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wgcna module preseravtion taking too long?
WGCNA
2 days ago lamia11me • 0
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Clarification on counting in Rsubread (featureCounts)
Rsubread
3 days ago Luca • 0
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1
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Question about RE-agnostic mode for intact Hi-C and Micro-C normalization(HiCDCPlus)
HiC HiCDCPlus
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PFAM formats changed - is it still possible to use this with ISA?
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23 days ago bolusharris • 0
0
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1
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160
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DECIPHER DesignProbes unable to design FISH-probes
decipher FISH DECIPHER FISH-probe probe-design
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upstream git branches of bioc-release
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1
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333
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org.Ss.eg.db MAMDC4 maps to incorrect UNIPROT key
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0
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1
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316
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GOseq Probability Weight Function bad fit
goseq
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0
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2
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142
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APAlyzer
APAlyzer
updated 4 weeks ago by ★ 4.0k • written 4 weeks ago by ▴ 10
0
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1
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Co-occurrence Network Analysis between Algae and Bacteria
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6 months ago rajdeepboral00 • 0
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getQC(RGset.raw) from IlluminaHumanMethylationMSAmanifest
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updated 6 months ago by 4.2k • written 6 months ago by • 0
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0
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DiffBind plot.profile error
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6 months ago this_is_me_trying • 0
0
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1
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644
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Using EBI Image on Ranged Bar Chart
EBImage
written 6 months ago by • 0
1
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3
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Possible issue following the logNormCounts(filtered) with resulted fit
single-cell SingleCell SingleCellExperiment SingleCellWorkflow SingleCellData
7 months ago • updated 6 months ago Konstantinos Yeles ▴ 90
0
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2
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583
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GBCC2025: New Scholarship Opportunities Available!
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updated 3 months ago by • 0 • written 7 months ago by ▴ 110
0
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0
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Blank gene_id in featureCounts
featureCounts Rsubread
7 months ago Meg • 0
0
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1
reply
558
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FCS 32 support going backwards?
flowCore
updated 6 months ago by • 0 • written 7 months ago by • 0
0
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0
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353
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What Input-type do I use in decouplR::run_viper?
decoupleR viper
updated 6 months ago by 43k • written 7 months ago by • 0
0
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0
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326
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Combining COMBAT-seq result (raw count) with other raw count
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7 months ago dudwnsrla1 • 0
0
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534
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updated 7 months ago by 700 • written 7 months ago by • 0
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0
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Diffbind Analysis gives error during profile plotting stage. Error in value[[3L]](cond) : profileplyr error: Error: BiocParallel errors 1 remote…
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1
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700
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Combat-seq usage
sva
7 months ago • updated 6 months ago bbao ▴ 10
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1
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416
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What happened to the Joost2016 dataset
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2
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FlowSOM is unable to create Output
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Discrepancies in normalised count data vs unnormalised
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7 months ago • updated 6 months ago AMgroup • 0
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0
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Significant Probes and Genes differ in Probe and Region level Differential Methylation Analyses
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0
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380
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Batch correction for microarray
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8 months ago Shaimaa Gamal • 0
0
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0
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GRaNIE with no internet
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8 months ago maia.malonzo • 0
0
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0
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Issue checking for convergence with the tutorial Dataset. EBseq 2.4.1
EBSeq
8 months ago Javier • 0
0
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0
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364
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I want my overlapping peaks to stop merging by default doing read counting (using DiffBind in R-studio)
peakoverlap mergingpeaks ChIPseq DiffBind
8 months ago atlanta • 0
1
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1
reply
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Differential expression analysis using two TCGA datasets
DifferentialExpression TCGAbiolinks RNASeq
updated 8 months ago by ★ 5.0k • written 8 months ago by • 0
1
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0
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559
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Modelling gene program dynamics across time with {lemur}
lemur
8 months ago BiotechPedro ▴ 10
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584
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Intepretation of results
AUCell
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0
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4
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DiffBind can't find a DAR
dar ATACSeq DiffBind
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1
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3
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Error in H5Dclose(h5dataset) when trying to read in kallisto h5 files
tximport rhdf5
8 months ago Sofia • 0
1
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1
reply
1.0k
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ComBat with repeated measures
ComBat sva
updated 8 months ago by ★ 5.0k • written 8 months ago by • 0
0
votes
0
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248
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Correlation threshold
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8 months ago user_bioinfo • 0
0
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5
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908
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Bioconductor unable to update 'curl'
curl HELP
8 months ago kagodwi2 • 0
0
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4
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Ensembl site unresponsive via biomaRt
biomaRt
updated 8 months ago by • 0 • written 8 months ago by • 0
1,000 results • Page 1 of 20
Recent ...
Replies
Answer: How does contrasts.fit do in limma to extract comparisons with a model having in by Gordon Smyth 53k
The limma Users Guide explains how to test for interactions or to test for contrasts very easily. limma can work with any design matrix, bu…
Answer: NUPOP usage by shepherl 4.2k
You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
Comment: How can I correctly use phyloseq with Docker? by fnfgame • 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
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C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
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
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