Showing : Dexseq • reset
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deseq2: convert ensembl ID to gene symbol.
DEXSeq DESeq2 DEXSeq DESeq2
updated 4.4 years ago by • 0 • written 8.5 years ago by ▴ 970
0
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3
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3.8k
views
p-value vs adjusted p-value in DEXSeq
DEXSeq DEXSeq
updated 9.6 years ago by ★ 3.7k • written 9.6 years ago by ▴ 70
12
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2
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3.8k
views
DEXSeq Usage and Expression Confusion
dexseq
updated 8.1 years ago by ★ 3.7k • written 8.1 years ago by ▴ 360
0
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1
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3.5k
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RNA-seq analysis and two-way ANOVAs
edgeR baySeq DEGseq DESeq DEXSeq edgeR baySeq DEGseq DESeq DEXSeq
updated 10.4 years ago by 47k • written 10.4 years ago by ▴ 150
0
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3
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3.1k
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DESeq versus CuffDiff2 for RNA-seq expression quantification in parasite-infected blood
Normalization DESeq DEXSeq Normalization DESeq DEXSeq
updated 9.8 years ago by ★ 3.7k • written 9.8 years ago by ▴ 40
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31
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3.0k
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Error in find DEXSeq package
deseq dexseq
7.7 years ago engr.yahya602 • 0
1
vote
6
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3.0k
views
DEXSeq: question about usage coefficient and splicing plot
dexseq
updated 2.2 years ago by ▴ 20 • written 7.8 years ago by • 0
0
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7
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3.0k
views
DEXSeq Error in estimateExonFoldChanges: the matrix is either rank-deficient or indefinite
dexseq estimateexonfoldchanges
updated 6.8 years ago by ★ 1.8k • written 6.9 years ago by ▴ 20
3
votes
6
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3.0k
views
DEXSeq Error: unable to find an inherited method for function ‘mcols’ for signature ‘"matrix"’
DEXSeq
updated 6.8 years ago by ★ 1.8k • written 6.8 years ago by • 0
2
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6
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2.8k
views
DEXSeq Error in lf[[1]] : subscript out of bounds
DEXSeq
7.5 years ago rahel14350 ▴ 10
0
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2
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2.6k
views
DEXSeq on FeatureCounts output
dexseq featurecounts
7.4 years ago Vivek.b ▴ 100
0
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1
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2.6k
views
Error in estimateDispersions of DEXSeq
DEXSeq estimateDispersions
updated 8.1 years ago by 39k • written 8.1 years ago by • 0
1
vote
15
replies
2.6k
views
junction.bed to GTF to use in DEXSeq
junction.bed DEXSeq
updated 7.5 years ago by ▴ 360 • written 7.5 years ago by ▴ 10
15
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6
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2.5k
views
Reference paper or resource for limma::diffSplice and edgeR::diffSpliceDGE methods?
edgeR limma diffSplice DEXSeq
updated 6.5 years ago by ▴ 90 • written 6.5 years ago by ▴ 140
0
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13
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2.4k
views
Efficiently running DEXSeq for Large Cohorts
DEXSeq DEXSeq
updated 7.5 years ago by ▴ 10 • written 10.0 years ago by ▴ 320
2
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4
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2.4k
views
Simultaneously adding two different covariates in the model gives error in DESeq2.
deseq2 dexseq rnaseq differential gene expression differential exon usage
updated 6.1 years ago by 39k • written 6.1 years ago by ▴ 30
3
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2
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2.4k
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Subread FeatureCounts for Exon level quantification: Length estimate for Exons as low as 1 base-pair
subread featurecounts dexseq rnaseq
updated 4.5 years ago by 47k • written 4.5 years ago by • 0
0
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12
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2.3k
views
Error in strsplit() : non-character argument - using DEXSeq
dexseq_count DEXSeqDataSetFromHTSeq DEXSeq strsplit
updated 6.8 years ago by ▴ 20 • written 6.8 years ago by ▴ 10
0
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2
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2.3k
views
DEXSeq error: Count files do not correspond to the flattened annotation file
Annotation GO DEXSeq Annotation GO DEXSeq
updated 9.7 years ago by ★ 3.7k • written 9.7 years ago by ▴ 50
1
vote
7
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2.3k
views
DEXSeq - Where to find and download the appropriate GTF reference file for Python Script
dexseq gtf gff reference genome
updated 5.8 years ago by 62k • written 5.8 years ago by • 0
1
vote
15
replies
2.3k
views
DEXSeq: Error in FUN(X[[i]], ...) : subscript out of bounds
dexseq
updated 5 weeks ago by • 0 • written 5.8 years ago by • 0
0
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7
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2.3k
views
How to retrieve exon ID and gene ID from exon coordinates?
RNASeq DEXSeq RNASeq DEXSeq
updated 10.4 years ago by 62k • written 10.4 years ago by ▴ 340
6
votes
3
replies
2.2k
views
plotDEXSeq error in plot.window(xlim = c(0, 1), ylim = c(0, max(matr))) : need finite 'ylim' values
dexseq differential exon usage
6.0 years ago fizer ▴ 30
5
votes
18
replies
2.1k
views
Incongruencies between DEXSeq and BitSeq/Cuffdiff
dexseq bitseq cuffdiff Differential exon usage isoforms
7.7 years ago • updated 7.6 years ago elle ▴ 10
2
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2
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2.1k
views
DEXSeq prepare annotation on Stringtie outputGTF - KeyError: 'gene_id'
dexseq
5.7 years ago craigmonger ▴ 10
0
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2
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2.1k
views
DESeq vs DEXSeq
RNASeq Annotation DESeq DEXSeq RNASeq Annotation DESeq DEXSeq
updated 10.8 years ago by ★ 3.7k • written 10.8 years ago by ▴ 280
4
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4
replies
2.0k
views
DEXSeq and Independent filtering
dexseq deseq2 genefilter
updated 7.2 years ago by 13k • written 7.2 years ago by ▴ 20
0
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1
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2.0k
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Making a gff file for introns to be used with DEXSEQ
dexseq
updated 5.9 years ago by 16k • written 5.9 years ago by ▴ 40
0
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5
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2.0k
views
NA in padj in the DEXSeq package
dexseq padj
7.0 years ago gil.hornung • 0
1
vote
14
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2.0k
views
DEXSeq - dexseq_count.py issue
dexseq dexseq_count genomicfeatures
updated 4.8 years ago by • 0 • written 4.9 years ago by • 0
0
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3
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2.0k
views
DEXSeq Issue
Alignment Annotation GO Homo sapiens TranscriptDb PROcess GenomicFeatures DEXSeq Alignment
updated 9.7 years ago by 39k • written 9.7 years ago by ▴ 150
2
votes
10
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2.0k
views
Undefined log2Foldchanges within DEXSeq for significantly regulated exons
DEXSeq
7.9 years ago n.kreim ▴ 20
0
votes
12
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1.9k
views
problem with loading DESeq after upgrading from R 2.14 to R 2.15
GUI DESeq DEXSeq GUI DESeq DEXSeq
updated 10.8 years ago by ▴ 60 • written 10.8 years ago by ▴ 370
0
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3
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1.9k
views
interpreting DEXSeq output
DEXSeq DEXSeq
updated 10.6 years ago by ★ 1.8k • written 10.6 years ago by ▴ 150
0
votes
1
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1.9k
views
Detecting differential usage of introns from RNA-seq data.
Preprocessing DEXSeq Preprocessing DEXSeq
updated 9.6 years ago by ★ 1.8k • written 9.6 years ago by ▴ 70
0
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4
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1.8k
views
Error for plotDEXSeq and warning for estimateDispersions
graph DEXSeq
updated 8.3 years ago by ★ 1.8k • written 8.3 years ago by ▴ 20
0
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8
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1.8k
views
DEXSeq - too many exons in gene
Sequencing Annotation DEXSeq Sequencing Annotation DEXSeq
updated 9.0 years ago by 13k • written 9.0 years ago by ▴ 490
0
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3
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1.8k
views
DEXSeq on introns but exon overlap and error message
dexseq intron retention prepare annotation
7.6 years ago mat.lesche ▴ 80
5
votes
6
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1.8k
views
Translating model formula from DESeq to DEXSeq
dexseq linear model formula
updated 7.2 years ago by ★ 1.8k • written 7.2 years ago by ▴ 110
2
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3
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1.8k
views
DEXSeqDataSetFromHTSeq object creation error
dexseq
8.4 years ago • updated 8.3 years ago guffanti.alessandro • 0
0
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7
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1.8k
views
htseq and dexseq
DEXSeq DEXSeq
updated 9.6 years ago by 13k • written 9.6 years ago by ▴ 810
3
votes
4
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1.7k
views
having trouble with dexseq_prepare_annotation.py
dexseq gtf
updated 7.2 years ago by ★ 1.8k • written 7.2 years ago by ▴ 10
0
votes
1
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1.7k
views
illegal operand when I run DEXSeq
DEXSeq DEXSeq
updated 9.9 years ago by ★ 1.3k • written 9.9 years ago by 13k
2
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3
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1.7k
views
dexseq_count.py 'SAM optional field tag NH not found'
dexseq
updated 6.8 years ago by • 0 • written 7.2 years ago by ▴ 30
0
votes
3
replies
1.7k
views
dexseq read.HTSeqCounts error
DEXSeq DEXSeq
updated 8.8 years ago by ★ 1.8k • written 8.8 years ago by ▴ 550
0
votes
2
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1.7k
views
DEXSeq without replicates?
DEXSeq DEXSeq
updated 11.1 years ago by ★ 3.7k • written 11.1 years ago by ▴ 210
0
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5
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1.7k
views
DEXSeq - Error in estimateSizeFactorsForMatrix(featureCounts(object)
DEXSeq DESeq2 dexseq deseq2 alternative splicing
7.3 years ago Fahmi Nazarie • 0
0
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2
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1.7k
views
DEXSeq-Error in FUN(X[[i]], ...) : subscript out of bounds
dexseq
6.2 years ago Mthabisi Moyo ▴ 30
0
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5
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1.7k
views
DEXSeq: 0 reads for all exons for an expressed gene
dexseq
7.6 years ago Andrea Grilli ▴ 240
0
votes
2
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1.7k
views
DEXSeq filtering
DEXSeq DEXSeq
updated 10.7 years ago by ★ 3.7k • written 10.7 years ago by ▴ 370
50 results • Page 1 of 1
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Replies
Comment: Empty ChipQC Report by Okan • 0
Hi, I have the same issue. Have you found any solution or any reason why this is happening?
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by Gordon Smyth 47k
Am I understanding correctly that you have 24 RNA-seq libraries in total, 6 from the pooled samples and 18 from regular samples with biolog…
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by k.roelfs • 0
I'm sorry, I know it is kinda confusing... We have 6 pools in total: Phenotype A: T1a, T2, T1b, T1c Phenotype B: T1, T2 Each pool consist…
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by Gordon Smyth 47k
Sorry, I don't understand your experiment. You are reading the edgeR Section on on what to do without replicates, but your experiment appe…
Answer: MA plot by Nathalie • 0
Thank you very much for your help and comments. There is errors in my file. BaseMean is BaseMeanLog2. I don't know how insert a file.
Votes
Volcano Plot in R
Answer: Replicating iDEP parameters in DESeq2; two conditions and an interaction term.
Answer: Replicating iDEP parameters in DESeq2; two conditions and an interaction term.
Answer: MA plot
Answer: MA plot
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