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cameraPR() non directional test
CAMERA
GeneSetEnrichment
5 hours ago
Hugo Varet
▴ 80
0
votes
1
reply
78
views
Use of limma R package with targeted proteomics for DE analysis
DEanalysis
limma
olinktargetedproteomics
updated 7 hours ago by
Gordon Smyth
52k • written 1 day ago by
svlachavas
▴ 840
0
votes
1
reply
94
views
Does anyone have the command to download all of the core_nt using blast_db_get()
BiocFileCache
12 hours ago • updated 10 hours ago
Matthew Thornton
▴ 380
1
vote
2
replies
220
views
normalizatino of dna methylation EPIC data
DNA
minfiData
minfiDataEPIC
DNAMethylation
minfi
1 day ago • updated 22 hours ago
user_bioinfo
• 0
0
votes
0
replies
31
views
Error in retrieving clinical data
TCGAbiolinks
23 hours ago
silickas
• 0
0
votes
2
replies
137
views
WGCNA
WGCNA
Normalization
RNASeq
updated 10 hours ago by
pammelala304
• 0 • written 1 day ago by
Vishnu
• 0
0
votes
0
replies
25
views
News:
EuroBioC2025: Abstract Submissions Open!
EuroBioC2025
Community
Conference
Bioconductor
1 day ago
Maria Doyle
▴ 100
0
votes
2
replies
849
views
News:
EuroBioC2023 abstract submission is open!
presentation
EuroBioC2023
Conference
community
Bioconductor
updated 1 day ago by
cirwin009
• 0 • written 24 months ago by
Maria Doyle
▴ 100
0
votes
0
replies
37
views
News:
Gene Set Enrichment Analysis in Bioconductor course
cola
1 day ago
info
▴ 10
0
votes
1
reply
120
views
Pathview visualisation not including positive log2 fold changes
pathview
Proteomics
updated 1 day ago by
James W. MacDonald
68k • written 2 days ago by
Jessica
• 0
1
vote
0
replies
1.5k
views
Suggesting changing the "reply-to" field to the mailing list address.
updated 2 days ago by
shepherl
4.1k • written 15.6 years ago by
Peng Yu
▴ 950
0
votes
3
replies
244
views
Differential variance analysis - can i use deseq2
DESeq2
DifferentialExpression
RNASeq
RNASeqData
scRNAseq
updated 1 hour ago by
Michael Love
43k • written 2 days ago by
Marwan
• 0
1
vote
1
reply
251
views
UniProt.ws query for single UniRef90 ID takes several minutes
UniProt.ws
updated 2 days ago by
James W. MacDonald
68k • written 6 days ago by
Nina
• 0
0
votes
3
replies
326
views
batch effect removal for agilent microarray data
"
"Bioconductor"
Bioconductor
2 days ago • updated 23 hours ago
gaye.yilmaz
• 0
0
votes
2
replies
498
views
Automatically install dependencies
Install
dependencies
biocmanager
updated 3 days ago by
shepherl
4.1k • written 6 days ago by
jessica.gillespie
• 0
0
votes
2
replies
1.1k
views
Spam:
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updated 4 days ago by
xihaxiw582
• 0 • written 17.1 years ago by
Allison Hoskins
10
0
votes
1
reply
356
views
SingleR with multiple single cell references
SingleR
scran
updated 5 days ago by
Aaron Lun
★ 28k • written 5 days ago by
maltethodberg
▴ 180
0
votes
0
replies
43
views
Help with mouse cell type annotation
annotation
SingleR
mouse
SingleCellData
scRNAseq
5 days ago
Muhammad
• 0
0
votes
1
reply
508
views
To count or not to count multi-overlapping reads?
RNA-Seq
featureCounts
Rsubread
updated 6 days ago by
Gordon Smyth
52k • written 7 days ago by
Arindam
▴ 80
0
votes
0
replies
38
views
Unable to restore chromosome sequence lengths or other metadata in BSgenome.Mfascicularis.NCBI.6.0
BSgenome.Mfascicularis.NCBI.6.0
6 days ago
Genevieve
• 0
1
vote
2
replies
971
views
Weird p-values using DESeq2?
DESeq2
RNASeq
updated 6 days ago by
ATpoint
★ 4.7k • written 7 days ago by
ingrid.h
• 0
0
votes
0
replies
58
views
Job:
Research Software Engineer - Bioconductor tools for biological data science and AI
Bioconductor
7 days ago
Wolfgang Huber
★ 13k
0
votes
0
replies
29
views
Generating Biphasic Curves in Offline GR Metrics Package
GRmetrics
7 days ago
Jasmitha
• 0
3
votes
5
replies
977
views
Overcoming confounding in batch effect correction
sva
BiologicalQuestion
8 days ago • updated 7 days ago
bbao
▴ 10
3
votes
2
replies
931
views
Store Matrix in DataFrame Cell
S4Vectors
9 days ago • updated 7 days ago
Dario Strbenac
★ 1.6k
0
votes
7
replies
2.1k
views
DiffBind - question on the use of filtered or unfiltered input data
DiffBind
written 22 months ago by
Oscar
• 0
0
votes
5
replies
525
views
For some reason I can't update BiocManager to 3.20
Bioconductor
updated 2 days ago by
shepherl
4.1k • written 9 days ago by
azm.ana2
• 0
0
votes
0
replies
6
views
Spam:
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netresponse
hgu219.db
MantelCorr
IlluminaDataTestFiles
9 days ago
Abu
0
0
votes
0
replies
6
views
Spam:
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PhenoGeneRanker
BSgenome.Osativa.MSU.MSU7
mouse.db0
SIM
9 days ago
Abu
0
0
votes
0
replies
8
views
Spam:
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Qtlizer
ropls
TransOmicsData
MethylSeekR
9 days ago
Abu
0
0
votes
0
replies
10
views
Spam:
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proDA
org.Sc.sgd.db
TVTB
9 days ago
Abu
0
0
votes
0
replies
10
views
Spam:
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JobPosting
customCMPdb
TransOmicsData
9 days ago
Abu
0
0
votes
0
replies
12
views
Spam:
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GOTHiC
BubbleTree
PANR
9 days ago
Abu
0
0
votes
1
reply
122
views
KEGG GSEA using Clusterprofiler - ncbi-geneid missing?
clusterProfiler
KEGG
9 days ago
Jessica
• 0
0
votes
0
replies
35
views
News:
GBCC2025 Abstract Submissions & Registration Now Open!
Community
Conference
GBCC2025
Bioconductor
9 days ago
Maria Doyle
▴ 100
0
votes
1
reply
125
views
Comparing Mock vs Infected in WT and Knockout Cells
DESeq2
DifferentialExpression
DifferentialRegulation
RNASeq
GeneSetEnrichment
updated 9 days ago by
Michael Love
43k • written 14 days ago by
Sahil
• 0
0
votes
1
reply
283
views
In WGCNA, what networkType should be used in pickSoftThreshold for a Signed Nowick TomType
WGCNA
pickSoftThreshold
SignedNowick
updated 10 days ago by
ATpoint
★ 4.7k • written 17 days ago by
ddrummer0056
• 0
0
votes
1
reply
132
views
Error: lexical error: invalid char in json text (alevin-seurat)
tximpo
tximportData
alevinQC
updated 10 days ago by
ATpoint
★ 4.7k • written 14 days ago by
ptlsugam
• 0
0
votes
0
replies
49
views
Help with MetagenomeSeq, understanding the 75th quantile
metagenomeSeq
cumulativesumscaling
updated 9 days ago by
James W. MacDonald
68k • written 13 days ago by
boone5jones
• 0
0
votes
0
replies
130
views
Methylation data - different probes are classified differently based on transcript? (Illumina methylation arrays, using minfi)
minf
minfiDataEPIC
MethylationArrayData
MethylationArray
EPICv2manifest
13 days ago
charlie.wright
• 0
0
votes
3
replies
442
views
DESeq2 adujsted p-value cutoff seemingly not working
DESeq2
updated 10 days ago by
980linnet
• 0 • written 15 days ago by
Guilherme
• 0
0
votes
4
replies
391
views
Web accessibility of Bioconductor.org
website
Website
updated 9 days ago by
Sean Davis
21k • written 15 days ago by
lizhare
• 0
1
vote
2
replies
735
views
Issue with assigning transcript IDs to reads when using summarizeOverlaps(mode = IntersectionNotEmpty)
GenomicAlignments
summarizeOverlaps(
Smart-seq2
proteinvariantcounting
16 days ago • updated 15 days ago
SofieK
• 0
0
votes
2
replies
258
views
Meffil: error in functional normalization function (Error in rg.to.mu(rg, probes))
methylationArrayAnalysis
Normalization
Epigenetics
MethylationArrayData
16 days ago
a.alkema
• 0
0
votes
2
replies
335
views
accounting for vs. removing batch effects with DESeq2 in RNAseq analysis
DESeq2
updated 13 days ago by
Blair
• 0 • written 18 days ago by
A
• 0
0
votes
2
replies
303
views
displaying the differential expression with deseq2 over 4X2 samples with the individual changes in gene expression per sample
DESeq2
18 days ago • updated 17 days ago
Martijn
• 0
0
votes
3
replies
346
views
How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat
RNASeq
DESeq2
scRNAseq
updated 18 days ago by
jodan
• 0 • written 26 days ago by
Quang NN
▴ 10
5
votes
4
replies
802
views
Unused arguments error without used arguments in GSVA?
GSVA
updated 16 days ago by
Axel Klenk
★ 1.1k • written 21 days ago by
1sunmic2
• 0
0
votes
1
reply
995
views
Using genomicRanges / plyranges to calculate score of peaks within intervals
plyranges
GenomicRanges
updated 18 days ago by
Michael Love
43k • written 3.8 years ago by
alorsonmethyle
• 0
1
vote
1
reply
1.6k
views
Reducing and aggregating GRanges with gaps using plyranges
GenomicRanges
plyranges
updated 18 days ago by
Michael Love
43k • written 4.4 years ago by
r.a.policastro
• 0
46,352 results • Page
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Comment: Differential variance analysis - can i use deseq2
by
Michael Love
43k
VST is valid for working with expression data on a variance stabilized scale, so yes. There are many papers that have used VST and then com…
Answer: Use of limma R package with targeted proteomics for DE analysis
by
Gordon Smyth
52k
It is usual to analyse log normalized values from Olink in limma. Just a straight log transformation should be sufficient. We find that `tr…
Comment: WGCNA
by
pammelala304
• 0
Thank you for your time and effort. I am so grateful! Play game [block blast](https://blockblastpuzzle.io) free.
Comment: Does anyone have the command to download all of the core_nt using blast_db_get()
by
Matthew Thornton
▴ 380
Ok. So I guess the core_nt is over 300Gb compressed. I can do it, but maybe it is better to just use ncbi-tools over the internet and just…
Comment: normalizatino of dna methylation EPIC data
by
user_bioinfo
• 0
yes actually that's why I did, and its all good! thank you for your response
Votes
Comment: Different annotation packages (org.Mm.eg.db, EnsDb.Mmusculus.v79, BiomaRt) retu
Answer: normalizatino of dna methylation EPIC data
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
Suggesting changing the "reply-to" field to the mailing list address.
Answer: UniProt.ws query for single UniRef90 ID takes several minutes
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