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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 29 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 10 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 15 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 14 days ago by
Garrett
• 0 • written 9.1 years ago by
brohawndg
▴ 150
7
votes
36
replies
5.6k
views
Ensembl plants at annotationHub?
ensembl
ensembldb
plant
arabidopsis thaliana
annotationhub
updated 29 days ago by
Shiva
• 0 • written 5.4 years ago by
Guido Hooiveld
★ 3.9k
0
votes
4
replies
5.3k
views
SingleR Label.Ont
SingleR
updated 17 days ago by
lisia
• 0 • written 7 months ago by
saeed.khalili
• 0
6
votes
12
replies
4.8k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache
AnnotationHub
ExperimentHub
6 months ago • updated 11 days ago
shepherl
3.9k
1
vote
2
replies
3.1k
views
Extract genes from ggvenn?
ggvenn
updated 27 days ago by
Michael
▴ 10 • written 2.0 years 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 15 days ago
shepherl
3.9k
5
votes
6
replies
2.8k
views
Although I successfully installed the package "simpleaffy'' , I cannot library it. Why?
simpleaffy
updated 22 hours ago by
James W. MacDonald
65k • written 2.3 years ago by
yanchangjian2019
• 0
0
votes
18
replies
2.5k
views
problem installing ENmix package
ENmix
Bioconductor
rtracklayer
written 3.2 years ago by
lea
• 0
6
votes
19
replies
2.4k
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
Sey R.
• 0 • written 4.6 years ago by
hsbio
▴ 10
6
votes
10
replies
2.2k
views
overlapsAny for elements in GRangesList
granges
grangeslist
overlapsAny
updated 19 days ago by
Samuel Ahuno
• 0 • written 8.0 years ago by
maltethodberg
▴ 180
15
votes
23
replies
1.9k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
4 weeks ago • updated 2 days ago
Chris
• 0
1
vote
7
replies
1.8k
views
Error using champ.import
ChAMP
EPICv2
updated 16 days ago by
shilpa
• 0 • written 10 months ago by
medha.suman
• 0
8
votes
6
replies
1.7k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq
rnaseq
updated 2 days ago by
Leonard Goldstein
▴ 200 • written 6.7 years ago by
Sylvain Foisy
▴ 80
0
votes
5
replies
1.7k
views
blockwiseModule crashes in the end and doesn't generate modules
WGCNA
written 12 months ago by
mauricio.microbiol
• 0
6
votes
10
replies
1.6k
views
Which input file is used for DGEList in EgdeR?
salmon
edgeR
tximport
nf-core
gene_counts
updated 14 days ago by
i.atanasoai
• 0 • written 15 months ago by
mohammedtoufiq91
▴ 10
0
votes
3
replies
1.5k
views
Limma, eBayes different sample size of groups and adjustment
limma
limma
updated 2 days ago by
XW
• 0 • written 13.0 years ago by
Babara Mueller
▴ 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
Tutorial:
Online workshop "Working with ChatGPT in R" 2023-03-09
chatgpt
programming
updated 20 days ago by
gptnederlands.nl
• 0 • written 14 months ago by
Wolfgang Huber
★ 13k
5
votes
9
replies
1.3k
views
Batch correction and repeated measures
RUVSeq
sva
limma
updated 15 days ago by
Gordon Smyth
50k • written 7 months ago by
Jonathan
▴ 10
0
votes
3
replies
1.2k
views
News:
European Bioconductor Conference 2023 planning
Europe
Conference
EuroBioC
Events
News
updated 11 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 16 days ago by
Ashley
• 0 • written 10 months ago by
zxc741xb
• 0
14
votes
17
replies
1.1k
views
Why p value inconsistent when using different number of pathway score?
limma
13 days ago • updated 1 day ago
Chris
• 0
2
votes
2
replies
1.1k
views
limma for gene expression analysis with big and unbalanced sample size
limma
microarray
statistics
updated 2 days ago by
XW
• 0 • written 7.9 years ago by
tati6406
• 0
2
votes
5
replies
1.0k
views
STRINGdb R package reference class instantiation with v12.0
STRINGdb
updated 28 days ago by
damian.szk
▴ 80 • written 5 months ago by
Abhishek
• 0
1
vote
2
replies
985
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 10 days ago by
Tim Peters
▴ 170 • written 14 months ago by
jose.ramirez1
▴ 10
0
votes
2
replies
918
views
Problem for loading Bioconductor package in R
Bioconductor
written 4.2 years ago by
araaaju
• 0
8
votes
23
replies
914
views
Convert Seurat Object to Summarised Experiment or ExpressionSet
SummarizedExperiment
ExpressionSet
updated 21 days ago by
Robert Castelo
★ 3.3k • written 22 days ago by
Bine
▴ 40
0
votes
2
replies
909
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell
RNASeq
RNASeqData
scRNAseq
updated 15 days ago by
wichaidi
• 0 • written 17 months ago by
irvin.ng
• 0
5
votes
9
replies
901
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
22 days ago • updated 15 days ago
Chris
• 0
5
votes
25
replies
886
views
limma models out of memory issue on Slurm HPC
Regression
limma
STATISITICS
HPC
updated 28 days ago by
Gordon Smyth
50k • written 5 weeks ago by
Jitendra
▴ 10
1
vote
3
replies
852
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler
RNASeq
updated 9 days ago by
Guangchuang Yu
★ 1.2k • written 14 months ago by
ruiqi.li
▴ 10
0
votes
2
replies
782
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
2
replies
756
views
error in install immunedeconv
Install
updated 29 days ago by
Arash
• 0 • written 13 months ago by
fenglingao
• 0
3
votes
1
reply
752
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
5
replies
739
views
DESeq2 setting significant p-value
DESeq2
updated 14 days ago by
Michael Love
41k • written 5.0 years ago by
Merlin
▴ 10
0
votes
1
reply
700
views
Query regarding phyloseq object construct with QIIME output
phyloseq
microbiome
Metagenomics
updated 20 days ago by
President Gamer
• 0 • written 11 months ago by
abhisek001
• 0
1
vote
2
replies
696
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
16 days ago • updated 7 days ago
ussarizona
▴ 10
0
votes
7
replies
690
views
News:
List of Deprecated Packages for Bioc3.19
Release
Devel
ExperimentData
Software
9 weeks ago • updated 9 days ago
shepherl
3.9k
0
votes
4
replies
592
views
How to correct for known and surrogate variables in DESeq2?
DESeq2
BatchEffect
sva
limma
updated 16 days ago by
Michael Love
41k • written 6 months ago by
Crystal571
• 0
0
votes
1
reply
552
views
CopywriteR output
CopywriteR
updated 27 days ago by
fer_talavera
• 0 • written 2.5 years ago by
Joshua
• 0
0
votes
1
reply
508
views
Cibersort phenotype file
cibersort
deconvR
immune
updated 24 days ago by
ivorychan7777
• 0 • written 15 months ago by
609b0d25
• 0
1
vote
2
replies
495
views
GSVA error
GSVA
19 days ago • updated 17 days ago
Alex
• 0
1
vote
6
replies
481
views
GSVA on separate healthy and disease datasets
GSVA
updated 23 days ago by
James W. MacDonald
65k • written 24 days ago by
Lucy
▴ 60
1
vote
4
replies
462
views
DEseq2 coefficient
DESeq2
coefficient
9 weeks ago • updated 1 day ago
JKim
• 0
1
vote
10
replies
446
views
Obtaining pheno data from CEL files
GEO
affy
4 weeks ago • updated 24 days ago
Kurtis
• 0
1
vote
4
replies
431
views
Using a change in a continuous explanatory variable to test changes in gene expression with limma
limma
updated 28 days ago by
Gordon Smyth
50k • written 4 weeks ago by
jari.karppinen
• 0
6
votes
5
replies
423
views
Estimating Cell Counts for EPIC V2 array data
FlowSorted.Blood.EPIC
minifi
written 9 weeks ago by
Kim
• 0
202 results • Page
1 of 5
Recent ...
Replies
Comment: Once again a "Model matrix not full rank"
by
James W. MacDonald
65k
You already ran a temporal assay. Now you can compare each time point to the baseline. The interaction term is only applicable if you have…
Comment: Timecourse RNASeq analysis
by
Aurora
• 0
I managed to run ImpulseDE2 as I am interested in getting significant gene changes over time. Now I would like to run deseq as well and com…
Comment: Once again a "Model matrix not full rank"
by
arfranco
▴ 130
But.. How to run a temporal assay?
Comment: Deseq2 and Normalization of RNA sequencing data
by
kcarey
• 0
Noise in terms of expression...to make sure that the information reported is not due to artifacts and actually expression. When I had FPKM …
Answer: NEED FOR NESSASORY HELP
by
Gordon Smyth
50k
Is this quesion related to your earlier question? https://support.bioconductor.org/p/9157127/ If you've already done an edgeR analysis, yo…
Votes
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
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