Showing : bioconductor • reset
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26
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Are individual-mouse-based statistics possible in CellChat?
Bioconductor CellChat
1 day ago Omer • 0
0
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0
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59
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MSstatsPTM-SpectronauttoMSstatsPTMFormat-failing with TAIR10 Locus Tags: Issue with UniProt-centric protein ID parsing
Bioconductor MSstatsPTM
2 days ago srkingwu • 0
1
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0
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70
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News: Bioconductor Maintainer Application
maintainer policy Bioconductor Devel devel
6 days ago shepherl 4.3k
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1
reply
320
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News: Announcing a New Journal - Bioinformatics Methods and Applications - Now Open for Submissions
Bioconductor
written 6 months ago by ★ 3.6k
2
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3
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182
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please provide a BibTeX citation for "Advanced Single-Cell Analysis with Bioconductor"
Bioconductor
written 10 days ago by ▴ 10
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1
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230
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News: Opportunity to host EuroBioC2026 Preconference workshops!
Conference Workshop Bioconductor
written 29 days ago by • 0
0
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1
reply
307
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News: EuroBioC2026 abstract submission is open!
Conference Bioconductor
written 7 weeks ago by • 0
3
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5
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549
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upstream git branches of bioc-release
Bioconductor
written 7 weeks ago by ▴ 10
0
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1
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438
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Guidance Requested on GCN Network Analysis and Module Enrichment in R
BioNERO Bioconductor Arabidopsis_thaliana_Data
updated 7 weeks ago by ★ 4.0k • written 6 months ago by • 0
0
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2
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503
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After running samtools, the featureCounts command crashed.
RNASeqData Bioconductor RNASeq
updated 6 weeks ago by • 0 • written 4 months ago by • 0
0
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2
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610
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Problem with the TMB plot
Bioconductor
written 3 months ago by • 0
2
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3
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568
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DESeq2 design for haplotype MPRA
Bioconductor
written 3 months ago by • 0
0
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0
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327
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Problem with viewGO(ref_path) in SpliceWiz
Bioconductor SpliceWiz
updated 8 weeks ago by ★ 4.0k • written 3 months ago by • 0
0
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2
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245
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Alternative to BrainArray custom CDF packages for Affymetrix chips?
Bioconductor
updated 8 weeks ago by ★ 4.1k • written 8 weeks ago by ▴ 600
1
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0
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117
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News: Bioconductor Seminar Series - Dec 2: Deep-learning Gene Perturbation Effect Prediction
Bioconductor
8 weeks ago Maria Doyle ▴ 110
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2
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342
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featureCounts -L: high unassigned:mapq fraction
Bioconductor
written 3 months ago by • 0
1
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2
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474
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Streamlining the computing time for MiloDE p-value correction in large dataset?
SingleCellExperiment edgeR miloR Bioconductor
updated 9 weeks ago by ★ 4.0k • written 3 months ago by • 0
1
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2
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449
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incomplete imputation of missing values with LEA impute() function
Bioconductor LEA
updated 9 weeks ago by ★ 4.0k • written 3 months ago by • 0
2
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2
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590
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What R/Bioconductor tools would you recommend for the analysis of sncRNA, specifically piRNA?
Bioconductor
3 months ago • updated 9 weeks ago Matthew Thornton ▴ 390
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3
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313
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Integration: Paired-end vs healthy single-end from a different source
Bioconductor
written 10 weeks ago by • 0
1
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4
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453
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"Watched Tags" are being erased rather than updated
Bioconductor
updated 8 weeks ago by • 0 • written 11 weeks ago by ▴ 10
0
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1
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256
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Question about collapsing ASVs by genus level during DESeq2 analysis
Bioconductor
updated 10 weeks ago by 43k • written 3 months ago by • 0
0
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7
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2.2k
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News: EuroBioC2023 abstract submission is open!
presentation EuroBioC2023 Conference community Bioconductor
written 2.9 years ago by ▴ 110
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0
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12
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Spam: The Neon Code PolyTrack
Bioconductor
10 weeks ago residentialplayt 0
2
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1
reply
532
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News: Bioconductor 3.22 Released!
release Release Bioconductor Software
written 11 weeks ago by 4.3k
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1
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458
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News: Save the Date: BioC2026
Bioconductor
written 11 weeks ago by 4.3k
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3
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277
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Using DESeq2 for age prediction
Bioconductor
updated 11 weeks ago by ★ 5.0k • written 11 weeks ago by • 0
4
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3
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643
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DESeq2 for candidate gene analysis
Bioconductor
written 3 months ago by ▴ 20
0
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3
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335
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"organism" missing in BSgenome.Hsapiens.UCSC.hg38 slotNames
Bioconductor
3 months ago ubjw24 • 0
0
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3
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473
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NA values for DESeq2 p-values and adjusted p-values using large sample sizes
Bioconductor
3 months ago Gabriel • 0
0
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1
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190
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Gatins Set error
flowCore Bioconductor
updated 3 months ago by 68k • written 3 months ago by • 0
0
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1
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259
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Job: Senior Teaching Fellow (MSc Computational Biomedicine)
Bioconductor
written 3 months ago by • 0
0
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1
reply
729
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News: Bioconductor 3.22 Release Schedule
Devel Release Bioconductor
written 4 months ago by 4.3k
1
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2
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377
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Error Loading Experiment from SimBenchData Package
Bioconductor
3 months ago ksankaran • 0
0
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3
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386
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Sharing a collection of datasets in ExperimentHub
Bioconductor
updated 3 months ago by ★ 29k • written 3 months ago by ▴ 600
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6
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595
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GO.db and others package Download failure
GO.db Bioconductor
updated 3 months ago by 68k • written 4 months ago by • 0
0
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1
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225
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Job: Research and Service Group Leader positions in AI in Biology at EMBL
Bioconductor
written 4 months ago by ★ 13k
0
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1
reply
402
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News: Bioconductor Board Nominations Open
TAB Bioconductor CAB
written 6 months ago by 4.3k
0
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3
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2.5k
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Applying lmFit(), eBayes() and topTable() for modeling associations between NMR-derived metabolic measures and various traits
limma Bioconductor Metabolomics
updated 6 months ago by 53k • written 6 months ago by • 0
0
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2
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1.1k
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Starting with a clean bioconductor rstudio container
Bioconductor
updated 6 months ago by ★ 5.0k • written 7 months ago by • 0
0
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9
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13k
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Bioconductor version cannot be validated
BiocManager Bioconductor
updated 7 months ago by • 0 • written 4.5 years ago by ▴ 10
0
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0
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373
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Job: Lab Head positions at the WEHI, Melbourne, Australia
JobPosting Bioconductor
7 months ago Gordon Smyth 53k
0
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4
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9.2k
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Bioconductor version cannot be validated
Bioconductor Annotation Ann
written 2.3 years ago by • 0
0
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2
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612
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GBCC2025: New Scholarship Opportunities Available!
Community Conference GBCC2025 Bioconductor
updated 4 months ago by • 0 • written 7 months ago by ▴ 110
0
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1
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501
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Best tximport quant.genes.sf
tximport tximeta Bioconductor
updated 8 months ago by ★ 5.0k • written 8 months ago by • 0
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2
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861
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Version conflict when pushing to scQTLtools devel branch
Bioconductor
written 9 months ago by • 0
1
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5
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1.9k
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Package developing and interoperation with Bioconductor
Package Bioconductor
written 9 months ago by • 0
0
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5
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2.8k
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News: EuroBioC2024 abstract submission is open!
Conference Bioconductor EuroBioC2024
written 23 months ago by ▴ 110
0
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1
reply
931
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News: List of Deprecated Packages for Bioc3.20
Release Devel Bioconductor
15 months ago • updated 9 months ago shepherl 4.3k
0
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0
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625
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News: EuroBioC2025: Abstract Submissions Open!
EuroBioC2025 Community Conference Bioconductor
10 months ago Maria Doyle ▴ 110
915 results • Page 1 of 19
Recent ...
Replies
Answer: When to use edgeR or limma by Gordon Smyth 53k
The short answer is that we generally prefer edgeR for applications with lots of small counts and limma for complex designs with random eff…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
I updated the above answer today.
Answer: When to use edgeR or limma by James W. MacDonald 68k
I would use edgeR's quasi-likelihood model for any analysis with a smaller number of observations (like 3 vs 3 or similar), but if you have…
Answer: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
The short answer is that limpa reads standard feature-level intensities from Spectronaut or other quantifications tools. limpa is designed …
Comment: Question about the filterByExpr function inputs in edgeR by mohammedtoufiq91 ▴ 10
@gordonsmyth Noted, thank you very much.
Votes
A: deseq2 - paired samples in 2 sequencing types with very different library sizes
Comment: Question about the filterByExpr function inputs in edgeR
Answer: Question about the filterByExpr function inputs in edgeR
Answer: Question about the filterByExpr function inputs in edgeR
A: DESeq2: What is the unit of DESeq2 normalized read count (VST)? Is it tag per mi
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