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News:
Gene Set Enrichment Analysis in Bioconductor course
GSEABase
GeneSetEnrichment
goseq
10 months ago
info
▴ 10
0
votes
1
reply
437
views
Pathview visualisation not including positive log2 fold changes
pathview
Proteomics
updated 10 months ago by
James W. MacDonald
68k • written 10 months ago by
Jessica
• 0
1
vote
0
replies
1.8k
views
Suggesting changing the "reply-to" field to the mailing list address.
updated 10 months ago by
shepherl
4.2k • written 16.4 years ago by
Peng Yu
▴ 950
0
votes
3
replies
1.1k
views
Differential variance analysis - can i use deseq2
DESeq2
DifferentialExpression
RNASeq
RNASeqData
scRNAseq
updated 10 months ago by
Michael Love
43k • written 10 months ago by
Marwan
• 0
1
vote
1
reply
684
views
UniProt.ws query for single UniRef90 ID takes several minutes
UniProt.ws
updated 10 months ago by
James W. MacDonald
68k • written 10 months ago by
Nina
• 0
0
votes
3
replies
699
views
batch effect removal for agilent microarray data
"
"Bioconductor"
Bioconductor
10 months ago
gaye.yilmaz
• 0
0
votes
2
replies
1.3k
views
Automatically install dependencies
Install
dependencies
biocmanager
updated 10 months ago by
shepherl
4.2k • written 10 months ago by
jessica.gillespie
• 0
0
votes
2
replies
1.1k
views
Spam:
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updated 10 months ago by
xihaxiw582
• 0 • written 18.0 years ago by
Allison Hoskins
10
2
votes
2
replies
1.1k
views
SingleR with multiple single cell references
SingleR
scran
10 months ago • updated 8 months ago
maltethodberg
▴ 180
0
votes
0
replies
422
views
Help with mouse cell type annotation
annotation
SingleR
mouse
SingleCellData
scRNAseq
10 months ago
Muhammad
• 0
0
votes
1
reply
1.0k
views
To count or not to count multi-overlapping reads?
RNA-Seq
featureCounts
Rsubread
updated 10 months ago by
Gordon Smyth
53k • written 10 months ago by
Arindam
▴ 80
0
votes
0
replies
230
views
Unable to restore chromosome sequence lengths or other metadata in BSgenome.Mfascicularis.NCBI.6.0
BSgenome.Mfascicularis.NCBI.6.0
10 months ago
Genevieve
• 0
1
vote
2
replies
1.4k
views
Weird p-values using DESeq2?
DESeq2
RNASeq
updated 10 months ago by
ATpoint
★ 5.0k • written 10 months ago by
ingrid.h
• 0
0
votes
0
replies
629
views
Job:
Research Software Engineer - Bioconductor tools for biological data science and AI
Bioconductor
10 months ago
Wolfgang Huber
★ 13k
0
votes
0
replies
208
views
Generating Biphasic Curves in Offline GR Metrics Package
GRmetrics
10 months ago
Jasmitha
• 0
3
votes
5
replies
1.7k
views
Overcoming confounding in batch effect correction
sva
BiologicalQuestion
10 months ago
bbao
▴ 10
3
votes
2
replies
1.2k
views
Store Matrix in DataFrame Cell
S4Vectors
10 months ago
Dario Strbenac
★ 1.6k
0
votes
5
replies
2.1k
views
For some reason I can't update BiocManager to 3.20
Bioconductor
updated 10 months ago by
shepherl
4.2k • written 10 months ago by
azm.ana2
• 0
0
votes
0
replies
6
views
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netresponse
hgu219.db
MantelCorr
IlluminaDataTestFiles
10 months ago
Abu
0
0
votes
0
replies
6
views
Spam:
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PhenoGeneRanker
BSgenome.Osativa.MSU.MSU7
mouse.db0
SIM
10 months ago
Abu
0
0
votes
0
replies
8
views
Spam:
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Qtlizer
ropls
TransOmicsData
MethylSeekR
10 months ago
Abu
0
0
votes
0
replies
10
views
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proDA
org.Sc.sgd.db
TVTB
10 months ago
Abu
0
0
votes
0
replies
10
views
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JobPosting
customCMPdb
TransOmicsData
10 months ago
Abu
0
0
votes
0
replies
12
views
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GOTHiC
BubbleTree
PANR
10 months ago
Abu
0
0
votes
1
reply
790
views
KEGG GSEA using Clusterprofiler - ncbi-geneid missing?
clusterProfiler
KEGG
10 months ago
Jessica
• 0
0
votes
0
replies
518
views
News:
GBCC2025 Abstract Submissions & Registration Now Open!
Community
Conference
GBCC2025
Bioconductor
10 months ago
Maria Doyle
▴ 110
0
votes
1
reply
429
views
Comparing Mock vs Infected in WT and Knockout Cells
DESeq2
DifferentialExpression
DifferentialRegulation
RNASeq
GeneSetEnrichment
updated 10 months ago by
Michael Love
43k • written 10 months ago by
Sahil
• 0
0
votes
1
reply
796
views
In WGCNA, what networkType should be used in pickSoftThreshold for a Signed Nowick TomType
WGCNA
pickSoftThreshold
SignedNowick
updated 10 months ago by
ATpoint
★ 5.0k • written 10 months ago by
ddrummer0056
• 0
0
votes
1
reply
448
views
Error: lexical error: invalid char in json text (alevin-seurat)
tximpo
tximportData
alevinQC
updated 10 months ago by
ATpoint
★ 5.0k • written 10 months ago by
ptlsugam
• 0
0
votes
0
replies
235
views
Help with MetagenomeSeq, understanding the 75th quantile
metagenomeSeq
cumulativesumscaling
updated 10 months ago by
James W. MacDonald
68k • written 10 months ago by
boone5jones
• 0
0
votes
0
replies
366
views
Methylation data - different probes are classified differently based on transcript? (Illumina methylation arrays, using minfi)
minf
minfiDataEPIC
MethylationArrayData
MethylationArray
EPICv2manifest
10 months ago
charlie.wright
• 0
0
votes
3
replies
857
views
DESeq2 adujsted p-value cutoff seemingly not working
DESeq2
updated 10 months ago by
980linnet
• 0 • written 10 months ago by
Guilherme
• 0
0
votes
4
replies
720
views
Web accessibility of Bioconductor.org
website
Website
updated 10 months ago by
Sean Davis
21k • written 10 months ago by
lizhare
• 0
1
vote
2
replies
1.3k
views
Issue with assigning transcript IDs to reads when using summarizeOverlaps(mode = IntersectionNotEmpty)
GenomicAlignments
summarizeOverlaps(
Smart-seq2
proteinvariantcounting
10 months ago
SofieK
• 0
0
votes
2
replies
557
views
Meffil: error in functional normalization function (Error in rg.to.mu(rg, probes))
methylationArrayAnalysis
Normalization
Epigenetics
MethylationArrayData
10 months ago
a.alkema
• 0
0
votes
2
replies
939
views
accounting for vs. removing batch effects with DESeq2 in RNAseq analysis
DESeq2
updated 10 months ago by
Blair
• 0 • written 10 months ago by
A
• 0
0
votes
3
replies
630
views
displaying the differential expression with deseq2 over 4X2 samples with the individual changes in gene expression per sample
DESeq2
updated 10 months ago by
Leonard
• 0 • written 10 months ago by
Martijn
• 0
0
votes
3
replies
926
views
How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat
RNASeq
DESeq2
scRNAseq
updated 10 months ago by
jodan
• 0 • written 11 months ago by
Quang NN
▴ 10
5
votes
5
replies
2.1k
views
Unused arguments error without used arguments in GSVA?
GSVA
updated 9 months ago by
michaelarringtony
• 0 • written 11 months ago by
1sunmic2
• 0
0
votes
1
reply
1.3k
views
Using genomicRanges / plyranges to calculate score of peaks within intervals
plyranges
GenomicRanges
updated 11 months ago by
Michael Love
43k • written 4.7 years ago by
alorsonmethyle
• 0
1
vote
1
reply
2.0k
views
Reducing and aggregating GRanges with gaps using plyranges
GenomicRanges
plyranges
updated 11 months ago by
Michael Love
43k • written 5.2 years ago by
r.a.policastro
• 0
4
votes
3
replies
635
views
plyranges: find exact GRanges match keeping metadata columns
plyranges
updated 10 months ago by
Michael Love
43k • written 11 months ago by
alexis.weinreb
• 0
0
votes
0
replies
412
views
News:
Mass Spectrometry and Proteomics with R/Bioconductor course
cadd.v1.6.hg38
11 months ago
info
▴ 10
0
votes
1
reply
436
views
Restricting differential binding analysis to only TSS-proximal regions
ChIP
csaw
updated 11 months ago by
Aaron Lun
★ 29k • written 11 months ago by
Luca
• 0
0
votes
0
replies
300
views
Batch Correction while implementing QSEA package
qsea
MEDIPS
MEDIPSData
DNAMethylation
11 months ago
User3088
• 0
0
votes
0
replies
305
views
News:
Announcing the GBCC2025 Logo Design Winner!
Community
Conference
GBCC2025
Bioconductor
11 months ago
Maria Doyle
▴ 110
0
votes
1
reply
470
views
building samplesheet and plot profile
DiffBind
11 months ago
yf
• 0
0
votes
0
replies
211
views
DBT JRF & PhD Scholar
BiologicalQuestion
OmicsMLRepoR
11 months ago
Manisha
• 0
0
votes
1
reply
429
views
I am having issues with bowtie2_build
genomes
bowtiew
Index
updated 11 months ago by
James W. MacDonald
68k • written 11 months ago by
eduardo.pastor
• 0
0
votes
1
reply
683
views
DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression
RNASeq
DESeq2
updated 11 months ago by
Michael Love
43k • written 11 months ago by
Sim
• 0
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I recommend that you always use voomLmFit() instead of the earlier voom() or voomWithQualityWeights() functions. Personally, I would use sa…
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Error in SummarizedExperiment(assays = SimpleList(counts = countData)
Answer: DESeq2 class error: superclass "ExpData" not defined in the environment of the o
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