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1
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1.9k
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intra-sample time series comparison using DESeq2
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updated 8.8 years ago by 43k • written 8.8 years ago by • 0
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understanding topGO enrichment
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8.8 years ago michael.steffen ▴ 20
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3
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DESeq2 not installing
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News: New Package Submission Deadline March 31
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8.8 years ago shepherl 4.2k
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2
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How to compare 10 GSMxxxxx from one GSE to 10 GSM from another GSE with GEOQuery
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champ.impute doesn't update beta matrix
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updated 8.8 years ago by ▴ 90 • written 8.8 years ago by ▴ 10
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3
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getBM to retrieve ensembl_gene_id's within a certain distance
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updated 8.8 years ago by 68k • written 8.8 years ago by • 0
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Basic question about updating information on Package Bioconductor Page
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8.8 years ago ines.desantiago • 0
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Gviz: Plot features with thin and thick lines
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8.8 years ago maltethodberg ▴ 180
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3
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getSeq human genomic sequences
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DiffBind for ATAC-seq
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updated 8.8 years ago by ▴ 70 • written 9.3 years ago by ▴ 50
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Experimental requirements and data preprocessing for transcriptome and translatome comparison
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8.8 years ago Benedikt • 0
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2
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updated 8.8 years ago by 25k • written 8.8 years ago by • 0
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RIPSeeker ripSeek does not produce any output
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8.8 years ago ofonov ▴ 10
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1
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Error in Heatmap...
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8.8 years ago baranikumar22 • 0
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Does TOPHAT-2 output works with EBSEQHMM ?
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8.8 years ago anshulmbi • 0
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RDAVIDWebService Input Incorrect
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8.8 years ago johntoomey • 0
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error with base-level DERfinder using large sample sizes
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updated 8.8 years ago by ★ 1.1k • written 8.8 years ago by • 0
2
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6
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updated 8.8 years ago by ★ 7.9k • written 8.8 years ago by • 0
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Differential Expression Analysis
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updated 8.8 years ago by 68k • written 8.8 years ago by • 0
3
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rtracklayer: how to export gff file with gene names included?
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updated 8.8 years ago by ★ 11k • written 8.8 years ago by ▴ 270
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FlowSOM and ConsensusClusterPlus: reproducibility issue
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8.8 years ago Lukas Weber • 0
0
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4
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miRNA-seq data analysis
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Normalising GenomicMethylSet / MethylSet in Minfi
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8.8 years ago SplittingInfinity ▴ 60
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8.8 years ago weiiioyo • 0
1
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1
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Error in valcano plot
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8.8 years ago baranikumar22 • 0
2
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3
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edgeR ANOVA-like analysis
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updated 8.8 years ago by ★ 29k • written 8.8 years ago by • 0
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XML installation error during step config status: creating inst/scripts/RSXML.bsh
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8.8 years ago adamhelm • 0
1
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2
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flowCore: 'truncate_max_range' argument in 'read.flowSet'
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8.8 years ago Lukas Weber • 0
22
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10
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Error in GRanges: could not find symbol "recursive" in environment of the generic function
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updated 8.8 years ago by ▴ 10 • written 8.8 years ago by ▴ 80
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3
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Unknown annotation in the RGChannelSetExtended object
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OmicCircos - Error in 1:scale.n : NA/NaN argument
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8.8 years ago Stefan Langenberg • 0
0
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0
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Gviz: control height of items within BiomartGeneRegionTrack (StackedTrack)
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8.8 years ago Kort, Eric ▴ 220
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999
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Cannot replace subset of DNAStringSet object
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3
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8.8 years ago Walter F. Baumann ▴ 10
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11
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DESEq2 Paired samples: Baseline Versus each Timepoint
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updated 8.8 years ago by 43k • written 8.8 years ago by • 0
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5
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error in installing bioconductor
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updated 8.8 years ago by ▴ 370 • written 8.8 years ago by • 0
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3
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unable to install bioconductor package
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bias correction (an example from ChIP-seq)
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8.8 years ago Bogdan ▴ 670
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2
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Trying to design a model(s) for a two factor RNA-seq experimental analysis in EdgeR with interaction
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updated 8.8 years ago by ★ 29k • written 8.8 years ago by • 0
3
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12
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Problem about use of TCGA rna-seq rsem gene results for regularized cox regression modeling
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8.8 years ago panagiotis.mokos ▴ 40
0
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1.9k
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Error raised during execution of MEDIPS package
medips
updated 8.8 years ago by ▴ 570 • written 8.8 years ago by • 0
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reply
3.1k
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Making a gff file for introns to be used with DEXSEQ
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updated 8.8 years ago by 16k • written 8.8 years ago by ▴ 40
1
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8
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[DESeq2] Automatic outlier detection and replacement with continuous variables
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8.8 years ago cajawe • 0
2
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4
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Error using Gviz and BiomartGeneRegionTrack, version problem?
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updated 8.8 years ago by ★ 1.6k • written 8.8 years ago by • 0
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reply
1.7k
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memory allocation error
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updated 8.8 years ago by 68k • written 8.8 years ago by ▴ 10
0
votes
0
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Tversky' alpha and beta should not be int, should they?
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8.8 years ago stephan.struckmann • 0
0
votes
2
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1.4k
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error in gcrma function
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updated 8.8 years ago by ★ 4.1k • written 8.8 years ago by • 0
0
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18
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WGCNA error in network construction ?
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8.8 years ago m.azhar ▴ 10
46,699 results • Page 342 of 934
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Answer: segfault in edgeR glmQLFit by Gordon Smyth 53k
Dear Mark, Thank you for providing a reproducible example. I confirm that I can reproduce the segfault myself on my own computer. We will …
Answer: DESeq2 - how many surrogate variables from svaseq, use of lfcshrink by aqeel • 0
Discover the pinnacle of Brazilian Jiu Jitsu gear at [Dragon][1] GI. [1]: https://dragongi.com/
Comment: How does contrasts.fit do in limma to extract comparisons with a model having in by Gordon Smyth 53k
I refered you to the DiffVar package 11 months ago. Did you consider it? Your clarification makes it clear that your issue is not with lim…
Comment: How does contrasts.fit do in limma to extract comparisons with a model having in by jtsy6383 • 0
Thanks for the reply Gordon. I am also working on the project and have been tasked to reformulate and add some details. We're interested i…
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…
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C: DESeq2 Following RSEM
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Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
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