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0
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13
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Error in render R qmd document (could not find function "process")
quantro
3 hours ago
Chutian
• 0
0
votes
0
replies
20
views
How to add Ensembl ids after Pseudobulk analysis by DESeq2
Seurat
DESeq2
single-cell
scRNA
Pseudobulk
9 hours ago
Sara
• 0
0
votes
4
replies
167
views
Volcano plot of scRNA-seq data not "centered"
DESeq2
updated 9 hours ago by
ATpoint
★ 4.2k • written 2 days ago by
tjl
• 0
0
votes
1
reply
58
views
Normalisation using clinical traits in RNA seq using DESeq2
DESeq2
clinicaltraits
Normalization
batchnormalisation
updated 9 hours ago by
ATpoint
★ 4.2k • written 2 days ago by
sukeshinik5
• 0
0
votes
0
replies
29
views
conumee with Infinium MethylationEPIC v2.0
conumee
1 day ago
Maximus
• 0
1
vote
4
replies
1.6k
views
conumee with Infinium MethylationEPIC v2.0
MethylationEPICv2.0
conumee
updated 1 day ago by
Maximus
• 0 • written 14 months ago by
luca.s
▴ 50
0
votes
4
replies
99
views
Cannot install oligo on Fedora
oligo
source
Install
updated 1 day ago by
James W. MacDonald
66k • written 2 days ago by
Guido Hooiveld
★ 4.0k
0
votes
1
reply
55
views
GSVA function
DESeq2
GSVA
ssGSEA
updated 2 days ago by
Robert Castelo
★ 3.3k • written 2 days ago by
michelafrancesconi8
• 0
0
votes
0
replies
24
views
News:
Legacy Bioconductor Installation
Installation
Bioconductor
2 days ago
shepherl
3.9k
0
votes
4
replies
13k
views
SingleR Label.Ont
SingleR
updated 2 days ago by
Anna
• 0 • written 8 months ago by
saeed.khalili
• 0
0
votes
1
reply
56
views
Error when running topGO with KS statistic and elim agorithm
topGO
updated 2 days ago by
James W. MacDonald
66k • written 2 days ago by
adendekk
• 0
0
votes
2
replies
66
views
Cluster columns in Pheatmap
geneexp
pheatmap
heatmaps
cluster
updated 2 days ago by
James W. MacDonald
66k • written 2 days ago by
pehove2385
• 0
0
votes
5
replies
421
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
25 days ago • updated 2 days ago
Ian D.
▴ 70
0
votes
0
replies
18
views
News:
Online course: Network Analysis in Systems Biology with R/Bioconductor
SystemsBiology
Bioconductor
Network
2 days ago
info
▴ 10
0
votes
4
replies
241
views
Using featureCounts with SAF annotation file gives "Error: only GTF files contain additional attributes"
RNASeq
Rsubread
updated 2 days ago by
Wei Shi
★ 3.6k • written 3 days ago by
atan
• 0
0
votes
0
replies
42
views
News:
Bioconductor Build System
Builds
Bioconductor
2 days ago
shepherl
3.9k
8
votes
6
replies
4.2k
views
Using the plotting functions of clusterProfiler / enrichplot with enrichment results from other programs
clusterProfiler
enrichplot
updated 3 days ago by
jovel_juan
▴ 30 • written 5.1 years ago by
charles.foster
▴ 160
0
votes
0
replies
35
views
News:
BioC2024 Bioconductor Carpentries RNA-Seq Workshop July 22-23
BioC2024
Conference
Bioconductor
Community
3 days ago
Maria Doyle
▴ 70
0
votes
5
replies
288
views
Running ENmix with mouse methylation manifest: readidat error - Error in readmanifest(manifestfile) : length(control.line) == 1 && is.integer(cont…
ENmix
Bioconductor
updated 3 days ago by
xuz
• 0 • written 5 days ago by
minardsmitha
▴ 10
3
votes
7
replies
914
views
Genes in open chromatin region
ChIPpeakAnno
DiffBind
written 8 months ago by
Chris
▴ 10
5
votes
6
replies
357
views
Not able to install any Bioconductor 3.18 package [unable to access index]
Install
updated 3 days ago by
merv
▴ 120 • written 3 days ago by
Lorena Pantano
▴ 140
0
votes
2
replies
126
views
Errors in chromosome annotation-biomaRt
org.Rn.eg.db
biomaRt
5 days ago • updated 3 days ago
landenshanie
▴ 40
2
votes
4
replies
159
views
Help with infinite recursion - non-zero exit status in installation of GenomeInfoDbData
Install
GenomeInfoDbData
GenomeInfoDb
updated 3 days ago by
James W. MacDonald
66k • written 3 days ago by
Brandon
▴ 20
1
vote
8
replies
1.8k
views
enrichGOgradient color change
clusterProfiler
updated 3 days ago by
Javier
• 0 • written 6 months ago by
inna.gur
• 0
2
votes
2
replies
100
views
unable to access bioconductor packages - qvalue installation failed...
Install
updated 3 days ago by
shepherl
3.9k • written 3 days ago by
gabry.scata
▴ 10
2
votes
2
replies
83
views
Get gene symbols for a set of hg19 coordinates
annotation
hg19
3 days ago
pcantalupo
▴ 10
0
votes
0
replies
25
views
Job:
Bioinformatics MSc University of York
bioinformatics
JobPosting
3 days ago
Daphne
• 0
0
votes
3
replies
117
views
pathview error
KEGGgraph
KEGG
updated 3 days ago by
Guido Hooiveld
★ 4.0k • written 4 days ago by
Fara
• 0
0
votes
0
replies
40
views
Problem in execuation of filterAndTrim command in DADA2
Bioconductor
dada2
4 days ago • updated 3 days ago
abhisek001
• 0
4
votes
11
replies
1.6k
views
can't open mghp.osn.xsede.org
GenomeInfoDbData
genomeinfodbdata
updated 3 days ago by
merv
▴ 120 • written 9 months ago by
15753563659
▴ 60
4
votes
3
replies
170
views
recount3 problem downloading data from source sra
recount3
updated 3 days ago by
Leonardo Collado Torres
★ 1.1k • written 5 days ago by
PABLO ANTONIO
▴ 10
1
vote
8
replies
167
views
Slightly different count plots from R and spreadsheet
DESeq2
ggplot2
4 days ago • updated 3 days ago
boczniak767
▴ 720
1
vote
3
replies
2.8k
views
WGNCA kME vs. kIM
WGCNA
updated 3 days ago by
Vitor
• 0 • written 8.7 years ago by
akridgerunner
▴ 30
2
votes
4
replies
1.8k
views
slingshot: error with plot3d.SlingshotDataSet
slingshot
plot3d.SlingshotDataSet
updated 4 days ago by
Kelly Street
• 0 • written 23 months ago by
manduchi
▴ 10
0
votes
7
replies
363
views
ChAMP installation issue
Cha
ChAMP
updated 4 days ago by
James W. MacDonald
66k • written 13 days ago by
e1271094
• 0
2
votes
4
replies
401
views
seqlevelsStyle() not working
ensembldb
genomei
GenomeInfoDb
written 3 months ago by
Kai Hu
▴ 70
10
votes
11
replies
1.9k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq
rnaseq
updated 4 days ago by
Sara
• 0 • written 6.8 years ago by
Sylvain Foisy
▴ 80
2
votes
2
replies
140
views
Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools
limma
ExpressionData
RNASeq
edgeR
5 days ago • updated 4 days ago
mohammedtoufiq91
▴ 10
8
votes
41
replies
5.9k
views
Ensembl plants at annotationHub?
ensembl
ensembldb
plant
arabidopsis thaliana
annotationhub
updated 4 days ago by
Daniele
• 0 • written 5.5 years ago by
Guido Hooiveld
★ 4.0k
0
votes
0
replies
43
views
FindOverlaps, makeVennDiagram and "others"
ATACSeq
peaks
ATAC
ChIPpeakAnno
5 days ago
Raghad
• 0
0
votes
1
reply
735
views
How to arrange multiple plots into one page in NOISeq?
noiseq
RNA-seq
quality control
updated 5 days ago by
baptiste.bidon
• 0 • written 4.8 years ago by
ag1805x
▴ 80
1
vote
1
reply
90
views
Documenting resources in an `ExperimentHub` package?
AnnotationHub
ExperimentHub
updated 5 days ago by
James W. MacDonald
66k • written 5 days ago by
Tim Barry
• 0
0
votes
0
replies
41
views
Conditional analysis
GENESIS
5 days ago
SuperDad
• 0
4
votes
3
replies
1.0k
views
BayesSpace parameters for DLPFC Visium data
BayesSpace
written 3.1 years ago by
aspangl1
▴ 30
0
votes
2
replies
239
views
Visium RNA
metaMSdata
written 9 weeks ago by
Karlison
• 0
0
votes
2
replies
764
views
Help with ENmix readidat
ENmix
IlluminaHumanMethylationEPICmanifest
updated 5 days ago by
James W. MacDonald
66k • written 2.0 years ago by
Daphna
• 0
1
vote
3
replies
157
views
LRT, more than two conditions and pairwise comparisons
DESeq2
updated 5 days ago by
James W. MacDonald
66k • written 7 days ago by
boczniak767
▴ 720
2
votes
4
replies
239
views
DESeq2- Mysterious interaction suppresses DEGs
DESeq2
PCAplot
RNA-Seq
DesignModel
updated 6 days ago by
Michael Love
42k • written 9 days ago by
shaunpeterson
• 0
1
vote
2
replies
106
views
How to run allelic imbalance in apeglm
apeglm
updated 6 days ago by
Michael Love
42k • written 7 days ago by
euge.eugenio
▴ 20
0
votes
6
replies
620
views
Numerical differences in DESeq2 output depending on different design matrix construction
DESeq2
9 days ago • updated 6 days ago
Ken C
• 0
174 results • Page
1 of 4
Recent ...
Replies
Comment: Volcano plot of scRNA-seq data not "centered"
by
ATpoint
★ 4.2k
My comment was generic. If your experiment causes drastic shifts then the situation might be different. The advise is the same: Try to use …
Comment: conumee with Infinium MethylationEPIC v2.0
by
Maximus
• 0
Hi Sole, If there is a combined mixture of MSet of 450K, EPIC and EPICv2, how should I create an annotation object? I tried to create anno…
Comment: Volcano plot of scRNA-seq data not "centered"
by
tjl
• 0
Thank you both. The code is below, simplified a bit for simplicity. ATpoint, your suggestion re: the top 20% of genes by baseMean makes me …
Comment: Cannot install oligo on Fedora
by
James W. MacDonald
66k
Wait a minute. The `oligo` package is *supposed to* be using `zlibbioc`, but apparently it is not. I get the same thing as you do, where it…
Comment: Cannot install oligo on Fedora
by
James W. MacDonald
66k
There is the `zlibbioc` package that provides the headers for zlib 1.2.5, that I think you should be able to use, although that would requi…
Votes
A: Analyzing data without replicates using DiffBind
A: Analyzing data without replicates using DiffBind
DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Gene symbol
DESeq2 swap ensembl gene id rownames with gene symbol column
A: DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Ge
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