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Votes
2
votes
2
replies
418
views
Selection of correct coefficients or contrasts in DESeq2
DESeq2
updated 21 days ago by
swbarnes2
★ 1.4k • written 24 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 8 months ago by
Stefano Mangiola
▴ 20
0
votes
4
replies
923
views
Why select top highly expressed genes based on normalized counts, but then plot VST-transformed values in DESeq2 pheatmap?
RNASeq
DESeq2
23 days ago • updated 20 days ago
Quang NN
▴ 10
1
vote
3
replies
641
views
Csaw normalization strategies - general inquiry
ChIPSeq
csaw
updated 21 days ago by
franknappi14
• 0 • written 24 days ago by
Luca
• 0
4
votes
9
replies
2.1k
views
Issues with seqlevelsStyle when making custom txdb objects for genomes/annotations from ToxoDB
txdbmaker
GenomeInfoDb
GenomicFeatures
Biostrings
gDNAx
updated 24 days ago by
Robert Castelo
★ 3.4k • written 8 weeks ago by
rohitsatyam102
▴ 20
0
votes
1
reply
165
views
WGCNA sample-data preprocessing order
Microarray
WGCNA
GeneExpression
updated 24 days ago by
ATpoint
★ 4.7k • written 29 days ago by
Reuben
• 0
0
votes
2
replies
170
views
WGCNA: Can we use high power (26) for signed network?
Networkanalysis
RNA-seqdata
Powerselection
WGCNA
28 days ago • updated 24 days ago
Vinesh
• 0
0
votes
1
reply
121
views
Ph.D. scholar
WGCNA
DataNormalization
MicroarrayData
updated 24 days ago by
ATpoint
★ 4.7k • written 25 days ago by
Harshul
• 0
0
votes
1
reply
146
views
Unable to find sample sheet file for ChAMP methylation data analysis
MethylationArray
MethylationArrayData
methylationArrayAnalysis
updated 25 days ago by
James W. MacDonald
68k • written 26 days ago by
Anki
• 0
0
votes
2
replies
340
views
How to generate circular cnetplot and color nodes and edges in the same plot ?
cnetplot
DESeq2
26 days ago • updated 24 days ago
Blandine
• 0
0
votes
5
replies
302
views
Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2
DifferentialExpression
RNASeqData
BatchEffect
written 27 days ago by
georgeyu703
• 0
0
votes
1
reply
132
views
affymetrix
genomes
Annotation
updated 27 days ago by
James W. MacDonald
68k • written 28 days ago by
aurel.popa2011
• 0
0
votes
1
reply
283
views
Problems with GSEA
GSEABase
updated 27 days ago by
Guido Hooiveld
★ 4.1k • written 27 days ago by
Sidra.Gull
• 0
0
votes
1
reply
202
views
Error compiling Rbowtie2 in R-4.4 (Bioconductor 3.20 and probably 3.19)
Rbowtie
4 weeks ago • updated 28 days ago
ja.garcia
• 0
1
vote
1
reply
216
views
SingleCellExperiment convenience function for metadata+expression?
SpatialExperiment
SingleCellExperiment
SpatialFeatureExperiment
updated 28 days ago by
Peter Hickey
▴ 750 • written 4 weeks ago by
sarah.williams
• 0
0
votes
4
replies
435
views
How to sort negative log2FC or FC in RNAseq for GSEA?
DESeq2
GSEA
clusterProfiler
28 days ago • updated 27 days ago
Quang NN
▴ 10
2
votes
4
replies
434
views
EdgeR Biological CVs
edgeR
updated 25 days ago by
Gordon Smyth
52k • written 29 days ago by
James
• 0
0
votes
1
reply
267
views
Curiously shaped volcano plot with using oarfish + swish to do differential gene expression on long-read RNA-seq
fishpond
fish
updated 4 weeks ago by
Michael Love
43k • written 4 weeks ago by
brown.annaleigh
• 0
0
votes
0
replies
52
views
Problem with PCAtool as dependencie
COTAN
PCAtools
4 weeks ago
Silvia
• 0
1
vote
2
replies
254
views
Detecting genomic signatures of drug resistance breast cancer in transcriptomic data
TransOmicsData
signatureSearchData
StatisticalMethod
written 12 weeks ago by
olusolaxx
• 0
0
votes
2
replies
47k
views
SingleR Label.Ont
SingleR
written 17 months ago by
saeed.khalili
• 0
0
votes
0
replies
63
views
cnvEQTL : Error in cpm.default(y, lib.size = lib.size) : NA counts not allowed
CNVRanger
4 weeks ago
xiaofeiwang18266
▴ 50
2
votes
5
replies
776
views
Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
limma
edgeR
biomaRt
updated 4 weeks ago by
James W. MacDonald
68k • written 4 weeks ago by
Jonathan
▴ 10
0
votes
1
reply
148
views
XCMS Data Processing
r
xcms
metabolomi
NTA
Metabolomics
updated 4 weeks ago by
James W. MacDonald
68k • written 4 weeks ago by
raklein
• 0
0
votes
2
replies
377
views
Error using useMart or useEnsembl
biomaRt
updated 4 weeks ago by
James W. MacDonald
68k • written 4 weeks ago by
rayanelkholdi
• 0
2
votes
1
reply
564
views
Error in download.file for TCGAutils::symbolsToRanges
TCGAutils
updated 4 weeks ago by
James W. MacDonald
68k • written 4 weeks ago by
xiaofeiwang18266
▴ 50
0
votes
11
replies
706
views
Problems with oarfish + tximport + swish
fishpond
tximport
tximeta
updated 28 days ago by
Im
• 0 • written 4 weeks ago by
brown.annaleigh
• 0
0
votes
2
replies
312
views
DESeq2 Heatmap
heatmaps
updated 4 weeks ago by
swbarnes2
★ 1.4k • written 4 weeks ago by
pm_25
• 0
0
votes
4
replies
465
views
Biomart and ensembl not working?
ensembldb
biomaRt
updated 4 weeks ago by
James W. MacDonald
68k • written 4 weeks ago by
Zuzer
• 0
0
votes
1
reply
136
views
Unknown gene transcripts after annotatr
annotatr
updated 4 weeks ago by
James W. MacDonald
68k • written 4 weeks ago by
Zach
• 0
0
votes
1
reply
128
views
Improve performance of qusage aggregateGeneSet
qusage
updated 4 weeks ago by
James W. MacDonald
68k • written 4 weeks ago by
oliverd
• 0
0
votes
0
replies
111
views
gsameth GSA: probe annotation to multiple genes
missMethyl
gsameth
5 weeks ago • updated 4 weeks ago
nurkenber
• 0
0
votes
0
replies
148
views
Testing Differential Expression with Interaction Effect Between Categorical and Continuous Variable with Repeated (Paired) Measures using variancePar…
limma
variancePartition
5 weeks ago
GJ
• 0
0
votes
1
reply
114
views
promoters_txdb <- promoters(txdb, upstream = 2000) is not 2000
TxDb.Hsapiens.UCSC.hg38.knownGene
updated 5 weeks ago by
James W. MacDonald
68k • written 5 weeks ago by
linouhao
▴ 20
0
votes
0
replies
108
views
News:
Online course: Gene set enrichment analysis in R/Bioconductor
GSEABenchmarkeR
5 weeks ago
info
▴ 10
0
votes
1
reply
192
views
org.Hs.eg.db issue
org.Hs.eg.db
updated 5 weeks ago by
shepherl
4.1k • written 5 weeks ago by
k.panov
• 0
0
votes
2
replies
399
views
Paired analysis in proteomics data for DE while interested in only a particular subset of the data
limma
modelmatrix
pairedanalysis
Proteomics
written 5 weeks ago by
svlachavas
▴ 840
0
votes
2
replies
350
views
iam not able to do retrive data using GEOquery R package
HELP
updated 5 weeks ago by
James W. MacDonald
68k • written 5 weeks ago by
ramya20kumar20
• 0
2
votes
5
replies
357
views
Differential variability modelling with vst() expression
limma
DESeq2
written 5 weeks ago by
jtsy6383
• 0
0
votes
2
replies
176
views
Installation error for Rsamtools.
Rsamtools
updated 5 weeks ago by
ATpoint
★ 4.7k • written 5 weeks ago by
Sheila
• 0
2
votes
9
replies
716
views
Different annotation packages (org.Mm.eg.db, EnsDb.Mmusculus.v79, BiomaRt) returning drastically different numbers of transcripts
AnnotationDbi
EnsDb.Mmusculus.v79
biomaRt
org.Mm.eg.db
updated 13 days ago by
franknappi14
• 0 • written 5 weeks ago by
Nicholas
• 0
0
votes
3
replies
510
views
DESeq2 analysis with transcript counts
Transcriptomics
RNASeq
DESeq2
written 5 weeks ago by
sindhuri
• 0
0
votes
0
replies
87
views
Issue when attempting to use output from DECIPHER IDtaxa (pr2 V5) with dada2/phyloseq
DECIPHER
taxonomyassignment
phyloseq
dada2
Pr2V5
5 weeks ago
Maggie
• 0
2
votes
9
replies
885
views
Why did PCA plots look exactly the same after adjusting for batch covariate in DESeq2 design?
DESeq2
BatchEffect
5 weeks ago • updated 28 days ago
Quang NN
▴ 10
0
votes
5
replies
307
views
Diffbind interpretation of data - fold change
DiffBind
5 weeks ago
Vera
• 0
1
vote
1
reply
351
views
Considerations behind the choice of RNAseq Differential Expression Analysis Tools
fishpond
DESeq2
rnaseqDTU
updated 5 weeks ago by
Michael Love
43k • written 5 weeks ago by
muhammadsohailraza
• 0
0
votes
1
reply
149
views
No preprocessing allowed for EPICv2 with DMRcate
missMethyl
DMRcate
updated 5 weeks ago by
James W. MacDonald
68k • written 6 weeks ago by
maximuscfyeung
• 0
1
vote
2
replies
889
views
Package `not available for Bioconductor version '3.20'` when it should be
consensusOV
genefu
5 weeks ago
Levi Waldron
★ 1.1k
0
votes
0
replies
86
views
Trouble with double delimiters in .fcs file (flowCore package)
flowCore
FlowCytometry
FlowCytometryData
6 weeks ago
vpochic
• 0
0
votes
4
replies
296
views
Newbie Question - adding metadata to an analysis
Biobase
6 weeks ago • updated 5 weeks ago
Bryan H
• 0
1,000 results • Page
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Comment: For some reason I can't update BiocManager to 3.20
by
azm.ana2
• 0
Sorry i apologize for the delay. Thank you very much for the answer. I have two supervisers and the one who knows about the computer is com…
Comment: For some reason I can't update BiocManager to 3.20
by
azm.ana2
• 0
Sorry i apologize for the delay. Thank you very much for the answer. I have two supervisers and the one who knows about the computer is com…
Answer: Welcome Bonus of USD 999 for free, join today!
by
xihaxiw582
• 0
Hello! If you're looking for online casinos where you can start playing with a small deposit, I recently found a great resource. Check out …
Answer: SingleR with multiple single cell references
by
Aaron Lun
★ 28k
> Is it necessary to piece together the individual steps manually (e.g. aggregateReference, trainSingleR, classifySingleR, combineRecompute…
Answer: Automatically install dependencies
by
ATpoint
★ 4.7k
The BiocManager, which is sort of an extended wrapper around `install.packages`, installs all R dependencies. If you see errors then this i…
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Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
A: Volcanoplot with limma - RAW P-values or Adj.P-Values
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