Showing : DEXSEq • reset
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Exonic part number of genes on the reverse strand
DEXSeq DEXSeq
12.4 years ago Guest User ★ 13k
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DEXSeq: PlotMA issues
graph DESeq DEXSeq graph DESeq DEXSeq
12.4 years ago Alejandro Reyes ★ 1.9k
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2
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1.2k
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a question in merging sam files for DEXSeq
DEXSeq DEXSeq
updated 12.4 years ago by ★ 3.8k • written 12.4 years ago by ▴ 80
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1
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1.1k
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DEXSeq troubles
DEXSeq DEXSeq
updated 12.4 years ago by ★ 1.9k • written 12.4 years ago by ▴ 150
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3
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2.9k
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DEXSeq Issue
Alignment Annotation GO Homo sapiens TranscriptDb PROcess GenomicFeatures DEXSeq Alignment
updated 12.4 years ago by 43k • written 12.4 years ago by ▴ 150
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6
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2.0k
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DEXSeq for 1 gene
DEXSeq DEXSeq
updated 12.4 years ago by ★ 1.9k • written 12.5 years ago by ▴ 120
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809
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DEXSeq: Creating sample
DEXSeq DEXSeq
12.4 years ago Bio152 ▴ 150
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1
reply
988
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DEXSeq User Friendly Guide (Start to Finish)
DEXSeq DEXSeq
updated 12.4 years ago by ★ 13k • written 12.4 years ago by ▴ 150
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2
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3.2k
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DEXSeq error: Count files do not correspond to the flattened annotation file
Annotation GO DEXSeq Annotation GO DEXSeq
updated 12.4 years ago by ★ 3.8k • written 12.5 years ago by ▴ 50
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4
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1.8k
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DEXSeq on two-exon genes: how to specify a formula without redundant terms
safe DEXSeq safe DEXSeq
12.5 years ago Narayanan, Manikandan NIH/NIAID [E] ▴ 60
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2
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1.3k
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DEXSeq: subsetting ExonCountSet ?
DESeq DEXSeq DESeq DEXSeq
updated 12.5 years ago by ★ 13k • written 12.5 years ago by ▴ 50
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3
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3.9k
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DESeq versus CuffDiff2 for RNA-seq expression quantification in parasite-infected blood
Normalization DESeq DEXSeq Normalization DESeq DEXSeq
updated 12.5 years ago by ★ 3.8k • written 12.5 years ago by ▴ 40
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1.2k
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DEXSeq html report error
puma DEXSeq puma DEXSeq
12.6 years ago Natasha ▴ 440
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1
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2.3k
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illegal operand when I run DEXSeq
DEXSeq DEXSeq
updated 12.7 years ago by ★ 1.3k • written 12.7 years ago by ★ 13k
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4
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1.9k
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illegal operand when I run DEXSeq
DEXSeq DEXSeq
updated 12.7 years ago by ★ 13k • written 12.7 years ago by ★ 1.3k
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0
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1.2k
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aggregate genes in DEXSeq
DEXSeq DEXSeq
12.7 years ago Alejandro Reyes ★ 1.9k
0
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7
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2.7k
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Detecting differential usage of introns from RNA-seq data.
DEXSeq DEXSeq
updated 12.7 years ago by ★ 1.9k • written 12.7 years ago by ▴ 320
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4
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1.2k
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DEXseq: several "1" and "NA" in padjust column
DEXSeq DEXSeq
updated 12.7 years ago by ★ 13k • written 12.7 years ago by ▴ 140
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1
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1.3k
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DEXSeq package - read.HTSeqCount function error
Annotation DEXSeq Annotation DEXSeq
updated 12.8 years ago by ★ 13k • written 12.8 years ago by ▴ 20
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3
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1.5k
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DEXSeq: building exon count set
DESeq DEXSeq DESeq DEXSeq
updated 12.8 years ago by ★ 1.9k • written 12.8 years ago by ▴ 140
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2
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1.3k
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DEXSeq and parallel, orphan processes.
GO DEXSeq GO DEXSeq
updated 12.8 years ago by ★ 1.9k • written 12.8 years ago by ▴ 30
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1
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1.2k
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DEXSeq package - read.HTSeqCount function error
DEXSeq DEXSeq
updated 12.8 years ago by ★ 1.9k • written 12.8 years ago by ▴ 20
0
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4
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1.2k
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DEXSeq all p-values are 1
GO DEXSeq GO DEXSeq
updated 12.9 years ago by ★ 13k • written 12.9 years ago by ★ 13k
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0
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1.6k
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get synthetic exon dataset with easyRNASeq
RNASeq Alignment Annotation Normalization GO PROcess GenomicRanges DEXSeq easyRNASeq GO
13.0 years ago delhomme@embl.de ★ 1.2k
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3
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1.3k
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DEXSeq offset term
Normalization PROcess DEXSeq Normalization PROcess DEXSeq
updated 13.1 years ago by ★ 1.9k • written 13.1 years ago by ★ 13k
1
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2
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1.4k
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DEXSeq: Difference in splicing
graph DEXSeq graph DEXSeq
updated 13.1 years ago by ★ 1.9k • written 13.1 years ago by ★ 13k
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9
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2.5k
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DEXSeq many exons marked as not testable
DEXSeq DEXSeq
updated 13.1 years ago by ▴ 10 • written 13.1 years ago by ▴ 70
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7
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3.5k
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How to retrieve exon ID and gene ID from exon coordinates?
RNASeq DEXSeq RNASeq DEXSeq
updated 13.2 years ago by 68k • written 13.2 years ago by ▴ 340
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1
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4.5k
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RNA-seq analysis and two-way ANOVAs
edgeR baySeq DEGseq DESeq DEXSeq edgeR baySeq DEGseq DESeq DEXSeq
updated 13.2 years ago by 53k • written 13.2 years ago by ▴ 160
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1
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1.2k
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DEXSeq: Error: all(unlist(lapply(design, class)) == "factor") is not TRUE
DEXSeq DEXSeq
updated 13.2 years ago by ★ 1.9k • written 13.2 years ago by ▴ 90
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4
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1.1k
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error in DEXSeq fitDispersionFunction()
DEXSeq DEXSeq
updated 13.2 years ago by ▴ 120 • written 13.2 years ago by ★ 1.9k
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1
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1.2k
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multicore and DEXSeq
DEXSeq DEXSeq
updated 13.3 years ago by ▴ 50 • written 13.3 years ago by ★ 1.9k
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1
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1.1k
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clarification on DEXSeq output
DEXSeq DEXSeq
updated 13.3 years ago by ★ 3.8k • written 13.3 years ago by ▴ 190
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1
reply
986
views
error in DEXSeq version 1.3.13
DEXSeq DEXSeq
updated 13.3 years ago by ★ 1.9k • written 13.3 years ago by ▴ 190
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2
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2.1k
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counts from HTSeq vs DEXSeq
DEXSeq DEXSeq
updated 13.3 years ago by ★ 3.8k • written 13.3 years ago by ▴ 190
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1
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2.2k
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Pasilla Package
DEXSeq DEXSeq
updated 13.3 years ago by ★ 1.9k • written 13.3 years ago by ★ 13k
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4
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1.8k
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DEXSeq error
DEXSeq DEXSeq
updated 13.3 years ago by ★ 1.9k • written 13.3 years ago by ▴ 140
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1
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991
views
DEXSeq question
DEXSeq DEXSeq
updated 13.4 years ago by ★ 1.9k • written 13.4 years ago by ▴ 190
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4
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1.9k
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A question with DEXSeq package: inconsistency between normalized counts vs. fitted expression, fitted splicing or fold changes
Cancer DEXSeq Cancer DEXSeq
updated 13.4 years ago by ★ 1.9k • written 13.4 years ago by ▴ 40
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1
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978
views
RnaSeqTutorial Package
Annotation BSgenome BSgenome DESeq DEXSeq Annotation BSgenome BSgenome DESeq DEXSeq
updated 13.4 years ago by ★ 13k • written 13.4 years ago by ★ 13k
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3
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2.8k
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interpreting DEXSeq output
DEXSeq DEXSeq
updated 13.4 years ago by ★ 1.9k • written 13.4 years ago by ▴ 160
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4
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1.7k
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DEXSeq package: Error in DEXSeqHTML
DEXSeq DEXSeq
updated 13.4 years ago by ★ 1.9k • written 13.4 years ago by ▴ 50
0
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2
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2.4k
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DEXSeq filtering
DEXSeq DEXSeq
updated 13.4 years ago by ★ 3.8k • written 13.4 years ago by ▴ 370
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0
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828
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DESeq error thrown during estimateDispersions w/ coxReid method
DESeq DEXSeq DESeq DEXSeq
13.4 years ago Simon Anders ★ 3.8k
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0
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902
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DESeq error thrown during estimateDispersions w/ coxReid method
Cancer DEXSeq Cancer DEXSeq
13.5 years ago Steve Lianoglou ★ 13k
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12
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3.1k
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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 13.5 years ago by ▴ 60 • written 13.5 years ago by ▴ 370
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3
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1.5k
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multifactorial analysis
DEXSeq DEXSeq
updated 13.6 years ago by 53k • written 13.6 years ago by ▴ 810
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2
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1.7k
views
DEXSeq error during fold change calculation
Alignment DEXSeq Alignment DEXSeq
updated 13.6 years ago by ★ 13k • written 13.6 years ago by ★ 13k
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1
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1.8k
views
DEXSeq with no biological replicate?
DEXSeq DEXSeq
updated 13.6 years ago by ★ 3.8k • written 13.6 years ago by ▴ 230
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2
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3.1k
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DESeq vs DEXSeq
RNASeq Annotation DESeq DEXSeq RNASeq Annotation DESeq DEXSeq
updated 13.6 years ago by ★ 3.8k • written 13.6 years ago by ▴ 280
363 results • Page 7 of 8
Recent ...
Replies
Comment: "Watched Tags" are being erased rather than updated by shepherl 4.2k
I can reproduce this and have opened an issue on the code base https://github.com/Bioconductor/support.bioconductor.org/issues/112
Comment: "Watched Tags" are being erased rather than updated by shepherl 4.2k
we can investigate this issue. thank you for bringing it to our attention
Comment: deseq2 filter the low counts by Michael Love 43k
> But within each comparison (contrast), if I trace some DEGs back to the original salmon merged gene counts (or even to normalised counts)…
Comment: deseq2 filter the low counts by empty_mt • 0
Thank you for you suggestion to look at the pre-filtering section in the DESeq2 vignettes - am I missing something? I have 6 treatments, …
Comment: deseq2 filter the low counts by Michael Love 43k
Have you seen this part: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#pre-filtering
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Bioconductor 3.22 Released!
Bioconductor 3.22 Released!
Comment: "Watched Tags" are being erased rather than updated
Comment: deseq2 filter the low counts
Answer: DESeq2 interactions
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