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156
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Design Matrix within group comparison more than two groups
DESeq2
7 days ago • updated 6 days ago
hemantcnaik
• 0
2
votes
2
replies
137
views
[DiffBind] Obtaining normalization factors
DiffBind
7 days ago • updated 3 days ago
Henry
▴ 10
2
votes
2
replies
135
views
ComplexHeatmap: change the names of a HeatmapAnnotation object
ComplexHeatmap
7 days ago • updated 4 days ago
daniel.carbajo
• 0
0
votes
3
replies
196
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 1 day ago by
W. Evan Johnson
▴ 850 • written 7 days ago by
schlumbohm
• 0
5
votes
9
replies
805
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
9 days ago • updated 1 day ago
Chris
• 0
0
votes
1
reply
115
views
compareCluster dotplot: how to modify the genesets order
DOSE
enrichplot
clusterProfiler
updated 5 days ago by
Guido Hooiveld
★ 3.9k • written 9 days ago by
Lucie
• 0
5
votes
6
replies
380
views
Not fully paired differential gene expression analysis
edgeR
DifferentialExpression
updated 6 days ago by
ATpoint
★ 4.0k • written 10 days ago by
nhaus
▴ 30
0
votes
2
replies
218
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
19 days ago • updated 12 hours ago
isaac.vock
• 0
14
votes
20
replies
1.7k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
21 days ago • updated 6 hours ago
Chris
• 0
6
votes
5
replies
380
views
Estimating Cell Counts for EPIC V2 array data
FlowSorted.Blood.EPIC
minifi
written 7 weeks ago by
Kim
• 0
0
votes
7
replies
352
views
DESeq filtering specific to contrasts
DESeq2
updated 11 hours ago by
Michael Love
41k • written 9 weeks ago by
Emma
• 0
0
votes
4
replies
556
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
5
votes
9
replies
1.2k
views
Batch correction and repeated measures
RUVSeq
sva
limma
updated 2 days ago by
Gordon Smyth
50k • written 6 months ago by
Jonathan
▴ 10
0
votes
4
replies
2.9k
views
SingleR Label.Ont
SingleR
updated 4 days ago by
lisia
• 0 • written 7 months ago by
saeed.khalili
• 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
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
1
vote
2
replies
752
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
1
vote
1
reply
823
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 hours ago by
russ.bainer
▴ 10 • written 13 months ago by
jose.ramirez1
▴ 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
6
votes
10
replies
1.5k
views
Which input file is used for DGEList in EgdeR?
salmon
edgeR
tximport
nf-core
gene_counts
updated 15 hours ago by
i.atanasoai
• 0 • written 14 months ago by
mohammedtoufiq91
▴ 10
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
0
votes
2
replies
888
views
Problem for loading Bioconductor package in R
Bioconductor
written 4.2 years ago by
araaaju
• 0
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 12 hours ago by
Seyram M.
• 0 • written 4.6 years ago by
hsbio
▴ 10
2
votes
5
replies
666
views
DESeq2 setting significant p-value
DESeq2
updated 13 hours ago by
Michael Love
41k • written 5.0 years ago by
Merlin
▴ 10
6
votes
10
replies
2.2k
views
overlapsAny for elements in GRangesList
granges
grangeslist
overlapsAny
updated 6 days ago by
Samuel Ahuno
• 0 • written 8.0 years ago by
maltethodberg
▴ 170
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 1 day ago by
Garrett
• 0 • written 9.1 years ago by
brohawndg
▴ 150
77 results • Page
2 of 2
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Answer: Cannabis and KEGGgraph
by
deeenes
▴ 30
Hello, I'm a developer of the `OmnipathR` package, and I wrote [a function][1] to access certain KEGG data: library(OmnipathR) cs…
Answer: RNAseq:Technical replicates from different batches
by
Gordon Smyth
50k
I am not entirely clear what you mean by "technical" replicates in this case. Are they resequencing of the same RNA samples or are they fre…
Comment: DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, param
by
russ.bainer
▴ 10
Hi, I'm hitting this too. As far as I can tell my DataTrack is fine, but perhaps I am missing something. Notably the same code works on o…
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions
by
Chris
• 0
Hi Robert, If I don't want to use all pathway in c2 gene set but only a few pathways of interested, how can I do that? So we try to get a …
Comment: How to retrieve detailed regression results from deseq2
by
Weiqian
▴ 10
Hi Michael, thanks for the answer! I'll have a look : )
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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