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0
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12
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wgcna module preseravtion taking too long?
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3 hours ago lamia11me • 0
0
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0
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29
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Clarification on counting in Rsubread (featureCounts)
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1 day ago Luca • 0
0
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1
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77
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NUPOP usage
TOAST
updated 5 days ago by 4.2k • written 5 days ago by • 0
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2
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260
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News: Important: Bioconductor Release 3.22 Delayed
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88
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Question about RE-agnostic mode for intact Hi-C and Micro-C normalization(HiCDCPlus)
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0
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2
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178
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BiocParallel (and DESeq2) - wrong args for environment subassignment
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updated 11 days ago by 43k • written 12 days ago by • 0
0
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148
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PTM analysis in LIMPA
limpa
updated 11 days ago by 53k • written 12 days ago by • 0
1
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152
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News: Upcoming Ensembl API and data access changes - new blog post available
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14 days ago Ensembl_Jorge ▴ 10
0
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2
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180
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problem reading bam files into nucleR
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0
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0
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13
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14 days ago Maya 0
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Highly similar RNA-seq samples in PCA - pooling or technical duplication?
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Question about DESeq2 Design for Paired Treatment Study
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updated 16 days ago by ★ 5.0k • written 17 days ago by • 0
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72
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19 days ago laurah ondari • 0
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PFAM formats changed - is it still possible to use this with ISA?
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20 days ago bolusharris • 0
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153
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DECIPHER DesignProbes unable to design FISH-probes
decipher FISH DECIPHER FISH-probe probe-design
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2
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p.adjust BH Question
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1
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4
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346
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Large logFC but somewhat high FDR
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22 days ago • updated 14 days ago JKim • 0
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151
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Job: Bioinformatician at the Lausanne University Hospital
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upstream git branches of bioc-release
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limpa - drivers for unusually high standard error?
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updated 22 days ago by 53k • written 22 days ago by • 0
1
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4
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How can I correctly use phyloseq with Docker?
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updated 3 days ago by • 0 • written 7 months ago by • 0
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398
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Boolean Gate Combination for Any 2 Positive Events in flowWorkspace
flowWorkspace FlowCytometry
updated 24 days ago by ★ 4.0k • written 5 months ago by • 0
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2
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Install old version of DESeq2
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updated 24 days ago by ★ 4.0k • written 5 months ago by • 0
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368
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Guidance Requested on GCN Network Analysis and Module Enrichment in R
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updated 24 days ago by ★ 4.0k • written 4 months ago by • 0
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BiocManager::install() doesn't work
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324
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Results with PON give more variants
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268
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Empty boxes in treemap plot rrvgo package
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266
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CRISPRSeek Question: changing weight and gRNA.size causes error
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updated 24 days ago by ★ 4.0k • written 4 months ago by • 0
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246
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sigDF object in sesame
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371
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Create consensusMatrix for codon bases
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updated 24 days ago by ★ 4.0k • written 4 months ago by • 0
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438
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updated 24 days ago by ★ 4.0k • written 4 months ago by • 0
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11
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1.6k
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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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0
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1
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263
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Finding duplicated entries in GRangesList
GenomicRanges
updated 25 days ago by ★ 4.0k • written 3 months ago by • 0
0
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1
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258
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DESeq2 on non-RNASeq counts data
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updated 25 days ago by ★ 4.0k • written 3 months ago by • 0
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2
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444
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After running samtools, the featureCounts command crashed.
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1
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509
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Problem with the TMB plot
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updated 25 days ago by ★ 4.0k • written 12 weeks ago by • 0
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1
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282
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mzR-Rcpp compiler version issue
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updated 27 days ago by 1.6k • written 3 months ago by • 0
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DESeq2 design for haplotype MPRA
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written 9 weeks ago by • 0
0
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214
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Must I do pseudobulk analysis on Cell Surface Protein Labeling data of Single Cell RNA Sequencing
scRNAseq
updated 27 days ago by ★ 4.0k • written 5 weeks ago by • 0
0
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0
replies
239
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Corrupted SQLite while trying to install PANTHER.db?
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updated 27 days ago by ★ 4.0k • written 3 months ago by • 0
0
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1
reply
330
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org.Ss.eg.db MAMDC4 maps to incorrect UNIPROT key
MAMDC4 org.Ss.eg.db AnnotationDbi
written 3 months ago by • 0
0
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1
reply
315
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Length of 'dimnames' [1] not equal to array extent
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updated 27 days ago by ★ 4.0k • written 3 months ago by • 0
0
votes
1
reply
331
views
Extract snp information from genomic regions with biomaRt -> "oaries_snp"
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updated 27 days ago by ★ 4.0k • written 3 months ago by • 0
46,695 results • Page 1 of 934
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Replies
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.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Votes
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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