohammedtoufiq91
▴ 10
0
votes
2
replies
1.3k
views
How to use spike-in information (sequences from another species) with DESeq2::DESeq()
DESeq2
SpikeIn
Normalization
updated 2 hours ago by
maria.soler
• 0 • written 15 months ago by
kalavattam
▴ 10
0
votes
2
replies
930
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
757
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
769
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 2 days 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 23 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 1 day 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 17 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 26 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
0
votes
3
replies
3.7k
views
[Mfuzz] Error in cmeans(exprs(eset)
Mfuzz
Mfuzz
updated 3 days ago by
Caio
• 0 • written 13.1 years ago by
boczniak767
▴ 720
198 results • Page
4 of 4
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Comment: Extremely small p-values using Limma for proteomic data
by
James W. MacDonald
65k
If you ever find yourself using the `@` function, you should reconsider what you are doing. There are vanishingly small instances when an e…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
42k
Here is some example code <https://gist.github.com/mikelove/cbbc84634b6854c865cb5eb08ad9b245>
Comment: How to use spike-in information (sequences from another species) with DESeq2::DE
by
maria.soler
• 0
Hi, I have a question barely related to this topic. Do you use a custom reference genome combining your organism and the one used as a spik…
Answer: Differential gene expression analysis results
by
ATpoint
★ 4.1k
Pease do not open multiple posts for the same issue: https://support.bioconductor.org/p/9158194/#9158222 The support site is not meant f…
Comment: deseq2 results
by
sajadahmad41454
• 0
thank you for your response, should i remove or discard that sample? since the red outlier on left represents one of healthy samples.
Votes
Comment: Log-cpm values from limma
Comment: Log-cpm values from limma
Comment: deseq2 results
Comment: deseq2 results
Answer: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
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