Showing : Deseq • reset
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Recommended gene model for DESeq
DESeq DESeq
updated 13.7 years ago by ★ 3.8k • written 13.7 years ago by ▴ 30
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1.5k
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counts vs exprs
DESeq DESeq
updated 13.7 years ago by ★ 13k • written 13.7 years ago by ▴ 230
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DESeq countDataSets and arrayQualityMetrics (was: Re: DESeq estimateDispersion options for lower depth miRNA-seq)
Genetics Biobase arrayQualityMetrics DESeq Genetics Biobase arrayQualityMetrics DESeq
13.7 years ago Wolfgang Huber ★ 13k
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edgeR-DeSeq - inconsistency between Variance and Coefficient of Variation
Regression edgeR DESeq Regression edgeR DESeq
13.7 years ago Gordon Smyth 53k
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edgeR-DeSeq - inconsistency between Variance and Coefficient of Variation?
edgeR DESeq edgeR DESeq
13.7 years ago Miguel Gallach ▴ 50
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1
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1.4k
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DESeq estimateDispersion options for lower depth miRNA-seq
Genetics arrayQualityMetrics DESeq Genetics arrayQualityMetrics DESeq
updated 13.7 years ago by ★ 13k • written 13.7 years ago by ▴ 50
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13
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7.9k
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Up & Downregulated genes using DESeq
DESeq DESeq
updated 13.7 years ago by ▴ 80 • written 13.7 years ago by ▴ 40
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2.3k
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DESeq for two-factor models
GO DESeq GO DESeq
13.7 years ago Henning Wildhagen ▴ 30
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2
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Updating Package Versions from SVN
DESeq DESeq
updated 13.7 years ago by 68k • written 13.7 years ago by ▴ 210
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1
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1.2k
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DESeq estimateDispersion options for lower depth miRNA-seq
Sequencing miRNA DESeq Sequencing miRNA DESeq
updated 13.7 years ago by ★ 13k • written 13.7 years ago by ▴ 50
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2
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3.2k
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DESeq vs DEXSeq
RNASeq Annotation DESeq DEXSeq RNASeq Annotation DESeq DEXSeq
updated 13.7 years ago by ★ 3.8k • written 13.7 years ago by ▴ 280
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2.0k
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DeSeq Volcano plot- error
RNASeq DESeq RNASeq DESeq
updated 13.7 years ago by ★ 13k • written 13.7 years ago by ▴ 30
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3
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DESeq multi-factor export results
DESeq DESeq
updated 13.7 years ago by ★ 3.8k • written 13.7 years ago by ▴ 40
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2
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DESeq Question
DESeq DESeq
updated 13.7 years ago by ★ 3.8k • written 13.7 years ago by ▴ 40
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3
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edgeR i get 377 significant genes where in DESeq i got 0
edgeR DESeq edgeR DESeq
updated 13.7 years ago by 53k • written 13.8 years ago by ★ 13k
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1
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1.1k
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DESeq without replicates, Problem trying to obtain significant hits
DESeq DESeq
updated 13.8 years ago by ★ 3.8k • written 13.8 years ago by ▴ 30
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3
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Newer version of DESeq give much small list of DE genes
DESeq DESeq
updated 13.8 years ago by ▴ 410 • written 13.8 years ago by ▴ 30
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1.6k
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Checking RNAseq DESeq pipeline
Sequencing PROcess DESeq Sequencing PROcess DESeq
updated 13.8 years ago by ★ 13k • written 13.8 years ago by ▴ 280
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10
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2.0k
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re incomplete analysis in Deseq
DESeq DESeq
updated 13.8 years ago by ★ 13k • written 13.8 years ago by ★ 13k
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1.1k
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Standard error and confidence intervals in DESeq?
Genetics DESeq Genetics DESeq
updated 13.8 years ago by ★ 13k • written 13.8 years ago by ▴ 190
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2.1k
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Volcano plot
Sequencing DESeq Sequencing DESeq
updated 13.8 years ago by ★ 13k • written 13.8 years ago by ▴ 30
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1
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1.2k
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Installation errors for DESeq, Genomic Ranges etc.
rtracklayer DESeq GenomicRanges BiocInstaller rtracklayer DESeq GenomicRanges BiocInstaller
updated 13.8 years ago by 25k • written 13.8 years ago by ▴ 220
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1
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967
views
how to update DEseq package on windows?
DESeq DESeq
updated 13.8 years ago by ★ 1.2k • written 13.8 years ago by ★ 2.0k
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1
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766
views
DESeq dispersions for series
DESeq DESeq
updated 13.8 years ago by ★ 13k • written 13.8 years ago by ▴ 10
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6
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7.7k
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DeSeq vs current version of Cuffdiff
Sequencing Bayesian Cancer DESeq Sequencing Bayesian Cancer DESeq
updated 13.8 years ago by ▴ 290 • written 13.8 years ago by ★ 2.0k
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using easyRNASeq examples
RNASeq Annotation BSgenome convert biomaRt BSgenome IRanges DESeq easyRNASeq RNASeq
13.8 years ago delhomme@embl.de ★ 1.2k
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1
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984
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about library size and length of gene information in DEseq
edgeR DESeq edgeR DESeq
updated 13.8 years ago by ★ 13k • written 13.8 years ago by ★ 2.0k
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8
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4.5k
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DESeq and transcript-wise analysis
convert DESeq convert DESeq
13.8 years ago Elena Sorokin ▴ 160
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7
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1.8k
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package to count read prior to DESeq?
DESeq DESeq
updated 13.9 years ago by ★ 3.6k • written 13.9 years ago by ▴ 280
3
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5
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3.0k
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DESeq on transcripts v/s genes
DESeq DESeq
updated 13.9 years ago by ★ 13k • written 13.9 years ago by ▴ 410
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0
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BaseCounts & edgeR
limma edgeR DESeq limma edgeR DESeq
13.9 years ago Gordon Smyth 53k
0
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859
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DESeq estimateDispersion query
DESeq DESeq
13.9 years ago Michal Okoniewski ▴ 190
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1
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1.1k
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DESeq - ChIP-seq (including background reads)
DESeq DESeq
updated 13.9 years ago by ▴ 70 • written 13.9 years ago by ▴ 70
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BaseCounts & edgeR
edgeR DESeq edgeR DESeq
13.9 years ago Marco Groth ▴ 10
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1.3k
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DESeq estimateDispersion query
GO edgeR DESeq GO edgeR DESeq
13.9 years ago Iain Gallagher ▴ 930
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1.2k
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DESeq: how to get the variance information
DESeq DESeq
updated 13.9 years ago by ★ 3.8k • written 13.9 years ago by ▴ 60
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961
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DESeq mean,var
RNASeq GO DESeq RNASeq GO DESeq
updated 13.9 years ago by ★ 13k • written 13.9 years ago by ▴ 50
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3
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DESeq for an mRNA-seq time course
DESeq DESeq
13.9 years ago Elena Sorokin ▴ 160
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8
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2.6k
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Fwd: differential binding question
edgeR DESeq edgeR DESeq
updated 13.9 years ago by ▴ 100 • written 13.9 years ago by ▴ 370
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normalizing time course RNA-Seq data
Normalization edgeR DESeq Normalization edgeR DESeq
13.9 years ago Mark Robinson ▴ 880
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796
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residual variances in Deseq packages
DESeq DESeq
14.0 years ago Hubert Rehrauer ▴ 100
0
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3
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1.7k
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DESeq variance question
edgeR DESeq edgeR DESeq
updated 14.0 years ago by 53k • written 14.0 years ago by ▴ 10
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1.1k
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edgeR - R script - results compared to DESeq
GLAD edgeR DESeq GLAD edgeR DESeq
14.0 years ago Gordon Smyth 53k
0
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5
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2.3k
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edgeR - R script - results compared to DESeq
edgeR DESeq edgeR DESeq
updated 14.0 years ago by ▴ 40 • written 14.0 years ago by ▴ 40
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1
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1.4k
views
DESeq gene names under id
DESeq DESeq
updated 14.0 years ago by ★ 3.8k • written 14.0 years ago by ▴ 20
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4
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DESeq adjusted pvalue calculation / filtering data
Sequencing Organism qvalue DESeq Sequencing Organism qvalue DESeq
updated 14.0 years ago by ★ 6.0k • written 14.1 years ago by ▴ 20
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2
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1.8k
views
Block x Treatment interaction test with DeSeq
DESeq DESeq
updated 14.0 years ago by ★ 3.8k • written 14.0 years ago by ▴ 10
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1
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1.2k
views
DESeq Error: pobs == ps[kAs[i] + 1] is not TRUE
DESeq DESeq
updated 14.1 years ago by ★ 3.8k • written 14.1 years ago by ★ 3.4k
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1
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2.7k
views
TMM and calcNormFactors: Normalization in baySeq to match edgeR and DESeq
Normalization Bayesian edgeR baySeq DESeq Normalization Bayesian edgeR baySeq DESeq
updated 14.1 years ago by ▴ 40 • written 14.1 years ago by 53k
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1.4k
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TMM and calcNormFactors: Normalization in baySeq to match, edgeR and DESeq (Smith, Hilary A)
Normalization edgeR baySeq DESeq Normalization edgeR baySeq DESeq
14.1 years ago Thomas J Hardcastle ▴ 180
512 results • Page 9 of 11
Recent ...
Replies
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…
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
Awards • All
Popular Question to shepherl 4.2k
Popular Question to James W. MacDonald 68k
Popular Question to Gordon Smyth 53k
Commentator to sina.nassiri ▴ 130
Popular Question to Hervé Pagès 16k
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