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affymetrix
genomes
Annotation
just now
aurel.popa2011
• 0
0
votes
2
replies
53
views
How to sort negative log2FC or FC in RNAseq for GSEA?
DESeq2
GSEA
clusterProfiler
8 hours ago • updated 1 hour ago
QN
▴ 10
2
votes
4
replies
170
views
EdgeR Biological CVs
edgeR
updated 4 hours ago by
ATpoint
★ 4.6k • written 23 hours ago by
James
• 0
0
votes
0
replies
23
views
WGCNA sample-data preprocessing order
Microarray
WGCNA
GeneExpression
1 day ago
Reuben
• 0
0
votes
1
reply
196
views
Curiously shaped volcano plot with using oarfish + swish to do differential gene expression on long-read RNA-seq
fishpond
fish
updated 1 day ago by
Michael Love
43k • written 3 days ago by
brown.annaleigh
• 0
0
votes
0
replies
21
views
Problem with PCAtool as dependencie
COTAN
PCAtools
2 days ago
Silvia
• 0
0
votes
0
replies
32
views
Error compiling Rbowtie2 in R-4.4 (Bioconductor 3.20 and probably 3.19)
Rbowtie
3 days ago
ja.garcia
• 0
1
vote
2
replies
200
views
Detecting genomic signatures of drug resistance breast cancer in transcriptomic data
TransOmicsData
signatureSearchData
StatisticalMethod
written 8 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
26
views
cnvEQTL : Error in cpm.default(y, lib.size = lib.size) : NA counts not allowed
CNVRanger
3 days ago
xiaofeiwang18266
▴ 50
0
votes
0
replies
45
views
SingleCellExperiment convenience function for metadata+expression?
SpatialExperiment
SingleCellExperiment
SpatialFeatureExperiment
3 days ago
sarah.williams
• 0
2
votes
5
replies
633
views
Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
limma
edgeR
biomaRt
updated 3 days ago by
James W. MacDonald
67k • written 4 days ago by
Jonathan
▴ 10
0
votes
1
reply
88
views
XCMS Data Processing
r
xcms
metabolomi
NTA
Metabolomics
updated 4 days ago by
James W. MacDonald
67k • written 5 days ago by
raklein
• 0
0
votes
2
replies
137
views
Error using useMart or useEnsembl
biomaRt
updated 4 days ago by
James W. MacDonald
67k • written 4 days ago by
rayanelkholdi
• 0
2
votes
1
reply
274
views
Error in download.file for TCGAutils::symbolsToRanges
TCGAutils
updated 4 days ago by
James W. MacDonald
67k • written 4 days ago by
xiaofeiwang18266
▴ 50
0
votes
12
replies
558
views
Problems with oarfish + tximport + swish
fishpond
tximport
tximeta
updated 6 hours ago by
Im
• 0 • written 5 days ago by
brown.annaleigh
• 0
0
votes
2
replies
205
views
DESeq2 Heatmap
heatmaps
updated 5 days ago by
swbarnes2
★ 1.4k • written 5 days ago by
pm_25
• 0
0
votes
4
replies
228
views
Biomart and ensembl not working?
ensembldb
biomaRt
updated 5 days ago by
James W. MacDonald
67k • written 5 days ago by
Zuzer
• 0
0
votes
1
reply
85
views
Unknown gene transcripts after annotatr
annotatr
updated 5 days ago by
James W. MacDonald
67k • written 5 days ago by
Zach
• 0
0
votes
1
reply
82
views
Improve performance of qusage aggregateGeneSet
qusage
updated 5 days ago by
James W. MacDonald
67k • written 6 days ago by
oliverd
• 0
0
votes
0
replies
62
views
gsameth GSA: probe annotation to multiple genes
missMethyl
gsameth
6 days ago
nurkenber
• 0
0
votes
0
replies
59
views
Testing Differential Expression with Interaction Effect Between Categorical and Continuous Variable with Repeated (Paired) Measures using variancePar…
limma
variancePartition
7 days ago
GJ
• 0
0
votes
1
reply
73
views
promoters_txdb <- promoters(txdb, upstream = 2000) is not 2000
TxDb.Hsapiens.UCSC.hg38.knownGene
updated 7 days ago by
James W. MacDonald
67k • written 7 days ago by
linouhao
▴ 20
0
votes
0
replies
48
views
News:
Online course: Gene set enrichment analysis in R/Bioconductor
GSEABenchmarkeR
8 days ago
info
▴ 10
0
votes
1
reply
130
views
org.Hs.eg.db issue
org.Hs.eg.db
updated 7 days ago by
shepherl
4.1k • written 9 days ago by
k.panov
• 0
0
votes
2
replies
347
views
Paired analysis in proteomics data for DE while interested in only a particular subset of the data
limma
modelmatrix
pairedanalysis
Proteomics
written 10 days ago by
svlachavas
▴ 840
0
votes
2
replies
215
views
iam not able to do retrive data using GEOquery R package
HELP
updated 10 days ago by
James W. MacDonald
67k • written 10 days ago by
ramya20kumar20
• 0
2
votes
5
replies
283
views
Differential variability modelling with vst() expression
limma
DESeq2
written 10 days ago by
jtsy6383
• 0
0
votes
2
replies
122
views
Installation error for Rsamtools.
Rsamtools
updated 10 days ago by
ATpoint
★ 4.6k • written 11 days ago by
Sheila
• 0
2
votes
8
replies
501
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 10 days ago by
James W. MacDonald
67k • written 11 days ago by
Nicholas
• 0
0
votes
2
replies
342
views
DESeq2 analysis with transcript counts
Transcriptomics
RNASeq
DESeq2
11 days ago • updated 9 days ago
sindhuri
• 0
0
votes
0
replies
51
views
Issue when attempting to use output from DECIPHER IDtaxa (pr2 V5) with dada2/phyloseq
DECIPHER
taxonomyassignment
phyloseq
dada2
Pr2V5
12 days ago
Maggie
• 0
2
votes
9
replies
709
views
Why did PCA plots look exactly the same after adjusting for batch covariate in DESeq2 design?
DESeq2
BatchEffect
12 days ago • updated 8 hours ago
QN
▴ 10
0
votes
5
replies
217
views
Diffbind interpretation of data - fold change
DiffBind
13 days ago
Vera
• 0
1
vote
1
reply
270
views
Considerations behind the choice of RNAseq Differential Expression Analysis Tools
fishpond
DESeq2
rnaseqDTU
updated 13 days ago by
Michael Love
43k • written 13 days ago by
muhammadsohailraza
• 0
0
votes
1
reply
79
views
No preprocessing allowed for EPICv2 with DMRcate
missMethyl
DMRcate
updated 13 days ago by
James W. MacDonald
67k • written 13 days ago by
maximuscfyeung
• 0
1
vote
2
replies
340
views
Package `not available for Bioconductor version '3.20'` when it should be
consensusOV
genefu
13 days ago
Levi Waldron
★ 1.1k
0
votes
0
replies
47
views
Trouble with double delimiters in .fcs file (flowCore package)
flowCore
FlowCytometry
FlowCytometryData
14 days ago
vpochic
• 0
0
votes
4
replies
214
views
Newbie Question - adding metadata to an analysis
Biobase
14 days ago • updated 12 days ago
Bryan H
• 0
0
votes
1
reply
149
views
Want numbers in DESeq to be seen as numerical, not categorical
DESeq2
updated 14 days ago by
swbarnes2
★ 1.4k • written 14 days ago by
natalievillafranca
• 0
0
votes
2
replies
245
views
MissMethyl failed to use gometh function for EPICv2
missMethyl
EPICv2manifest
updated 14 days ago by
James W. MacDonald
67k • written 14 days ago by
maximuscfyeung
• 0
0
votes
1
reply
106
views
Correlation between gene clusters
genomes
RNASeqData
written 14 days ago by
Le
• 0
0
votes
2
replies
210
views
Mean variance curve troubleshoot filtering
limmavoom
filtering
edgeR
RNASeqData
meanvariancetrend
15 days ago • updated 13 days ago
gingergeiger22
• 0
0
votes
0
replies
66
views
Error ("could not find function "EM_estimate"") when running ENmix mpreprocess() on Microsoft Azure
Preprocessing
ENmix
16 days ago
balf0020
• 0
0
votes
1
reply
332
views
Please, I desperately need help with DESeq2. Three groups of repeated measures with two timepoints... (plus an additional group)
edgeR
DESeq2
updated 16 days ago by
Michael Love
43k • written 27 days ago by
Jimmy Mak
• 0
2
votes
1
reply
335
views
Is it possible to work with DESeq2 where data is not properly matched for sex and age
DESeq2
RNASeqData
updated 16 days ago by
Michael Love
43k • written 24 days ago by
KR
• 0
0
votes
1
reply
1.3k
views
How to increase font for gene name and increase arrow size for GVIZ's ( UcscTrack function ) track?
DMRcate
Gviz
updated 18 days ago by
ming
• 0 • written 3.1 years ago by
Ahdee
▴ 50
6
votes
5
replies
525
views
How do I fix an odd voom plot in a combined dataset?
limma
Normalization
voom
updated 13 days ago by
James W. MacDonald
67k • written 19 days ago by
1sunmic2
• 0
1
vote
8
replies
800
views
Incorporating Salmon offset matrix into Wilcoxon DEG analysis
edgeR
20 days ago • updated 12 days ago
Andre
• 0
0
votes
2
replies
252
views
DESeq error: counts matrix should be numeric, currently it has mode: character
DESeq2
22 days ago • updated 20 days ago
Kucsera
• 0
46,299 results • Page
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Comment: How to sort negative log2FC or FC in RNAseq for GSEA?
by
QN
▴ 10
Thank you ATpoint for your response! In the result of GSEA, like you indicated, there will be gene sets that have positive NES and gene se…
Comment: EdgeR Biological CVs
by
ATpoint
★ 4.6k
"Joseph" is a spam bot...
Comment: Problems with oarfish + tximport + swish
by
Im
• 0
Office ta kemon
Answer: How to sort negative log2FC or FC in RNAseq for GSEA?
by
ATpoint
★ 4.6k
GSEA asks whether there are general shifts in gene expression towards certain terms. Hence, you would not split your results tables but ord…
Comment: EdgeR Biological CVs
by
James
• 0
Thank you Gordon and Joseph. I presume question (1) would be answered by using a prior G0 of 0? For question (2), I was expecting a biolog…
Votes
How to correct for tumor purity using DESeq2 to analyze TCGA tumor sample expression.
Answer: EdgeR Biological CVs
Comment: EdgeR Biological CVs
Answer: Error in download.file for TCGAutils::symbolsToRanges
Answer: Error in download.file for TCGAutils::symbolsToRanges
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