Showing : Deseq • reset
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Fwd: DESeq plotting graphs.
Cancer DESeq Cancer DESeq
13.2 years ago Steve Lianoglou ★ 13k
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RNAseq object
RNASeq DESeq easyRNASeq RNASeq DESeq easyRNASeq
updated 13.2 years ago by ★ 4.2k • written 13.2 years ago by ★ 13k
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Differential expression analysis of CAGE data
Transcription Annotation convert edgeR DESeq Transcription Annotation convert edgeR DESeq
updated 13.2 years ago by ★ 13k • written 13.2 years ago by ▴ 30
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DESeq cuont table normalization
Normalization DESeq Normalization DESeq
updated 13.2 years ago by ★ 13k • written 13.2 years ago by ▴ 260
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DESeq - Estimating Dispersion with Technical Replicates
GLAD DESeq GLAD DESeq
updated 13.2 years ago by ★ 13k • written 13.2 years ago by ▴ 20
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DESeq error
DESeq DESeq
updated 13.2 years ago by ★ 3.8k • written 13.2 years ago by ▴ 50
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DESeq - working with more than 2 conditions
DESeq DESeq
updated 13.2 years ago by ★ 13k • written 13.2 years ago by ▴ 140
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Estimating Size Factors in DESeq Package
DESeq DESeq
updated 13.3 years ago by ★ 3.8k • written 13.3 years ago by ▴ 20
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DESeq Fold-Change calculation
DESeq DESeq
updated 13.3 years ago by ★ 3.8k • written 13.3 years ago by ★ 1.3k
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RNA-seq analysis and two-way ANOVAs
edgeR baySeq DEGseq DESeq DEXSeq edgeR baySeq DEGseq DESeq DEXSeq
updated 13.3 years ago by 53k • written 13.3 years ago by ▴ 160
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how to set parameter of DESeq function estimateDispersions
DESeq DESeq
13.3 years ago wang peter ★ 2.0k
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1.5k
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deseq within and between group variation
DESeq DESeq
updated 13.3 years ago by ★ 3.8k • written 13.3 years ago by ▴ 60
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DESeq normalization
Normalization DESeq Normalization DESeq
13.4 years ago • updated 13.3 years ago sudeep s ▴ 60
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EasyRNASeq issue (missing bai files)
GO PROcess DESeq easyRNASeq GO PROcess DESeq easyRNASeq
updated 13.4 years ago by ▴ 10 • written 13.4 years ago by ★ 1.2k
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how to design model in DESeq
DESeq DESeq
13.4 years ago wang peter ★ 2.0k
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801
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FW: Reproducibility in DESeq
convert DESeq convert DESeq
13.4 years ago Fatemehsadat Seyednasrollah ▴ 260
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DESeq installation problems
DESeq BiocInstaller DESeq BiocInstaller
updated 13.4 years ago by ★ 8.2k • written 13.4 years ago by ▴ 10
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how to get normalized counts from edgeR
DESeq DESeq
updated 13.4 years ago by ▴ 880 • written 13.4 years ago by ★ 2.0k
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easyRNAseq question
Category DESeq easyRNASeq Category DESeq easyRNASeq
updated 13.4 years ago by ★ 13k • written 13.4 years ago by ▴ 190
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down-expression and high-expression in single cell + amplification
DESeq DESeq
13.4 years ago Dror Hibsh ▴ 40
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Very Different group sizes in DE of two conditions
miRNA Cancer edgeR DESeq miRNA Cancer edgeR DESeq
updated 13.4 years ago by 53k • written 13.4 years ago by ★ 13k
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DESeq analysis
edgeR DESeq edgeR DESeq
updated 13.4 years ago by ★ 13k • written 13.4 years ago by ▴ 260
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Differential gene expression: EdgeR / DESeq and identifying noise/outliers
Sequencing edgeR DESeq Sequencing edgeR DESeq
13.5 years ago Gordon Smyth 53k
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FW: DESeq analysis
edgeR DESeq edgeR DESeq
13.5 years ago Fatemehsadat Seyednasrollah ▴ 260
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Differential gene expression: EdgeR / DESeq and identifying noise/outliers
Sequencing edgeR DESeq Sequencing edgeR DESeq
13.5 years ago Michael Salbaum ▴ 80
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pvalue and padj in DESeq
DESeq DESeq
updated 13.5 years ago by ★ 3.8k • written 13.5 years ago by ★ 13k
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DESeq analysis
DESeq DESeq
updated 13.5 years ago by ★ 13k • written 13.5 years ago by ★ 13k
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interactions between variables in DEXSeq
DESeq DESeq
updated 13.5 years ago by ★ 1.9k • written 13.5 years ago by ▴ 160
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estimateDispersions in DESeq
Genetics graph DESeq Genetics graph DESeq
updated 13.5 years ago by ★ 13k • written 13.5 years ago by ▴ 10
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DESeq and contrasts
DESeq DESeq
updated 13.5 years ago by 53k • written 13.5 years ago by ▴ 20
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990
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RnaSeqTutorial Package
Annotation BSgenome BSgenome DESeq DEXSeq Annotation BSgenome BSgenome DESeq DEXSeq
updated 13.5 years ago by ★ 13k • written 13.5 years ago by ★ 13k
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down-expression and high-expression in single cell + amplification
DESeq DESeq
updated 13.5 years ago by ★ 4.2k • written 13.5 years ago by ★ 13k
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paired analysis in RNA Seq data using DESeq
RNASeq edgeR DESeq RNASeq edgeR DESeq
13.5 years ago Natasha ▴ 440
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3.9k
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voom() vs. RPKM/FPKM or otherwise normalized counts, and GC correction, when fitting models to a small number of responses (per-feature counts)
Normalization graph limma convert edgeR DESeq Rsubread Normalization graph limma convert
updated 2.9 years ago by 53k • written 13.5 years ago by ★ 6.5k
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DESeq estimateDispersions() problem
DESeq DESeq
updated 13.5 years ago by ★ 13k • written 13.5 years ago by ★ 1.2k
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DESeq estimateDispersions() problem
DESeq DESeq
13.5 years ago Karl Lundén ▴ 20
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DESeq error thrown during estimateDispersions w/ coxReid method
DESeq DEXSeq DESeq DEXSeq
13.6 years ago Simon Anders ★ 3.8k
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DESeq error with glm.fit during estimateDispersions
DESeq DESeq
updated 13.6 years ago by ★ 3.8k • written 13.6 years ago by ▴ 210
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How to use DESeq output to convert raw counts to normalized data
convert DESeq convert DESeq
updated 13.6 years ago by ★ 3.8k • written 13.6 years ago by ▴ 30
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How to use DESeq to normalize and estimate variance in a RNAseq timecourse analysis
Normalization DESeq Normalization DESeq
updated 13.6 years ago by ★ 13k • written 13.6 years ago by ▴ 50
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DESeq Package Questions
Network edgeR DESeq Network edgeR DESeq
13.6 years ago Xin Davis ▴ 30
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2.4k
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DESeq
DESeq DESeq
updated 13.6 years ago by ★ 13k • written 13.6 years ago by ▴ 440
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problem with loading DESeq after upgrading from R 2.14 to R 2.15
GUI DESeq DEXSeq GUI DESeq DEXSeq
updated 13.6 years ago by ▴ 60 • written 13.6 years ago by ▴ 370
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823
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回复： TMM factors
Normalization edgeR DESeq Normalization edgeR DESeq
13.6 years ago Mark Robinson ▴ 880
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DESeq without replicates, Problem trying to obtain significant hits
DESeq DESeq
13.7 years ago Asma ▴ 10
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2.4k
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DeSeq - How to get the Biological Coefficient of Variation
edgeR DESeq edgeR DESeq
updated 13.7 years ago by ★ 3.8k • written 13.7 years ago by ▴ 50
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error in dispersion estimate
DESeq DESeq
13.7 years ago mariangela bonizzoni ▴ 20
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1.7k
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Genominator error when calling syste.time
Genominator DESeq Genominator DESeq
updated 13.7 years ago by ★ 6.5k • written 13.7 years ago by ▴ 200
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question about DESeq or tissue-specific expression
DESeq DESeq
updated 13.7 years ago by ★ 13k • written 13.7 years ago by ▴ 450
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810
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Checking output of DESeq package analysis
DESeq DESeq
updated 13.7 years ago by ★ 3.8k • written 13.7 years ago by ★ 13k
512 results • Page 8 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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