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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 15 days ago by
Amruta
• 0 • written 5.2 years ago by
r.tor
• 0
17
votes
4
replies
8.9k
views
Tutorial:
Updated Support Site Editor
support.bioconductor.org
editor
markdown
updates
Tutorial
updated 24 days ago by
Mj.A.
• 0 • written 5.2 years ago by
shepherl
3.8k
9
votes
12
replies
7.7k
views
Multi factor design edgeR/Deseq2
deseq2
edgeR
rna-seq
updated 1 day 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 22 hours ago by
Garrett
• 0 • written 9.1 years ago by
brohawndg
▴ 150
4
votes
16
replies
7.3k
views
Normalised counts from RUVg in RUVSeq
RUVg
ruvseq
rnaseq
updated 28 days ago by
Shaimaa Gamal
• 0 • written 8.9 years ago by
Pauly Lin
▴ 150
10
votes
10
replies
6.4k
views
biomaRt not working - lazy table error
error
lazy
R
biomaRt
table
updated 29 days ago by
juo5
• 0 • written 5 months ago by
Abhishek
▴ 10
7
votes
36
replies
5.5k
views
Ensembl plants at annotationHub?
ensembl
ensembldb
plant
arabidopsis thaliana
annotationhub
updated 15 days ago by
Shiva
• 0 • written 5.4 years ago by
Guido Hooiveld
★ 3.9k
4
votes
4
replies
3.7k
views
Function simplify fails when argument ont is set to "ALL" in enrichGO function in package clusterProfiler
clusterProfiler
GO
GO enrichment
genesetenrichment
updated 29 days ago by
jandrade
• 0 • written 6.3 years ago by
Huang, Lei [BSD] - CRI
▴ 20
0
votes
6
replies
3.1k
views
limma, analysis on subset of data gives completely different results
limma
limma
updated 17 days ago by
Gordon Smyth
50k • written 9.8 years ago by
Arvid Sondén
▴ 40
1
vote
2
replies
3.0k
views
Extract genes from ggvenn?
ggvenn
updated 14 days ago by
Michael
▴ 10 • written 23 months ago by
axe880
• 0
3
votes
18
replies
2.8k
views
News:
List of Deprecated Packages for Bioc3.18
Deprecation
devel
Bioconductor
Devel
9 months ago • updated 2 days ago
shepherl
3.8k
0
votes
4
replies
2.8k
views
SingleR Label.Ont
SingleR
updated 4 days ago by
lisia
• 0 • written 7 months ago by
saeed.khalili
• 0
0
votes
3
replies
2.3k
views
internal error in trio library when trying to use lfmm() in LEA package
lfmm
LEA
updated 26 days ago by
m.charters
• 0 • written 2.9 years ago by
valentinarov
• 0
6
votes
10
replies
2.2k
views
overlapsAny for elements in GRangesList
granges
grangeslist
overlapsAny
updated 5 days ago by
Samuel Ahuno
• 0 • written 8.0 years ago by
maltethodberg
▴ 170
5
votes
14
replies
2.1k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 4 hours ago by
Seyram M.
• 0 • written 4.6 years ago by
hsbio
▴ 10
0
votes
5
replies
1.8k
views
EdgeR: paired samples together with independant samples
RNASeq
edgeR
RNASeq
edgeR
updated 17 days ago by
Gordon Smyth
50k • written 11.5 years ago by
Maria Keays
▴ 30
14
votes
19
replies
1.7k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
21 days ago • updated 11 days ago
Chris
• 0
1
vote
7
replies
1.7k
views
Error using champ.import
ChAMP
EPICv2
updated 2 days ago by
shilpa
• 0 • written 9 months ago by
medha.suman
• 0
2
votes
2
replies
1.6k
views
Running featureCounts() in 'IntersectionStrict' mode
rsubread
featurecounts
summarizeoverlaps
updated 19 days ago by
isaac.vock
• 0 • written 7.8 years ago by
Jon Manning
▴ 90
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
6
votes
10
replies
1.5k
views
Which input file is used for DGEList in EgdeR?
salmon
edgeR
tximport
nf-core
gene_counts
updated 7 hours ago by
i.atanasoai
• 0 • written 14 months ago by
mohammedtoufiq91
▴ 10
0
votes
1
reply
1.3k
views
Tutorial:
Online workshop "Working with ChatGPT in R" 2023-03-09
chatgpt
programming
updated 6 days ago by
gptnederlands.nl
• 0 • written 14 months ago by
Wolfgang Huber
★ 13k
2
votes
6
replies
1.3k
views
How to get DMR for Infinium methylation EPIC v2
ChAMP
DMRcate
minfi
updated 16 days ago by
Tim Peters
▴ 170 • written 4 months ago by
rae.alshammari
▴ 10
5
votes
9
replies
1.2k
views
Batch correction and repeated measures
RUVSeq
sva
limma
updated 1 day ago by
Gordon Smyth
50k • written 6 months ago by
Jonathan
▴ 10
1
vote
8
replies
1.2k
views
DESeq2 test for synergistic vs additive effects
synergistic
additive
DESeq2
updated 18 days ago by
Wolfgang Huber
★ 13k • written 9 months ago by
Jane
▴ 10
1
vote
4
replies
1.1k
views
Issue with Biomart- cannot access ensembl
biomaRT
updated 29 days ago by
James W. MacDonald
65k • written 4.0 years ago by
RJW63
• 0
2
votes
5
replies
1.1k
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 2 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 20 days ago by
Gordon Smyth
50k • written 12.4 years ago by
Bogdan
▴ 670
0
votes
2
replies
1.0k
views
error when using M-values in ChAMP
ChAMP
updated 22 days ago by
hortense96
• 0 • written 6.2 years ago by
a.mcneill
• 0
2
votes
5
replies
995
views
STRINGdb R package reference class instantiation with v12.0
STRINGdb
updated 14 days ago by
damian.szk
▴ 80 • written 4 months ago by
Abhishek
• 0
0
votes
2
replies
888
views
Problem for loading Bioconductor package in R
Bioconductor
written 4.2 years ago by
araaaju
• 0
0
votes
2
replies
871
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell
RNASeq
RNASeqData
scRNAseq
updated 2 days ago by
wichaidi
• 0 • written 17 months ago by
irvin.ng
• 0
5
votes
9
replies
798
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
8 days ago • updated 1 day ago
Chris
• 0
5
votes
25
replies
784
views
limma models out of memory issue on Slurm HPC
Regression
limma
STATISITICS
HPC
updated 14 days ago by
Gordon Smyth
50k • written 24 days ago by
Jitendra
▴ 10
8
votes
23
replies
766
views
Convert Seurat Object to Summarised Experiment or ExpressionSet
SummarizedExperiment
ExpressionSet
updated 8 days ago by
Robert Castelo
★ 3.2k • written 9 days ago by
Bine
▴ 40
1
vote
2
replies
750
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler
RNASeq
updated 1 day ago by
sredemption
• 0 • written 13 months ago by
ruiqi.li
▴ 10
3
votes
1
reply
733
views
News:
[Pre-print] Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex
biorxiv
spatialLIBD
News
written 4.1 years ago by
Leonardo Collado Torres
★ 1.0k
0
votes
2
replies
728
views
error in install immunedeconv
Install
updated 15 days ago by
Arash
• 0 • written 13 months ago by
fenglingao
• 0
2
votes
5
replies
707
views
Looking for equivalent EPIC chip v1 vs. v2 annotation variables
sesame
IlluminaHumanMethylationEPICv2anno.20a1.hg38
methylationEPICv2.0
EpicV2
updated 29 days ago by
aldea85
• 0 • written 5 months ago by
Courtney
• 0
0
votes
2
replies
688
views
biomart not ound some prevous release
biomart
rnaseq
written 5.2 years ago by
jarod_v6@libero.it
▴ 40
0
votes
1
reply
668
views
Query regarding phyloseq object construct with QIIME output
phyloseq
microbiome
Metagenomics
updated 6 days ago by
President Gamer
• 0 • written 10 months ago by
abhisek001
• 0
5
votes
3
replies
664
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR
DifferentialExpression
updated 22 days ago by
Gordon Smyth
50k • written 29 days ago by
Jack S.
▴ 50
2
votes
5
replies
661
views
DESeq2 setting significant p-value
DESeq2
updated 5 hours ago by
Michael Love
41k • written 5.0 years ago by
Merlin
▴ 10
0
votes
4
replies
554
views
How to correct for known and surrogate variables in DESeq2?
DESeq2
BatchEffect
sva
limma
updated 3 days ago by
Michael Love
41k • written 5 months ago by
Crystal571
• 0
0
votes
6
replies
552
views
News:
List of Deprecated Packages for Bioc3.19
Release
Devel
ExperimentData
Software
7 weeks ago • updated 3 hours ago
shepherl
3.8k
0
votes
2
replies
552
views
ageData (minfi pipeline)
ageData
missMethyl
differentialvariability
minfi
updated 25 days ago by
CHEN
• 0 • written 11 months ago by
Saanchi
• 0
0
votes
1
reply
528
views
CopywriteR output
CopywriteR
updated 14 days ago by
fer_talavera
• 0 • written 2.5 years ago by
Joshua
• 0
0
votes
1
reply
486
views
Cibersort phenotype file
cibersort
deconvR
immune
updated 10 days ago by
ivorychan7777
• 0 • written 14 months ago by
609b0d25
• 0
2
votes
8
replies
473
views
Microarray Limma Model fitting and DEG
limma
DGEanalysis
updated 22 days ago by
Gordon Smyth
50k • written 24 days ago by
Amit
• 0
2
votes
6
replies
436
views
limma: vooma mean-variance trend and data filtration
MicroarrayData
limma
6 weeks ago • updated 24 days ago
Lily Cheang
▴ 10
200 results • Page
1 of 4
Recent ...
Replies
Comment: How to retrieve detailed regression results from deseq2
by
Weiqian
▴ 10
Hi Michael, thanks for the answer! I'll have a look : )
Comment: DESeq filtering specific to contrasts
by
Michael Love
41k
It will likely not filter it out, but really the per-dataset details would affect the results.
Comment: DESeq filtering specific to contrasts
by
Carlin95
• 0
Thanks for clarifying. Could I ask maybe one more thing for my sanity? Let's say you had a multi-factor experiment with contrasts including…
Comment: FilterByExpr low counts with small sample size
by
Jonathan
▴ 10
Thank you for your answer; However, I have some follow-up questions. Following up in In your [1-2-3 article][1], you say that > "... the…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa
by
Seyram M.
• 0
Thank you very much for your reply! I will do so. Kind regards, Seyram
Votes
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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