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0
votes
0
replies
4
views
Biomart and ensembl not working?
ensembldb
biomaRt
46 minutes ago
Zuzer
• 0
0
votes
1
reply
37
views
DESeq2 Heatmap
heatmaps
updated 4 hours ago by
James W. MacDonald
67k • written 5 hours ago by
pm_25
• 0
0
votes
1
reply
36
views
Improve performance of qusage aggregateGeneSet
qusage
updated 6 hours ago by
James W. MacDonald
67k • written 8 hours ago by
oliverd
• 0
0
votes
0
replies
20
views
XCMS Data Processing
r
xcms
metabolomi
NTA
Metabolomics
7 hours ago
raklein
• 0
0
votes
0
replies
39
views
gsameth GSA: probe annotation to multiple genes
missMethyl
gsameth
1 day ago • updated 17 hours ago
nurkenber
• 0
0
votes
0
replies
21
views
Testing Differential Expression with Interaction Effect Between Categorical and Continuous Variable with Repeated (Paired) Measures using variancePar…
limma
variancePartition
1 day ago
GJ
• 0
0
votes
1
reply
55
views
promoters_txdb <- promoters(txdb, upstream = 2000) is not 2000
TxDb.Hsapiens.UCSC.hg38.knownGene
updated 1 day ago by
James W. MacDonald
67k • written 1 day ago by
linouhao
▴ 20
0
votes
0
replies
29
views
News:
Online course: Gene set enrichment analysis in R/Bioconductor
GSEABenchmarkeR
2 days ago
info
▴ 10
0
votes
1
reply
104
views
org.Hs.eg.db issue
org.Hs.eg.db
updated 1 day ago by
shepherl
4.1k • written 3 days ago by
k.panov
• 0
0
votes
2
replies
329
views
Paired analysis in proteomics data for DE while interested in only a particular subset of the data
limma
modelmatrix
pairedanalysis
Proteomics
written 4 days ago by
svlachavas
▴ 840
0
votes
2
replies
194
views
iam not able to do retrive data using GEOquery R package
HELP
updated 4 days ago by
James W. MacDonald
67k • written 4 days ago by
ramya20kumar20
• 0
2
votes
4
replies
219
views
Differential variability modelling with vst() expression
limma
DESeq2
updated 4 days ago by
Michael Love
43k • written 5 days ago by
jtsy6383
• 0
0
votes
2
replies
103
views
Installation error for Rsamtools.
Rsamtools
updated 4 days ago by
ATpoint
★ 4.6k • written 5 days ago by
Sheila
• 0
2
votes
8
replies
455
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 4 days ago by
James W. MacDonald
67k • written 5 days ago by
Nicholas
• 0
0
votes
2
replies
304
views
DESeq2 analysis with transcript counts
Transcriptomics
RNASeq
DESeq2
6 days ago • updated 3 days ago
sindhuri
• 0
0
votes
0
replies
43
views
Issue when attempting to use output from DECIPHER IDtaxa (pr2 V5) with dada2/phyloseq
DECIPHER
taxonomyassignment
phyloseq
dada2
Pr2V5
6 days ago
Maggie
• 0
2
votes
8
replies
544
views
Why did PCA plots look exactly the same after adjusting for batch covariate in DESeq2 design?
DESeq2
BatchEffect
6 days ago • updated 4 days ago
Quang
▴ 10
0
votes
5
replies
201
views
Diffbind interpretation of data - fold change
DiffBind
7 days ago
Vera
• 0
1
vote
1
reply
255
views
Considerations behind the choice of RNAseq Differential Expression Analysis Tools
fishpond
DESeq2
rnaseqDTU
updated 7 days ago by
Michael Love
43k • written 7 days ago by
muhammadsohailraza
• 0
0
votes
1
reply
69
views
No preprocessing allowed for EPICv2 with DMRcate
missMethyl
DMRcate
updated 7 days ago by
James W. MacDonald
67k • written 7 days ago by
maximuscfyeung
• 0
1
vote
2
replies
229
views
Package `not available for Bioconductor version '3.20'` when it should be
consensusOV
genefu
7 days ago
Levi Waldron
★ 1.1k
0
votes
0
replies
42
views
Trouble with double delimiters in .fcs file (flowCore package)
flowCore
FlowCytometry
FlowCytometryData
8 days ago
vpochic
• 0
0
votes
4
replies
195
views
Newbie Question - adding metadata to an analysis
Biobase
8 days ago • updated 6 days ago
Bryan H
• 0
0
votes
1
reply
133
views
Want numbers in DESeq to be seen as numerical, not categorical
DESeq2
updated 8 days ago by
swbarnes2
★ 1.4k • written 8 days ago by
natalievillafranca
• 0
0
votes
2
replies
222
views
MissMethyl failed to use gometh function for EPICv2
missMethyl
EPICv2manifest
updated 8 days ago by
James W. MacDonald
67k • written 8 days ago by
maximuscfyeung
• 0
0
votes
1
reply
94
views
Correlation between gene clusters
genomes
RNASeqData
written 9 days ago by
Le
• 0
0
votes
2
replies
180
views
Mean variance curve troubleshoot filtering
limmavoom
filtering
edgeR
RNASeqData
meanvariancetrend
10 days ago • updated 8 days ago
gingergeiger22
• 0
0
votes
0
replies
59
views
Error ("could not find function "EM_estimate"") when running ENmix mpreprocess() on Microsoft Azure
Preprocessing
ENmix
10 days ago
balf0020
• 0
0
votes
1
reply
325
views
Please, I desperately need help with DESeq2. Three groups of repeated measures with two timepoints... (plus an additional group)
edgeR
DESeq2
updated 11 days ago by
Michael Love
43k • written 21 days ago by
Jimmy Mak
• 0
2
votes
1
reply
329
views
Is it possible to work with DESeq2 where data is not properly matched for sex and age
DESeq2
RNASeqData
updated 11 days ago by
Michael Love
43k • written 18 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 12 days ago by
ming
• 0 • written 3.1 years ago by
Ahdee
▴ 50
6
votes
5
replies
513
views
How do I fix an odd voom plot in a combined dataset?
limma
Normalization
voom
updated 7 days ago by
James W. MacDonald
67k • written 13 days ago by
1sunmic2
• 0
1
vote
8
replies
773
views
Incorporating Salmon offset matrix into Wilcoxon DEG analysis
edgeR
15 days ago • updated 7 days ago
Andre
• 0
0
votes
2
replies
239
views
DESeq error: counts matrix should be numeric, currently it has mode: character
DESeq2
17 days ago • updated 15 days ago
Kucsera
• 0
0
votes
1
reply
165
views
combining raw counts and estimated counts
RNASeqData
GEO
TCGAbiolinks
updated 19 days ago by
O'Brien
• 0 • written 21 days ago by
Noor
• 0
0
votes
3
replies
1.2k
views
News:
EuroBioC2023 abstract submission closing soon!
presentation
EuroBioc2023
Conference
community
Bioconductor
written 21 months ago by
Maria Doyle
▴ 90
0
votes
5
replies
1.1k
views
News:
EuroBioC2024 abstract submission is open!
Conference
Bioconductor
EuroBioC2024
updated 19 days ago by
Alan Downey
• 0 • written 11 months ago by
Maria Doyle
▴ 90
0
votes
2
replies
434
views
Cross-validation with multiple control subgroups in limma
limma
multtest
25 days ago • updated 24 days ago
Ali Barry
▴ 40
1
vote
1
reply
355
views
Can DESeq2's design compensate for sequencing experimental design shortcomings?
DESeq2
updated 25 days ago by
Michael Love
43k • written 4 weeks ago by
txema.heredia
• 0
0
votes
0
replies
87
views
Job:
Postdoctoral Researcher in Spatial Gene Regulatory Networks underlying Stomatal Patterning
JobPosting
26 days ago
Jenny Drnevich
★ 2.0k
0
votes
1
reply
312
views
ChAMP.DMR error - Error in makeGenomicRatioSetFromMatrix
ChAMP
updated 19 days ago by
O'Brien
• 0 • written 27 days ago by
André
• 0
4
votes
8
replies
1.5k
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 27 days ago by
rohitsatyam102
▴ 20
1
vote
9
replies
765
views
Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma
DESeq2
edgeR
written 28 days ago by
anna.cot.anna.cot
▴ 30
0
votes
2
replies
228
views
Error in get_anno_data(ontology) : ontology not supported yet...
EnrichDO
28 days ago • updated 27 days ago
GODseeker
• 0
0
votes
2
replies
293
views
Standardization of rlog transformed counts before PCA
RNASeq
DESeq2
Visualization
updated 28 days ago by
ATpoint
★ 4.6k • written 4 weeks ago by
bbao
• 0
0
votes
2
replies
260
views
Build error on kunpeng2 Linux aarch64
Bioconductor
updated 13 days ago by
wise
• 0 • written 29 days ago by
Hongxiang
• 0
0
votes
3
replies
1.3k
views
Limma - using both array and spot weights in lmFit
Genetics
Genetics
written 17.7 years ago by
Jakob Hedegaard
▴ 170
0
votes
2
replies
449
views
Margins for gene_set_enrichment_plot
spatialLIBD
updated 4 weeks ago by
Leonardo Collado Torres
★ 1.1k • written 5 weeks ago by
Oliver
• 0
0
votes
1
reply
155
views
Errors running learn.bn function from Pigengene in windows environment
Pigengene
written 4 weeks ago by
Thomas
• 0
0
votes
1
reply
262
views
Need new version : tx2gene.gencode.v47.csv
tximportData
updated 4 weeks ago by
Guido Hooiveld
★ 4.1k • written 4 weeks ago by
gauravbcbp22
• 0
46,285 results • Page
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Answer: DESeq2 Heatmap
by
James W. MacDonald
67k
Two things. First, `scale` is already vectorized, so you don't have to use `apply`. You can instead just do `t(scale(t(mat)))` . Second, th…
Answer: Improve performance of qusage aggregateGeneSet
by
James W. MacDonald
67k
This support site is meant mostly to help people with questions about using Bioconductor packages rather than posting code improvements. I …
Answer: promoters_txdb <- promoters(txdb, upstream = 2000) is not 2000
by
James W. MacDonald
67k
If you use `promoters` and do not provide an argument for something that has a default, you will get the default argument. Your last call t…
Comment: org.Hs.eg.db issue
by
k.panov
• 0
installed R on another PC, works perfectly. ergo, problem outside of R probably..... :-(
Comment: MBDseq analysis using qsea package
by
Lukas
▴ 20
Hi, I checked in with Matthias and here is his response: You need to indicate "samples": "The indices of the samples for which individu…
Votes
Comment: DESeq2 for single cell pseudobulk processing
C: Limma: how to get same output as topTable but for all the genes ?
A: Processing agilent data by limma
A: Linear regression in DESeq2
Answer: Is there any chance to solve "the model matrix is not full rank" in DESeq2?
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