Showing : DESEq • reset
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Recommended gene model for DESeq
DESeq DESeq
updated 13.5 years ago by ★ 3.8k • written 13.5 years ago by ▴ 30
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1
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1.5k
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counts vs exprs
DESeq DESeq
updated 13.5 years ago by ★ 13k • written 13.5 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
13.5 years ago Wolfgang Huber ★ 13k
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edgeR-DeSeq - inconsistency between Variance and Coefficient of Variation
Regression edgeR DESeq Regression edgeR DESeq
13.5 years ago Gordon Smyth 53k
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1.5k
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edgeR-DeSeq - inconsistency between Variance and Coefficient of Variation?
edgeR DESeq edgeR DESeq
13.5 years ago Miguel Gallach ▴ 50
0
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1
reply
1.3k
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DESeq estimateDispersion options for lower depth miRNA-seq
Genetics arrayQualityMetrics DESeq Genetics arrayQualityMetrics DESeq
updated 13.5 years ago by ★ 13k • written 13.5 years ago by ▴ 50
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13
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7.8k
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Up & Downregulated genes using DESeq
DESeq DESeq
updated 13.5 years ago by ▴ 80 • written 13.5 years ago by ▴ 40
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2.2k
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DESeq for two-factor models
GO DESeq GO DESeq
13.5 years ago Henning Wildhagen ▴ 30
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2
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1.0k
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Updating Package Versions from SVN
DESeq DESeq
updated 13.5 years ago by 68k • written 13.5 years ago by ▴ 210
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1
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1.1k
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DESeq estimateDispersion options for lower depth miRNA-seq
Sequencing miRNA DESeq Sequencing miRNA DESeq
updated 13.5 years ago by ★ 13k • written 13.5 years ago by ▴ 50
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2
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3.1k
views
DESeq vs DEXSeq
RNASeq Annotation DESeq DEXSeq RNASeq Annotation DESeq DEXSeq
updated 13.5 years ago by ★ 3.8k • written 13.5 years ago by ▴ 280
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1
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1.9k
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DeSeq Volcano plot- error
RNASeq DESeq RNASeq DESeq
updated 13.6 years ago by ★ 13k • written 13.6 years ago by ▴ 30
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3
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DESeq multi-factor export results
DESeq DESeq
updated 13.6 years ago by ★ 3.8k • written 13.6 years ago by ▴ 40
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2
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1.5k
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DESeq Question
DESeq DESeq
updated 13.6 years ago by ★ 3.8k • written 13.6 years ago by ▴ 40
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3
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1.5k
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edgeR i get 377 significant genes where in DESeq i got 0
edgeR DESeq edgeR DESeq
updated 13.6 years ago by 53k • written 13.6 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 13.6 years ago by ★ 3.8k • written 13.6 years ago by ▴ 30
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3
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1.0k
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Newer version of DESeq give much small list of DE genes
DESeq DESeq
updated 13.6 years ago by ▴ 410 • written 13.6 years ago by ▴ 30
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1
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1.5k
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Checking RNAseq DESeq pipeline
Sequencing PROcess DESeq Sequencing PROcess DESeq
updated 13.6 years ago by ★ 13k • written 13.6 years ago by ▴ 280
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10
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1.9k
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re incomplete analysis in Deseq
DESeq DESeq
updated 13.6 years ago by ★ 13k • written 13.6 years ago by ★ 13k
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1
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1.0k
views
Standard error and confidence intervals in DESeq?
Genetics DESeq Genetics DESeq
updated 13.6 years ago by ★ 13k • written 13.6 years ago by ▴ 190
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1
reply
2.0k
views
Volcano plot
Sequencing DESeq Sequencing DESeq
updated 13.6 years ago by ★ 13k • written 13.6 years ago by ▴ 30
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1
reply
1.2k
views
Installation errors for DESeq, Genomic Ranges etc.
rtracklayer DESeq GenomicRanges BiocInstaller rtracklayer DESeq GenomicRanges BiocInstaller
updated 13.6 years ago by 25k • written 13.6 years ago by ▴ 220
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1
reply
941
views
how to update DEseq package on windows?
DESeq DESeq
updated 13.6 years ago by ★ 1.2k • written 13.7 years ago by ★ 2.0k
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1
reply
729
views
DESeq dispersions for series
DESeq DESeq
updated 13.7 years ago by ★ 13k • written 13.7 years ago by ▴ 10
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6
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7.6k
views
DeSeq vs current version of Cuffdiff
Sequencing Bayesian Cancer DESeq Sequencing Bayesian Cancer DESeq
updated 13.7 years ago by ▴ 290 • written 13.7 years ago by ★ 2.0k
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using easyRNASeq examples
RNASeq Annotation BSgenome convert biomaRt BSgenome IRanges DESeq easyRNASeq RNASeq
13.7 years ago delhomme@embl.de ★ 1.2k
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1
reply
962
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about library size and length of gene information in DEseq
edgeR DESeq edgeR DESeq
updated 13.7 years ago by ★ 13k • written 13.7 years ago by ★ 2.0k
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8
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4.4k
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DESeq and transcript-wise analysis
convert DESeq convert DESeq
13.7 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 13.7 years ago by ★ 3.6k • written 13.7 years ago by ▴ 280
3
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5
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2.9k
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DESeq on transcripts v/s genes
DESeq DESeq
updated 13.7 years ago by ★ 13k • written 13.7 years ago by ▴ 410
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0
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BaseCounts & edgeR
limma edgeR DESeq limma edgeR DESeq
13.7 years ago Gordon Smyth 53k
0
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0
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824
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DESeq estimateDispersion query
DESeq DESeq
13.7 years ago Michal Okoniewski ▴ 190
0
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1
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1.1k
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DESeq - ChIP-seq (including background reads)
DESeq DESeq
updated 13.7 years ago by ▴ 70 • written 13.7 years ago by ▴ 70
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1.1k
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BaseCounts & edgeR
edgeR DESeq edgeR DESeq
13.7 years ago Marco Groth ▴ 10
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1.3k
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DESeq estimateDispersion query
GO edgeR DESeq GO edgeR DESeq
13.7 years ago Iain Gallagher ▴ 930
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1
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1.1k
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DESeq: how to get the variance information
DESeq DESeq
updated 13.7 years ago by ★ 3.8k • written 13.7 years ago by ▴ 60
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1
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907
views
DESeq mean,var
RNASeq GO DESeq RNASeq GO DESeq
updated 13.7 years ago by ★ 13k • written 13.7 years ago by ▴ 50
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3
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2.6k
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DESeq for an mRNA-seq time course
DESeq DESeq
13.8 years ago Elena Sorokin ▴ 160
0
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8
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2.5k
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Fwd: differential binding question
edgeR DESeq edgeR DESeq
updated 13.8 years ago by ▴ 100 • written 13.8 years ago by ▴ 370
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0
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1.8k
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normalizing time course RNA-Seq data
Normalization edgeR DESeq Normalization edgeR DESeq
13.8 years ago Mark Robinson ▴ 880
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0
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767
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residual variances in Deseq packages
DESeq DESeq
13.8 years ago Hubert Rehrauer ▴ 100
0
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3
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1.6k
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DESeq variance question
edgeR DESeq edgeR DESeq
updated 13.8 years ago by 53k • written 13.9 years ago by ▴ 10
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0
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1.1k
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edgeR - R script - results compared to DESeq
GLAD edgeR DESeq GLAD edgeR DESeq
13.9 years ago Gordon Smyth 53k
0
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5
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2.2k
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edgeR - R script - results compared to DESeq
edgeR DESeq edgeR DESeq
updated 13.9 years ago by ▴ 40 • written 13.9 years ago by ▴ 40
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1
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1.4k
views
DESeq gene names under id
DESeq DESeq
updated 13.9 years ago by ★ 3.8k • written 13.9 years ago by ▴ 20
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4
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8.7k
views
DESeq adjusted pvalue calculation / filtering data
Sequencing Organism qvalue DESeq Sequencing Organism qvalue DESeq
updated 13.9 years ago by ★ 6.0k • written 13.9 years ago by ▴ 20
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2
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1.7k
views
Block x Treatment interaction test with DeSeq
DESeq DESeq
updated 13.9 years ago by ★ 3.8k • written 13.9 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 13.9 years ago by ★ 3.8k • written 13.9 years ago by ★ 3.4k
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1
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2.6k
views
TMM and calcNormFactors: Normalization in baySeq to match edgeR and DESeq
Normalization Bayesian edgeR baySeq DESeq Normalization Bayesian edgeR baySeq DESeq
updated 13.9 years ago by ▴ 40 • written 13.9 years ago by 53k
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0
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1.3k
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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
13.9 years ago Thomas J Hardcastle ▴ 180
512 results • Page 9 of 11
Recent ...
Replies
Comment: Check removeBatchEffect effectiveness by massimo • 0
I would kindly ask for additional support. When not including the design_timepoint argument in removeBatchEffect and thus keeping the inter…
Comment: Error Loading Experiment from SimBenchData Package by ksankaran • 0
Aha, that was it! The object was class Seurat, but I didn't have it installed. After installing, everything works as expected.
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset? by ATpoint ★ 5.0k
Is a method that is so computationally expensive really beneficial and necessary? You seem to have biological replication, don't you, so ps…
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes by ATpoint ★ 5.0k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
Comment: R course in Boston December 19-20 by eja.gaasa2e.r.m • 0
The upcoming XLSolutions R course in Boston on December 19 20 is a great opportunity to enhance your data skills. Whether you re a beginner…
Votes
Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
Comment: Error Loading Experiment from SimBenchData Package
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
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