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0
votes
3
replies
106
views
Volcano plot of scRNA-seq data not "centered"
DESeq2
1 day ago • updated 6 hours ago
tjl
• 0
0
votes
4
replies
68
views
Cannot install oligo on Fedora
oligo
source
Install
updated 7 hours ago by
James W. MacDonald
66k • written 12 hours ago by
Guido Hooiveld
★ 4.0k
0
votes
1
reply
34
views
GSVA function
DESeq2
GSVA
ssGSEA
updated 10 hours ago by
Robert Castelo
★ 3.3k • written 11 hours ago by
michelafrancesconi8
• 0
0
votes
0
replies
13
views
News:
Legacy Bioconductor Installation
Installation
Bioconductor
9 hours ago
shepherl
3.9k
0
votes
4
replies
12k
views
SingleR Label.Ont
SingleR
updated 12 hours ago by
Anna
• 0 • written 8 months ago by
saeed.khalili
• 0
0
votes
1
reply
41
views
Error when running topGO with KS statistic and elim agorithm
topGO
updated 13 hours ago by
James W. MacDonald
66k • written 1 day ago by
adendekk
• 0
0
votes
2
replies
51
views
Cluster columns in Pheatmap
geneexp
pheatmap
heatmaps
cluster
updated 14 hours ago by
James W. MacDonald
66k • written 17 hours ago by
pehove2385
• 0
0
votes
1
reply
39
views
Normalisation using clinical traits in RNA seq using DESeq2
DESeq2
clinicaltraits
Normalization
batchnormalisation
updated 16 hours ago by
ATpoint
★ 4.2k • written 16 hours ago by
sukeshinik5
• 0
0
votes
5
replies
418
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
23 days ago • updated 17 hours ago
Ian D.
▴ 70
0
votes
0
replies
13
views
News:
Online course: Network Analysis in Systems Biology with R/Bioconductor
SystemsBiology
Bioconductor
Network
17 hours ago
info
▴ 10
0
votes
4
replies
224
views
Using featureCounts with SAF annotation file gives "Error: only GTF files contain additional attributes"
RNASeq
Rsubread
updated 20 hours ago by
Wei Shi
★ 3.6k • written 1 day ago by
atan
• 0
0
votes
0
replies
25
views
News:
Bioconductor Build System
Builds
Bioconductor
1 day 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 1 day ago by
jovel_juan
▴ 30 • written 5.0 years ago by
charles.foster
▴ 160
0
votes
0
replies
27
views
News:
BioC2024 Bioconductor Carpentries RNA-Seq Workshop July 22-23
BioC2024
Conference
Bioconductor
Community
1 day ago
Maria Doyle
▴ 70
0
votes
5
replies
260
views
Running ENmix with mouse methylation manifest: readidat error - Error in readmanifest(manifestfile) : length(control.line) == 1 && is.integer(cont…
ENmix
Bioconductor
updated 1 day ago by
xuz
• 0 • written 3 days ago by
minardsmitha
▴ 10
3
votes
7
replies
911
views
Genes in open chromatin region
ChIPpeakAnno
DiffBind
written 8 months ago by
Chris
▴ 10
5
votes
6
replies
310
views
Not able to install any Bioconductor 3.18 package [unable to access index]
Install
updated 1 day ago by
merv
▴ 120 • written 2 days ago by
Lorena Pantano
▴ 140
0
votes
2
replies
114
views
Errors in chromosome annotation-biomaRt
org.Rn.eg.db
biomaRt
4 days ago • updated 1 day ago
landenshanie
▴ 40
2
votes
4
replies
143
views
Help with infinite recursion - non-zero exit status in installation of GenomeInfoDbData
Install
GenomeInfoDbData
GenomeInfoDb
updated 1 day ago by
James W. MacDonald
66k • written 2 days ago by
Brandon
▴ 20
1
vote
8
replies
1.8k
views
enrichGOgradient color change
clusterProfiler
updated 1 day ago by
Javier
• 0 • written 6 months ago by
inna.gur
• 0
2
votes
2
replies
89
views
unable to access bioconductor packages - qvalue installation failed...
Install
updated 1 day ago by
shepherl
3.9k • written 1 day ago by
gabry.scata
▴ 10
2
votes
2
replies
71
views
Get gene symbols for a set of hg19 coordinates
annotation
hg19
2 days ago • updated 1 day ago
pcantalupo
▴ 10
0
votes
0
replies
18
views
Job:
Bioinformatics MSc University of York
bioinformatics
JobPosting
1 day ago
Daphne
• 0
0
votes
3
replies
106
views
pathview error
KEGGgraph
KEGG
updated 1 day ago by
Guido Hooiveld
★ 4.0k • written 2 days ago by
Fara
• 0
0
votes
0
replies
30
views
Problem in execuation of filterAndTrim command in DADA2
Bioconductor
dada2
2 days ago • updated 1 day ago
abhisek001
• 0
4
votes
11
replies
1.6k
views
can't open mghp.osn.xsede.org
GenomeInfoDbData
genomeinfodbdata
updated 2 days ago by
merv
▴ 120 • written 9 months ago by
15753563659
▴ 60
4
votes
3
replies
150
views
recount3 problem downloading data from source sra
recount3
updated 2 days ago by
Leonardo Collado Torres
★ 1.1k • written 3 days ago by
PABLO ANTONIO
▴ 10
1
vote
8
replies
147
views
Slightly different count plots from R and spreadsheet
DESeq2
ggplot2
2 days ago
boczniak767
▴ 720
1
vote
3
replies
2.8k
views
WGNCA kME vs. kIM
WGCNA
updated 2 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 2 days ago by
Kelly Street
• 0 • written 23 months ago by
manduchi
▴ 10
0
votes
7
replies
341
views
ChAMP installation issue
Cha
ChAMP
updated 2 days ago by
James W. MacDonald
66k • written 11 days ago by
e1271094
• 0
2
votes
4
replies
396
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 2 days ago by
Sara
• 0 • written 6.8 years ago by
Sylvain Foisy
▴ 80
2
votes
2
replies
124
views
Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools
limma
ExpressionData
RNASeq
edgeR
3 days ago
mohammedtoufiq91
▴ 10
8
votes
41
replies
5.9k
views
Ensembl plants at annotationHub?
ensembl
ensembldb
plant
arabidopsis thaliana
annotationhub
updated 3 days ago by
Daniele
• 0 • written 5.5 years ago by
Guido Hooiveld
★ 4.0k
0
votes
0
replies
38
views
FindOverlaps, makeVennDiagram and "others"
ATACSeq
peaks
ATAC
ChIPpeakAnno
3 days ago
Raghad
• 0
0
votes
1
reply
732
views
How to arrange multiple plots into one page in NOISeq?
noiseq
RNA-seq
quality control
updated 3 days ago by
baptiste.bidon
• 0 • written 4.7 years ago by
ag1805x
▴ 80
1
vote
1
reply
83
views
Documenting resources in an `ExperimentHub` package?
AnnotationHub
ExperimentHub
updated 3 days ago by
James W. MacDonald
66k • written 4 days ago by
Tim Barry
• 0
0
votes
0
replies
36
views
Conditional analysis
GENESIS
3 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
234
views
Visium RNA
metaMSdata
written 9 weeks ago by
Karlison
• 0
0
votes
2
replies
761
views
Help with ENmix readidat
ENmix
IlluminaHumanMethylationEPICmanifest
updated 4 days ago by
James W. MacDonald
66k • written 2.0 years ago by
Daphna
• 0
1
vote
3
replies
145
views
LRT, more than two conditions and pairwise comparisons
DESeq2
updated 4 days ago by
James W. MacDonald
66k • written 5 days ago by
boczniak767
▴ 720
2
votes
4
replies
220
views
DESeq2- Mysterious interaction suppresses DEGs
DESeq2
PCAplot
RNA-Seq
DesignModel
updated 4 days ago by
Michael Love
42k • written 7 days ago by
shaunpeterson
• 0
1
vote
2
replies
93
views
How to run allelic imbalance in apeglm
apeglm
updated 4 days ago by
Michael Love
42k • written 5 days ago by
euge.eugenio
▴ 20
0
votes
6
replies
605
views
Numerical differences in DESeq2 output depending on different design matrix construction
DESeq2
7 days ago • updated 4 days ago
Ken C
• 0
0
votes
1
reply
84
views
ERROR; return code from pthread_create() is 22
affy
updated 4 days ago by
James W. MacDonald
66k • written 6 days ago by
pickingastar
• 0
1
vote
1
reply
190
views
How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC
BatchEffect
RNASeq
updated 4 days ago by
James W. MacDonald
66k • written 4 days ago by
ttt
• 0
1
vote
1
reply
89
views
Control group between 2 batches have different expression in RNAseq data
BatchQC
BatchEffect
rnaseqGene
Normalization
updated 4 days ago by
James W. MacDonald
66k • written 4 days ago by
Đình Vinh
• 0
0
votes
0
replies
31
views
Job:
Post-Doc: Development of a new method to study the distribution of the effect sizes of QTL
StatisticalMethod
Evolution
QuantitativeTrailLocus
Genetics
JobPosting
4 days ago
pierre.devillemereuil
• 0
181 results • Page
1 of 4
Recent ...
Replies
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…
Answer: GSVA function
by
Robert Castelo
★ 3.3k
Hi, We recommend to input normalized expression values in logarithmic scale to GSVA. We also recommend to use the latest release of the …
Comment: Cannot install oligo on Fedora
by
Guido Hooiveld
★ 4.0k
Aha, that is a good one! Starting from release 40, as I just found out, Fedora apparently is not including/using `zlib` as such anymore, b…
Votes
Answer: How to run allelic imbalance in apeglm
Answer: Not able to install any Bioconductor 3.18 package [unable to access index]
Answer: Documenting resources in an `ExperimentHub` package?
Answer: Not able to install any Bioconductor 3.18 package [unable to access index]
Seurat/DESeq2 - single cell RNA-seq differential expression
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