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0
votes
0
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13
views
Find exact GRanges match keeping metadata columns
plyranges
11 hours ago
alexis.weinreb
• 0
4
votes
2
replies
158
views
Unused arguments error without used arguments in GSVA?
GSVA
1 day ago • updated 14 hours ago
1sunmic2
• 0
0
votes
0
replies
16
views
News:
Mass Spectrometry and Proteomics with R/Bioconductor course
cadd.v1.6.hg38
1 day ago
info
▴ 10
0
votes
1
reply
72
views
Restricting differential binding analysis to only TSS-proximal regions
ChIP
csaw
updated 1 day ago by
Aaron Lun
★ 28k • written 2 days ago by
Luca
• 0
0
votes
0
replies
27
views
Batch Correction while implementing QSEA package
qsea
MEDIPS
MEDIPSData
DNAMethylation
1 day ago
User3088
• 0
0
votes
0
replies
17
views
News:
Announcing the GBCC2025 Logo Design Winner!
Community
Conference
GBCC2025
Bioconductor
1 day ago
Maria Doyle
▴ 100
0
votes
1
reply
64
views
building samplesheet and plot profile
DiffBind
1 day ago
yf
• 0
0
votes
0
replies
25
views
DBT JRF & PhD Scholar
BiologicalQuestion
OmicsMLRepoR
2 days ago
Manisha
• 0
0
votes
1
reply
120
views
I am having issues with bowtie2_build
genomes
bowtiew
Index
updated 2 days ago by
James W. MacDonald
67k • written 3 days ago by
eduardo.pastor
• 0
0
votes
1
reply
94
views
DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression
RNASeq
DESeq2
updated 2 days ago by
Michael Love
43k • written 3 days ago by
Sim
• 0
0
votes
0
replies
43
views
My DEXSeqDataSetFromSE is returning an Error, but all of my checks to seem to indicate that this error is not present
DifferentialSplicing
RNASeqData
DEXSeq
3 days ago
cftattersfield
• 0
1
vote
0
replies
85
views
News:
Bioconductor Course, Kenya 2025: Applications Open!
Events
Community
Training
Africa
Bioconductor
3 days ago
Maria Doyle
▴ 100
0
votes
1
reply
172
views
How to visualize these pathways using pathview
Salmo_salar
RNASeq
KEGG
pathview
updated 3 days ago by
Guido Hooiveld
★ 4.1k • written 3 days ago by
ingrid.h
• 0
2
votes
2
replies
370
views
Selection of correct coefficients or contrasts in DESeq2
DESeq2
updated 4 days ago by
swbarnes2
★ 1.4k • written 8 days ago by
Nathan
• 0
9
votes
3
replies
1.8k
views
Job:
Postdoc/RA position: Software Engineer For R and High-Performance Computing
JobPosting
CuratedAtlasQueryR
tidySpatialExperiment
tidyomics
tidySingleCellExperiment
written 7 months ago by
Stefano Mangiola
▴ 20
0
votes
4
replies
871
views
Why select top highly expressed genes based on normalized counts, but then plot VST-transformed values in DESeq2 pheatmap?
RNASeq
DESeq2
6 days ago • updated 3 days ago
Quang NN
▴ 10
1
vote
3
replies
411
views
Csaw normalization strategies - general inquiry
ChIPSeq
csaw
updated 4 days ago by
franknappi14
• 0 • written 7 days ago by
Luca
• 0
0
votes
2
replies
211
views
How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat
RNASeq
DESeq2
scRNAseq
6 days ago • updated 4 days ago
Quang NN
▴ 10
4
votes
9
replies
2.0k
views
Issues with seqlevelsStyle when making custom txdb objects for genomes/annotations from ToxoDB
txdbmaker
GenomeInfoDb
GenomicFeatures
Biostrings
gDNAx
updated 7 days ago by
Robert Castelo
★ 3.4k • written 6 weeks ago by
rohitsatyam102
▴ 20
0
votes
1
reply
131
views
WGCNA sample-data preprocessing order
Microarray
WGCNA
GeneExpression
updated 8 days ago by
ATpoint
★ 4.6k • written 12 days ago by
Reuben
• 0
0
votes
2
replies
129
views
WGCNA: Can we use high power (26) for signed network?
Networkanalysis
RNA-seqdata
Powerselection
WGCNA
11 days ago • updated 7 days ago
Vinesh
• 0
0
votes
1
reply
94
views
Ph.D. scholar
WGCNA
DataNormalization
MicroarrayData
updated 8 days ago by
ATpoint
★ 4.6k • written 8 days ago by
Harshul
• 0
0
votes
1
reply
120
views
Unable to find sample sheet file for ChAMP methylation data analysis
MethylationArray
MethylationArrayData
methylationArrayAnalysis
updated 8 days ago by
James W. MacDonald
67k • written 9 days ago by
Anki
• 0
0
votes
2
replies
257
views
How to generate circular cnetplot and color nodes and edges in the same plot ?
cnetplot
DESeq2
9 days ago • updated 7 days ago
Blandine
• 0
0
votes
4
replies
215
views
Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2
DifferentialExpression
RNASeqData
BatchEffect
10 days ago
georgeyu703
• 0
0
votes
1
reply
113
views
affymetrix
genomes
Annotation
updated 10 days ago by
James W. MacDonald
67k • written 11 days ago by
aurel.popa2011
• 0
0
votes
1
reply
162
views
Problems with GSEA
GSEABase
updated 10 days ago by
Guido Hooiveld
★ 4.1k • written 11 days ago by
Sidra.Gull
• 0
0
votes
1
reply
153
views
Error compiling Rbowtie2 in R-4.4 (Bioconductor 3.20 and probably 3.19)
Rbowtie
14 days ago • updated 11 days ago
ja.garcia
• 0
1
vote
1
reply
177
views
SingleCellExperiment convenience function for metadata+expression?
SpatialExperiment
SingleCellExperiment
SpatialFeatureExperiment
updated 11 days ago by
Peter Hickey
▴ 750 • written 15 days ago by
sarah.williams
• 0
0
votes
4
replies
384
views
How to sort negative log2FC or FC in RNAseq for GSEA?
DESeq2
GSEA
clusterProfiler
12 days ago • updated 10 days ago
Quang NN
▴ 10
2
votes
4
replies
362
views
EdgeR Biological CVs
edgeR
updated 8 days ago by
Gordon Smyth
52k • written 12 days ago by
James
• 0
0
votes
1
reply
232
views
Curiously shaped volcano plot with using oarfish + swish to do differential gene expression on long-read RNA-seq
fishpond
fish
updated 13 days ago by
Michael Love
43k • written 15 days ago by
brown.annaleigh
• 0
0
votes
0
replies
34
views
Problem with PCAtool as dependencie
COTAN
PCAtools
13 days ago
Silvia
• 0
1
vote
2
replies
229
views
Detecting genomic signatures of drug resistance breast cancer in transcriptomic data
TransOmicsData
signatureSearchData
StatisticalMethod
written 10 weeks ago by
olusolaxx
• 0
0
votes
2
replies
46k
views
SingleR Label.Ont
SingleR
written 16 months ago by
saeed.khalili
• 0
0
votes
0
replies
42
views
cnvEQTL : Error in cpm.default(y, lib.size = lib.size) : NA counts not allowed
CNVRanger
15 days ago
xiaofeiwang18266
▴ 50
2
votes
5
replies
721
views
Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
limma
edgeR
biomaRt
updated 15 days ago by
James W. MacDonald
67k • written 15 days ago by
Jonathan
▴ 10
0
votes
1
reply
114
views
XCMS Data Processing
r
xcms
metabolomi
NTA
Metabolomics
updated 15 days ago by
James W. MacDonald
67k • written 17 days ago by
raklein
• 0
0
votes
2
replies
238
views
Error using useMart or useEnsembl
biomaRt
updated 15 days ago by
James W. MacDonald
67k • written 16 days ago by
rayanelkholdi
• 0
2
votes
1
reply
539
views
Error in download.file for TCGAutils::symbolsToRanges
TCGAutils
updated 15 days ago by
James W. MacDonald
67k • written 16 days ago by
xiaofeiwang18266
▴ 50
0
votes
11
replies
649
views
Problems with oarfish + tximport + swish
fishpond
tximport
tximeta
updated 12 days ago by
Im
• 0 • written 16 days ago by
brown.annaleigh
• 0
0
votes
2
replies
247
views
DESeq2 Heatmap
heatmaps
updated 16 days ago by
swbarnes2
★ 1.4k • written 17 days ago by
pm_25
• 0
0
votes
4
replies
307
views
Biomart and ensembl not working?
ensembldb
biomaRt
updated 16 days ago by
James W. MacDonald
67k • written 17 days ago by
Zuzer
• 0
0
votes
1
reply
112
views
Unknown gene transcripts after annotatr
annotatr
updated 16 days ago by
James W. MacDonald
67k • written 17 days ago by
Zach
• 0
0
votes
1
reply
100
views
Improve performance of qusage aggregateGeneSet
qusage
updated 17 days ago by
James W. MacDonald
67k • written 17 days ago by
oliverd
• 0
0
votes
0
replies
92
views
gsameth GSA: probe annotation to multiple genes
missMethyl
gsameth
18 days ago
nurkenber
• 0
0
votes
0
replies
126
views
Testing Differential Expression with Interaction Effect Between Categorical and Continuous Variable with Repeated (Paired) Measures using variancePar…
limma
variancePartition
18 days ago
GJ
• 0
0
votes
1
reply
98
views
promoters_txdb <- promoters(txdb, upstream = 2000) is not 2000
TxDb.Hsapiens.UCSC.hg38.knownGene
updated 18 days ago by
James W. MacDonald
67k • written 19 days ago by
linouhao
▴ 20
0
votes
0
replies
84
views
News:
Online course: Gene set enrichment analysis in R/Bioconductor
GSEABenchmarkeR
20 days ago
info
▴ 10
0
votes
1
reply
159
views
org.Hs.eg.db issue
org.Hs.eg.db
updated 18 days ago by
shepherl
4.1k • written 20 days ago by
k.panov
• 0
46,311 results • Page
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Comment: Unused arguments error without used arguments in GSVA?
by
1sunmic2
• 0
It was due to the comma. Thank you!
Answer: Unused arguments error without used arguments in GSVA?
by
Axel Klenk
★ 1.1k
Hi, here is a good place to ask questions when encountering problems with GSVA. I cannot reproduce this behaviour with the current release…
Answer: Restricting differential binding analysis to only TSS-proximal regions
by
Aaron Lun
★ 28k
Seems reasonable to filter out windows outside of the TSS if you don't care about those events. IIRC the `discard` option will ignore any f…
Comment: Sample-specific methylation values using QSEA
by
User3088
• 0
Thanks Simon. I got the sample-specific methylation values by using '**samples=getSampleNames**' ``` result=makeTable(qs=prad_QSEAset, glm=…
Comment: input for singR function
by
iamin053
• 0
Hi Paria, I'm wondering if you were able to get an answer on this please. I would greatly appreciate any comments!
Votes
Answer: Unused arguments error without used arguments in GSVA?
Answer: Unused arguments error without used arguments in GSVA?
Answer: Unused arguments error without used arguments in GSVA?
Unused arguments error without used arguments in GSVA?
Answer: Is it always preferable to recount library sizes of DGEList object in edgeR afte
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