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3
votes
3
replies
13k
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How to fix 'long vectors not supported yet' error in R
r
updated 24 days ago by
Amruta
• 0 • written 5.2 years ago by
r.tor
• 0
5
votes
8
replies
8.8k
views
Limma design with continuous and categorical covariates
limma
batch effect
covariates
microarray
updated 5 days ago by
hortense96
• 0 • written 7.7 years ago by
dmcleanuk
▴ 30
9
votes
12
replies
7.8k
views
Multi factor design edgeR/Deseq2
deseq2
edgeR
rna-seq
updated 10 days ago by
Elizabeth
• 0 • written 8.8 years ago by
gthm
▴ 30
11
votes
5
replies
7.3k
views
Theoretical WGCNA Question
WGCNA
Theory
Scale-Free Topology
updated 9 days ago by
Garrett
• 0 • written 9.1 years ago by
brohawndg
▴ 150
7
votes
36
replies
5.5k
views
Ensembl plants at annotationHub?
ensembl
ensembldb
plant
arabidopsis thaliana
annotationhub
updated 24 days ago by
Shiva
• 0 • written 5.4 years ago by
Guido Hooiveld
★ 3.9k
6
votes
12
replies
4.7k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache
AnnotationHub
ExperimentHub
6 months ago • updated 6 days ago
shepherl
3.8k
0
votes
4
replies
4.4k
views
SingleR Label.Ont
SingleR
updated 12 days ago by
lisia
• 0 • written 7 months ago by
saeed.khalili
• 0
0
votes
6
replies
3.1k
views
limma, analysis on subset of data gives completely different results
limma
limma
updated 26 days ago by
Gordon Smyth
50k • written 9.8 years ago by
Arvid Sondén
▴ 40
1
vote
2
replies
3.1k
views
Extract genes from ggvenn?
ggvenn
updated 22 days ago by
Michael
▴ 10 • written 24 months ago by
axe880
• 0
3
votes
18
replies
2.9k
views
News:
List of Deprecated Packages for Bioc3.18
Deprecation
devel
Bioconductor
Devel
10 months ago • updated 10 days ago
shepherl
3.8k
0
votes
18
replies
2.5k
views
problem installing ENmix package
ENmix
Bioconductor
rtracklayer
written 3.2 years ago by
lea
• 0
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 5 days ago by
Michael Love
41k • written 4.6 years ago by
hsbio
▴ 10
6
votes
10
replies
2.2k
views
overlapsAny for elements in GRangesList
granges
grangeslist
overlapsAny
updated 14 days ago by
Samuel Ahuno
• 0 • written 8.0 years ago by
maltethodberg
▴ 170
15
votes
22
replies
1.8k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
29 days ago • updated 8 days ago
Chris
• 0
0
votes
5
replies
1.8k
views
EdgeR: paired samples together with independant samples
RNASeq
edgeR
RNASeq
edgeR
updated 26 days ago by
Gordon Smyth
50k • written 11.5 years ago by
Maria Keays
▴ 30
1
vote
7
replies
1.7k
views
Error using champ.import
ChAMP
EPICv2
updated 11 days ago by
shilpa
• 0 • written 10 months ago by
medha.suman
• 0
0
votes
5
replies
1.6k
views
blockwiseModule crashes in the end and doesn't generate modules
WGCNA
written 12 months ago by
mauricio.microbiol
• 0
2
votes
2
replies
1.6k
views
Running featureCounts() in 'IntersectionStrict' mode
rsubread
featurecounts
summarizeoverlaps
updated 28 days ago by
isaac.vock
• 0 • written 7.9 years ago by
Jon Manning
▴ 90
6
votes
10
replies
1.6k
views
Which input file is used for DGEList in EgdeR?
salmon
edgeR
tximport
nf-core
gene_counts
updated 9 days ago by
i.atanasoai
• 0 • written 14 months ago by
mohammedtoufiq91
▴ 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
2
votes
6
replies
1.3k
views
How to get DMR for Infinium methylation EPIC v2
ChAMP
DMRcate
minfi
updated 25 days ago by
Tim Peters
▴ 170 • written 5 months ago by
rae.alshammari
▴ 10
0
votes
1
reply
1.3k
views
Tutorial:
Online workshop "Working with ChatGPT in R" 2023-03-09
chatgpt
programming
updated 15 days ago by
gptnederlands.nl
• 0 • written 14 months ago by
Wolfgang Huber
★ 13k
5
votes
9
replies
1.2k
views
Batch correction and repeated measures
RUVSeq
sva
limma
updated 10 days ago by
Gordon Smyth
50k • written 7 months ago by
Jonathan
▴ 10
1
vote
8
replies
1.2k
views
DESeq2 test for synergistic vs additive effects
synergistic
additive
DESeq2
updated 27 days ago by
Wolfgang Huber
★ 13k • written 10 months ago by
Jane
▴ 10
0
votes
3
replies
1.2k
views
News:
European Bioconductor Conference 2023 planning
Europe
Conference
EuroBioC
Events
News
updated 6 days ago by
lauryfriese932
• 0 • written 18 months ago by
Maria Doyle
▴ 70
2
votes
5
replies
1.1k
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 11 days ago by
Ashley
• 0 • written 10 months ago by
zxc741xb
• 0
0
votes
2
replies
1.1k
views
library size and fold changes
edgeR
edgeR
updated 29 days ago by
Gordon Smyth
50k • written 12.4 years ago by
Bogdan
▴ 670
2
votes
5
replies
1.0k
views
STRINGdb R package reference class instantiation with v12.0
STRINGdb
updated 23 days ago by
damian.szk
▴ 80 • written 5 months ago by
Abhishek
• 0
1
vote
2
replies
946
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 5 days ago by
Tim Peters
▴ 170 • written 14 months ago by
jose.ramirez1
▴ 10
0
votes
2
replies
905
views
Problem for loading Bioconductor package in R
Bioconductor
written 4.2 years ago by
araaaju
• 0
0
votes
2
replies
894
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell
RNASeq
RNASeqData
scRNAseq
updated 11 days ago by
wichaidi
• 0 • written 17 months ago by
irvin.ng
• 0
8
votes
23
replies
881
views
Convert Seurat Object to Summarised Experiment or ExpressionSet
SummarizedExperiment
ExpressionSet
updated 17 days ago by
Robert Castelo
★ 3.3k • written 18 days ago by
Bine
▴ 40
5
votes
9
replies
873
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
17 days ago • updated 10 days ago
Chris
• 0
12
votes
13
replies
870
views
Why p value inconsistent when using different number of pathway score?
limma
8 days ago • updated 21 hours ago
Chris
• 0
5
votes
25
replies
836
views
limma models out of memory issue on Slurm HPC
Regression
limma
STATISITICS
HPC
updated 23 days ago by
Gordon Smyth
50k • written 4 weeks ago by
Jitendra
▴ 10
1
vote
3
replies
823
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler
RNASeq
updated 4 days ago by
Guangchuang Yu
★ 1.2k • written 14 months ago by
ruiqi.li
▴ 10
0
votes
2
replies
771
views
Job:
Bioinformatics Laboratory Head in AI or machine learning (WEHI, Australia)
bioconductor
artificialintelligence
JobPosting
machinelearning
written 8 months ago by
Gordon Smyth
50k
3
votes
1
reply
748
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
745
views
error in install immunedeconv
Install
updated 24 days ago by
Arash
• 0 • written 13 months ago by
fenglingao
• 0
2
votes
5
replies
706
views
DESeq2 setting significant p-value
DESeq2
updated 9 days ago by
Michael Love
41k • written 5.0 years ago by
Merlin
▴ 10
0
votes
2
replies
693
views
biomart not ound some prevous release
biomart
rnaseq
written 5.2 years ago by
jarod_v6@libero.it
▴ 40
0
votes
1
reply
686
views
Query regarding phyloseq object construct with QIIME output
phyloseq
microbiome
Metagenomics
updated 15 days ago by
President Gamer
• 0 • written 10 months ago by
abhisek001
• 0
0
votes
7
replies
643
views
News:
List of Deprecated Packages for Bioc3.19
Release
Devel
ExperimentData
Software
8 weeks ago • updated 4 days ago
shepherl
3.8k
0
votes
4
replies
578
views
How to correct for known and surrogate variables in DESeq2?
DESeq2
BatchEffect
sva
limma
updated 11 days ago by
Michael Love
41k • written 6 months ago by
Crystal571
• 0
0
votes
1
reply
543
views
CopywriteR output
CopywriteR
updated 22 days ago by
fer_talavera
• 0 • written 2.5 years ago by
Joshua
• 0
0
votes
1
reply
501
views
Cibersort phenotype file
cibersort
deconvR
immune
updated 19 days ago by
ivorychan7777
• 0 • written 15 months ago by
609b0d25
• 0
1
vote
2
replies
486
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
11 days ago • updated 2 days ago
ussarizona
▴ 10
1
vote
6
replies
468
views
GSVA on separate healthy and disease datasets
GSVA
updated 18 days ago by
James W. MacDonald
65k • written 19 days ago by
Lucy
▴ 60
1
vote
2
replies
421
views
GSVA error
GSVA
14 days ago • updated 13 days ago
Alex
• 0
1
vote
4
replies
417
views
Using a change in a continuous explanatory variable to test changes in gene expression with limma
limma
updated 23 days ago by
Gordon Smyth
50k • written 25 days ago by
jari.karppinen
• 0
190 results • Page
1 of 4
Recent ...
Replies
Comment: Why p value inconsistent when using different number of pathway score?
by
Chris
• 0
Hi Robert, if two conditions don't have hundreds of differential express genes ( in some conditions such as peripheral blood Alzheimer vs n…
Answer: Dominance Index for Shotgun Metagenomics Data
by
Leo Lahti
▴ 40
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
pl23
• 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions
by
Michael Love
41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
by
ussarizona
▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Votes
Answer: Dominance Index for Shotgun Metagenomics Data
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
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