0
votes
4
replies
12k
views
SingleR Label.Ont
SingleR
updated 18 hours ago by • 0 • written 8 months ago by • 0
8
votes
41
replies
5.9k
views
Ensembl plants at annotationHub?
ensembl ensembldb plant arabidopsis thaliana annotationhub
updated 3 days ago by • 0 • written 5.5 years ago by ★ 4.0k
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 ▴ 30 • written 5.0 years ago by ▴ 160
1
vote
3
replies
2.8k
views
WGNCA kME vs. kIM
WGCNA
updated 2 days ago by • 0 • written 8.7 years ago by ▴ 30
10
votes
11
replies
1.9k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq rnaseq
updated 3 days ago by • 0 • written 6.8 years ago by ▴ 80
2
votes
4
replies
1.8k
views
slingshot: error with plot3d.SlingshotDataSet
slingshot plot3d.SlingshotDataSet
updated 2 days ago by • 0 • written 23 months ago by ▴ 10
1
vote
8
replies
1.8k
views
enrichGOgradient color change
clusterProfiler
updated 1 day ago by • 0 • written 6 months ago by • 0
1
vote
4
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1.6k
views
conumee with Infinium MethylationEPIC v2.0
MethylationEPICv2.0 conumee
updated 1 hour ago by • 0 • written 14 months ago by ▴ 50
4
votes
11
replies
1.6k
views
can't open mghp.osn.xsede.org
GenomeInfoDbData genomeinfodbdata
updated 2 days ago by ▴ 120 • written 9 months ago by ▴ 60
4
votes
3
replies
1.0k
views
BayesSpace parameters for DLPFC Visium data
BayesSpace
written 3.1 years ago by ▴ 30
3
votes
7
replies
912
views
Genes in open chromatin region
ChIPpeakAnno DiffBind
written 8 months ago by ▴ 10
0
votes
2
replies
762
views
Help with ENmix readidat
ENmix IlluminaHumanMethylationEPICmanifest
updated 4 days ago by 66k • written 2.0 years ago by • 0
0
votes
1
reply
733
views
How to arrange multiple plots into one page in NOISeq?
noiseq RNA-seq quality control
updated 3 days ago by • 0 • written 4.8 years ago by ▴ 80
7
votes
6
replies
673
views
Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it does not happen in Linux
GenomAutomorphism
written 19 days ago by • 0
0
votes
6
replies
606
views
Numerical differences in DESeq2 output depending on different design matrix construction
DESeq2
8 days ago • updated 4 days ago Ken C • 0
0
votes
5
replies
419
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
24 days ago • updated 23 hours ago Ian D. ▴ 70
2
votes
4
replies
396
views
seqlevelsStyle() not working
ensembldb genomei GenomeInfoDb
written 3 months ago by ▴ 70
0
votes
7
replies
344
views
ChAMP installation issue
Cha ChAMP
updated 2 days ago by 66k • written 12 days ago by • 0
5
votes
6
replies
328
views
Not able to install any Bioconductor 3.18 package [unable to access index]
Install
updated 1 day ago by ▴ 120 • written 2 days ago by ▴ 140
0
votes
5
replies
263
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 • 0 • written 3 days ago by ▴ 10
0
votes
2
replies
235
views
Visium RNA
metaMSdata
written 9 weeks ago by • 0
0
votes
4
replies
227
views
Using featureCounts with SAF annotation file gives "Error: only GTF files contain additional attributes"
RNASeq Rsubread
updated 1 day ago by ★ 3.6k • written 1 day ago by • 0
2
votes
4
replies
221
views
DESeq2- Mysterious interaction suppresses DEGs
DESeq2 PCAplot RNA-Seq DesignModel
updated 4 days ago by 42k • written 7 days ago by • 0
0
votes
5
replies
190
views
all variables in design formula must be columns in colData (Deseq2) error
BatchQC batchinDeseq2. columnsincolData.
6 days ago • updated 4 days ago Galina • 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 66k • written 5 days ago by • 0
4
votes
3
replies
151
views
recount3 problem downloading data from source sra
recount3
updated 2 days ago by ★ 1.1k • written 3 days ago by ▴ 10
1
vote
8
replies
148
views
Slightly different count plots from R and spreadsheet
DESeq2 ggplot2
2 days ago boczniak767 ▴ 720
1
vote
3
replies
148
views
LRT, more than two conditions and pairwise comparisons
DESeq2
updated 4 days ago by 66k • written 5 days ago by ▴ 720
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 66k • written 2 days ago by ▴ 20
2
votes
2
replies
128
views
Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
3 days ago mohammedtoufiq91 ▴ 10
1
vote
2
replies
127
views
Subsetting RNAseq data | voomaByGroup()
limma
6 days ago • updated 4 days ago Anna • 0
0
votes
2
replies
115
views
Errors in chromosome annotation-biomaRt
org.Rn.eg.db biomaRt
4 days ago • updated 1 day ago landenshanie ▴ 40
0
votes
3
replies
113
views
Volcano plot of scRNA-seq data not "centered"
DESeq2
1 day ago • updated 12 hours ago tjl • 0
0
votes
3
replies
106
views
pathview error
KEGGgraph KEGG
updated 2 days ago by ★ 4.0k • written 3 days ago by • 0
1
vote
2
replies
97
views
How to run allelic imbalance in apeglm
apeglm
updated 4 days ago by 42k • written 5 days ago by ▴ 20
1
vote
1
reply
92
views
Control group between 2 batches have different expression in RNAseq data
BatchQC BatchEffect rnaseqGene Normalization
updated 4 days ago by 66k • written 5 days ago by • 0
2
votes
2
replies
89
views
unable to access bioconductor packages - qvalue installation failed...
Install
updated 1 day ago by 3.9k • written 2 days ago by ▴ 10
1
vote
1
reply
85
views
Documenting resources in an `ExperimentHub` package?
AnnotationHub ExperimentHub
updated 3 days ago by 66k • written 4 days ago by • 0
0
votes
1
reply
84
views
ERROR; return code from pthread_create() is 22
affy
updated 4 days ago by 66k • written 6 days ago by • 0
0
votes
4
replies
73
views
Cannot install oligo on Fedora
oligo source Install
updated 14 hours ago by 66k • written 18 hours ago by ★ 4.0k
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
56
views
Minor allele data from grch38 giving NAs from getBM ?
BioMartGOGeneSets allele_freq biomaRt getBM
7 days ago • updated 6 days ago Abiologist • 0
0
votes
2
replies
54
views
Cluster columns in Pheatmap
geneexp pheatmap heatmaps cluster
updated 20 hours ago by 66k • written 23 hours ago by • 0
0
votes
0
replies
46
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq scRNAseq
5 days ago Bibi • 0
0
votes
1
reply
45
views
Normalisation using clinical traits in RNA seq using DESeq2
DESeq2 clinicaltraits Normalization batchnormalisation
updated 23 hours ago by ★ 4.2k • written 23 hours ago by • 0
0
votes
1
reply
43
views
Error when running topGO with KS statistic and elim agorithm
topGO
updated 19 hours ago by 66k • written 1 day ago by • 0
0
votes
0
replies
40
views
Processing of curatedmetagenomics
curatedMetagenomicData
5 days ago Edward • 0
0
votes
0
replies
39
views
FindOverlaps, makeVennDiagram and "others"
ATACSeq peaks ATAC ChIPpeakAnno
3 days ago Raghad • 0
0
votes
0
replies
37
views
Conditional analysis
GENESIS
3 days ago SuperDad • 0
0
votes
1
reply
36
views
GSVA function
DESeq2 GSVA ssGSEA
updated 16 hours ago by ★ 3.3k • written 18 hours ago by • 0
59 results • Page 1 of 2
Recent ...
Replies
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…
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 …
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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