3
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6
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416
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Highly similar RNA-seq samples in PCA - pooling or technical duplication?
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two questions about limma
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Question about DESeq2 Design for Paired Treatment Study
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updated 1 day ago by ★ 5.0k • written 2 days ago by • 0
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66
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problem reading bam files into nucleR
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3 days ago • updated 1 day ago efoss ▴ 10
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News: EuroBioC2026 abstract submission is open!
Conference Bioconductor
4 days ago laurah ondari • 0
0
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PFAM formats changed - is it still possible to use this with ISA?
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5 days ago bolusharris • 0
0
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0
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DECIPHER DesignProbes unable to design FISH-probes
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6 days ago vreinmuth • 0
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p.adjust BH Question
updated 6 days ago by 53k • written 14.2 years ago by ▴ 10
1
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4
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Large logFC but somewhat high FDR
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7 days ago • updated 6 days ago JKim • 0
0
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0
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Job: Bioinformatician at the Lausanne University Hospital
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7 days ago story.benjamin ▴ 20
3
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5
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289
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upstream git branches of bioc-release
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written 7 days ago by ▴ 10
0
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2
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111
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limpa - drivers for unusually high standard error?
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updated 7 days ago by 53k • written 7 days ago by • 0
1
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3
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How can I correctly use phyloseq with Docker?
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updated 9 days ago by ★ 4.0k • written 7 months ago by • 0
0
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363
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Boolean Gate Combination for Any 2 Positive Events in flowWorkspace
flowWorkspace FlowCytometry
updated 9 days ago by ★ 4.0k • written 4 months ago by • 0
0
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Install old version of DESeq2
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updated 9 days ago by ★ 4.0k • written 4 months ago by • 0
0
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324
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Guidance Requested on GCN Network Analysis and Module Enrichment in R
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updated 9 days ago by ★ 4.0k • written 4 months ago by • 0
0
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ORFik: spliced 5utr regions
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updated 9 days ago by ★ 4.0k • written 4 months ago by • 0
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updated 9 days ago by ★ 4.0k • written 4 months ago by • 0
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281
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Results with PON give more variants
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updated 9 days ago by ★ 4.0k • written 4 months ago by ▴ 10
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235
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Empty boxes in treemap plot rrvgo package
rrvgo
updated 9 days ago by ★ 4.0k • written 4 months ago by • 0
0
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1
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231
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CRISPRSeek Question: changing weight and gRNA.size causes error
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updated 9 days ago by ★ 4.0k • written 4 months ago by • 0
0
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Feedback needed on new user-friendly BED file tool
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updated 9 days ago by ★ 4.0k • written 4 months ago by • 0
0
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208
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updated 9 days ago by ★ 4.0k • written 3 months ago by • 0
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updated 9 days ago by ★ 4.0k • written 3 months ago by • 0
1
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11
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Using DESeq2 on single cell RNA Seq data of same cell type but different conditions that were pseudo bulked
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updated 9 days ago by ★ 4.0k • written 3 months ago by • 0
0
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updated 10 days ago by ★ 4.0k • written 3 months ago by • 0
0
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updated 10 days ago by ★ 4.0k • written 3 months ago by • 0
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updated 10 days ago by ★ 4.0k • written 10 weeks ago by • 0
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mzR-Rcpp compiler version issue
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2
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updated 11 days ago by • 0 • written 6 weeks ago by • 0
0
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187
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Must I do pseudobulk analysis on Cell Surface Protein Labeling data of Single Cell RNA Sequencing
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updated 12 days ago by ★ 4.0k • written 20 days ago by • 0
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updated 12 days ago by ★ 4.0k • written 3 months ago by • 0
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updated 12 days ago by ★ 4.0k • written 3 months ago by • 0
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270
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Length of 'dimnames' [1] not equal to array extent
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updated 12 days ago by ★ 4.0k • written 3 months ago by • 0
0
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291
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updated 12 days ago by ★ 4.0k • written 12 weeks ago by • 0
0
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updated 12 days ago by ★ 4.0k • written 11 weeks ago by • 0
0
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Questions about pseudo counts from RUVSeq
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updated 12 days ago by ★ 4.0k • written 11 weeks ago by • 0
0
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Problem with viewGO(ref_path) in SpliceWiz
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updated 12 days ago by ★ 4.0k • written 10 weeks ago by • 0
0
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updated 12 days ago by ★ 4.0k • written 9 weeks ago by • 0
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0
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updated 12 days ago by ★ 4.0k • written 18 days ago by • 0
0
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109
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APAlyzer
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updated 12 days ago by ★ 4.0k • written 14 days ago by ▴ 10
2
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2
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234
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Identifying differentially expressed genes in individual samples from a large cohort
limma DifferentialExpression
13 days ago • updated 12 days ago jamie.gearing ▴ 60
0
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161
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Alternative to BrainArray custom CDF packages for Affymetrix chips?
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updated 13 days ago by ★ 4.1k • written 17 days ago by ▴ 600
1
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2
replies
199
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Error installing Seqinfo
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updated 14 days ago by 4.2k • written 16 days ago by • 0
1
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0
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News: Bioconductor Seminar Series - Dec 2: Deep-learning Gene Perturbation Effect Prediction
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17 days ago Maria Doyle ▴ 110
0
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4
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182
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Getting a large intercept with DESeq2
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17 days ago • updated 14 days ago Denise • 0
2
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Post translational modifications and phosphoproteomics in limpa?
limpa
18 days ago • updated 11 days ago james.eapen • 0
0
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Add additional maintainer for MOFA2
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updated 21 days ago by 4.2k • written 21 days ago by • 0
46,683 results • Page 1 of 934
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Comment: Question about DESeq2 Design for Paired Treatment Study by ATpoint ★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Comment: problem reading bam files into nucleR by efoss ▴ 10
I thought I might be able to track down a problematic line in the bam file by repeatedly splitting the bam file in and then running the co…
Answer: two questions about limma by Gordon Smyth 53k
Answered here: https://support.bioconductor.org/p/16318/
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0
Thank you very much! will take that into consideration
Comment: Large logFC but somewhat high FDR by JKim • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments.
Votes
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
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