0
votes
1
reply
636
views
cytolib uses outdated boost call
cytolib
updated 4 months ago by 68k • written 4 months ago by • 0
4
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8
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1.9k
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Should Xenium pseudobulk experiments be analysed like microarrays (limma) or like RNASeq (edgeR,Deseq2, or limma-voom)
Deseq2 edgeR limma xenium Voom
5 months ago • updated 4 months ago richardallenfriedmanbrooklyn ▴ 30
0
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2
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340
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can't post
devel
updated 4 months ago by 4.2k • written 4 months ago by • 0
7
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9
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5.6k
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competitive enrichment test yields too few significant results, self-contained too many
limma DESeq2 fry edgeR
5 months ago • updated 4 months ago bbao ▴ 10
0
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1
reply
1.4k
views
How to avoid losing a sample as reference running an individual differential expression analysis (LIMMA)
Microarray limma BRAIN Microarray limma BRAIN
updated 5 months ago by 53k • written 16.8 years ago by ▴ 10
0
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1
reply
533
views
discrepancy in IDs from file and tx2gene (IDs don't match)
tximport DESeq2
updated 5 months ago by 68k • written 5 months ago by • 0
3
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9
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4.6k
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Best practice for handling large data (matrix with >2^31-1 non-zero elements) in SingleCellExperiment?
SingleCellExperiment
updated 6 weeks ago by • 0 • written 5 months ago by ▴ 10
0
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0
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224
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News: Announcing a New Journal - Bioinformatics Methods and Applications - Now Open for Submissions
Bioconductor
5 months ago Wei Shi ★ 3.6k
1
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3
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2.4k
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Regarding the issue of background genes in enrichment analysis
KEGG goTools seqTools
written 5 months ago by ▴ 10
0
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3
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2.4k
views
Applying lmFit(), eBayes() and topTable() for modeling associations between NMR-derived metabolic measures and various traits
limma Bioconductor Metabolomics
updated 5 months ago by 53k • written 5 months ago by • 0
2
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4
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3.3k
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I would like to perform differential expression analysis of lncRNAs using DESeq2 and edgeR.
diffGeneAnalysis lncRNA
5 months ago John ▴ 10
0
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2
replies
996
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gene detection across experiments
DESeq2 Normalization
5 months ago Mara • 0
0
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3
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1.7k
views
RNA-seq: TPM batch effect correction
rnaseqDTU Normalization
updated 5 months ago by 68k • written 5 months ago by • 0
5
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11
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3.3k
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parameters of filterByExpr
edgeR DESeq2 filterByExpr
written 7 months ago by ▴ 10
0
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5
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2.0k
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compute_fasta_digest does not match Salmon index hash
tximeta
written 8 months ago by • 0
0
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5
replies
897
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WGCNA
WGCNA Normalization RNASeq
written 9 months ago by • 0
3
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4
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5.2k
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Analysis of clusters of a heatmap with enrichGO of clusterProfiler: choice fo the categories to visualize
clusterProfiler enrichGO ComplexHeatmap
updated 5 months ago by 68k • written 5 months ago by ▴ 10
0
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3
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1.2k
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TopGO question
topGO top
updated 5 months ago by 68k • written 5 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 5 months ago by ★ 5.0k • written 5 months ago by • 0
0
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1
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2.4k
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ChAMP pipeline error (champ.import)
software error
updated 5 months ago by • 0 • written 6.7 years ago by • 0
0
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2
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564
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Problem in Chip-seq data analysis using MACS3
chipseq MACSdata
updated 5 months ago by ★ 5.0k • written 5 months ago by • 0
1
vote
5
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4.6k
views
Pre-filtering, adjusting independent filtering, or lfcthreshold() on DESeq2? Low counts and dropouts produce interesting volcano plots.
DESeq2
updated 4 months ago by 43k • written 6 months ago by • 0
0
votes
1
reply
731
views
Which GTF file to use for creation of tx2gene files?
tximport
updated 5 months ago by 43k • written 5 months ago by • 0
1
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1
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2.2k
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DESeq2 LRT: Testing Effects of Treatment1, Treatment2, and Their Interaction in a Four-Factor Design
DESeq2 multifactorialdesign interaction InteractionSet
updated 5 months ago by 43k • written 5 months ago by • 0
0
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2
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1.2k
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6 groups to compare DESeq2 (Wald vs LRT)
DESeq2
updated 5 months ago by 43k • written 5 months ago by • 0
0
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3
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982
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Many transcripts missing from tx2gene created from Ensembl GTF file
kallisto tximport ensembl
updated 5 months ago by • 0 • written 5 months ago by • 0
1
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2
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3.8k
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Is voomByGroup available in limma?
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5 months ago richardallenfriedmanbrooklyn ▴ 30
0
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4
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How to use goana function with zebrafish genome from org.Dr.eg.db
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5 months ago Eric • 0
1
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3
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written 7 months ago by ▴ 30
0
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0
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Spam: wealthdt5
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5 months ago Enfurry 0
0
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0
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278
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Y-axis break ihn Volcano Plot
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6 months ago rajdeepboral00 • 0
0
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0
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264
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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
3
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2
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Biological replicates consideration in DESeq2 design formula.
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Deseq2 paired sample in the design is considered as "batch"?
DESeq2
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0
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0
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296
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Job: Job: Ensembl Dataflow Coordinator
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6 months ago Aleena_Ensembl ▴ 30
0
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1.4k
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Retrieve Salmon transcript quantification file from recount3
recount3
updated 6 months ago by ★ 1.1k • written 6 months ago by ▴ 10
0
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1
reply
1.1k
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error from library(IlluminaHumanMethylationMSAmanifest)
MSAarray25 hcg110.db
updated 6 months ago by 68k • written 6 months ago by • 0
0
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1
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897
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Source / binary version mismatch for rGADEM
rGADEM
updated 6 months ago by 4.2k • written 6 months ago by • 0
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9
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13k
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Bioconductor version cannot be validated
BiocManager Bioconductor
updated 6 months ago by • 0 • written 4.4 years ago by ▴ 10
3
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1
reply
3.8k
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DESeq2 empirical bayes: variance of the prior for log fold changes (LFC)
DESeq2
updated 6 months ago by 43k • written 6 months ago by ▴ 10
0
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2
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1.3k
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Interaction in Design Experimental
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6 months ago Ferdinand David • 0
0
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0
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346
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6 months ago Gordon Smyth 53k
1
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4
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Heatmap of the Count Matrix
rnaseqGene
updated 12 weeks ago by • 0 • written 6 months ago by • 0
0
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1
reply
610
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DESeq2 results
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updated 6 months ago by ★ 5.0k • 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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4
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8.9k
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Bioconductor version cannot be validated
Bioconductor Annotation Ann
written 2.2 years ago by • 0
0
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4
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925
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Position of the legend object in complexHeatmap
ComplexHeatmap
6 months ago caroline.zanchi ▴ 10
0
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4
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3.2k
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Drawing custom KEGG pathways
pathview KEGG
written 4.6 years ago by ▴ 10
1
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18
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error in ChAMP loading file
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updated 5 months ago by • 0 • written 3.1 years ago by • 0
1
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4
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2.0k
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How to left_join a tidySummarizedExperiment with a GRanges object by seqnames and start (tidyverse-style)?
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7 months ago • updated 12 weeks ago Kateřina • 0
46,692 results • Page 4 of 934
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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…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
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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
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