Showing : DEXseq • reset
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deseq2: convert ensembl ID to gene symbol.
DEXSeq DESeq2 DEXSeq DESeq2
updated 4.8 years ago by • 0 • written 8.8 years ago by ▴ 970
12
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2
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4.0k
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DEXSeq Usage and Expression Confusion
dexseq
updated 8.4 years ago by ★ 3.7k • written 8.4 years ago by ▴ 360
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3
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3.9k
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p-value vs adjusted p-value in DEXSeq
DEXSeq DEXSeq
updated 10.0 years ago by ★ 3.7k • written 10.0 years ago by ▴ 70
0
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1
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3.7k
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RNA-seq analysis and two-way ANOVAs
edgeR baySeq DEGseq DESeq DEXSeq edgeR baySeq DEGseq DESeq DEXSeq
updated 10.8 years ago by 47k • written 10.8 years ago by ▴ 150
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31
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3.3k
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Error in find DEXSeq package
deseq dexseq
8.1 years ago engr.yahya602 • 0
1
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6
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3.2k
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DEXSeq: question about usage coefficient and splicing plot
dexseq
updated 2.6 years ago by ▴ 20 • written 8.2 years ago by • 0
0
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7
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3.2k
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DEXSeq Error in estimateExonFoldChanges: the matrix is either rank-deficient or indefinite
dexseq estimateexonfoldchanges
updated 7.2 years ago by ★ 1.8k • written 7.2 years ago by ▴ 20
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 10.1 years ago by ★ 3.7k • written 10.1 years ago by ▴ 40
3
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6
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3.1k
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DEXSeq Error: unable to find an inherited method for function ‘mcols’ for signature ‘"matrix"’
DEXSeq
updated 7.2 years ago by ★ 1.8k • written 7.2 years ago by • 0
2
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6
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2.9k
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DEXSeq Error in lf[[1]] : subscript out of bounds
DEXSeq
7.9 years ago rahel14350 ▴ 10
0
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2
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2.8k
views
DEXSeq on FeatureCounts output
dexseq featurecounts
7.7 years ago Vivek.b ▴ 100
1
vote
15
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2.8k
views
junction.bed to GTF to use in DEXSeq
junction.bed DEXSeq
updated 7.8 years ago by ▴ 360 • written 7.8 years ago by ▴ 10
0
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1
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2.7k
views
Error in estimateDispersions of DEXSeq
DEXSeq estimateDispersions
updated 8.4 years ago by 40k • written 8.5 years ago by • 0
15
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6
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2.6k
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Reference paper or resource for limma::diffSplice and edgeR::diffSpliceDGE methods?
edgeR limma diffSplice DEXSeq
updated 6.8 years ago by ▴ 90 • written 6.8 years ago by ▴ 160
0
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13
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2.6k
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Efficiently running DEXSeq for Large Cohorts
DEXSeq DEXSeq
updated 7.9 years ago by ▴ 10 • written 10.4 years ago by ▴ 320
3
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2
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2.6k
views
Subread FeatureCounts for Exon level quantification: Length estimate for Exons as low as 1 base-pair
subread featurecounts dexseq rnaseq
updated 4.9 years ago by 47k • written 4.9 years ago by • 0
2
votes
4
replies
2.5k
views
Simultaneously adding two different covariates in the model gives error in DESeq2.
deseq2 dexseq rnaseq differential gene expression differential exon usage
updated 6.4 years ago by 40k • written 6.4 years ago by ▴ 30
1
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15
replies
2.5k
views
DEXSeq: Error in FUN(X[[i]], ...) : subscript out of bounds
dexseq
updated 5 months ago by • 0 • written 6.1 years ago by • 0
1
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7
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2.5k
views
DEXSeq - Where to find and download the appropriate GTF reference file for Python Script
dexseq gtf gff reference genome
updated 6.1 years ago by 63k • written 6.1 years ago by • 0
0
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12
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2.5k
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Error in strsplit() : non-character argument - using DEXSeq
dexseq_count DEXSeqDataSetFromHTSeq DEXSeq strsplit
updated 7.1 years ago by ▴ 20 • written 7.1 years ago by ▴ 10
0
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2
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2.4k
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DEXSeq error: Count files do not correspond to the flattened annotation file
Annotation GO DEXSeq Annotation GO DEXSeq
updated 10.0 years ago by ★ 3.7k • written 10.0 years ago by ▴ 50
0
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7
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2.4k
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How to retrieve exon ID and gene ID from exon coordinates?
RNASeq DEXSeq RNASeq DEXSeq
updated 10.7 years ago by 63k • written 10.7 years ago by ▴ 340
6
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3
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2.4k
views
plotDEXSeq error in plot.window(xlim = c(0, 1), ylim = c(0, max(matr))) : need finite 'ylim' values
dexseq differential exon usage
6.3 years ago fizer ▴ 30
5
votes
18
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2.3k
views
Incongruencies between DEXSeq and BitSeq/Cuffdiff
dexseq bitseq cuffdiff Differential exon usage isoforms
8.0 years ago • updated 7.9 years ago elle ▴ 10
1
vote
14
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2.3k
views
DEXSeq - dexseq_count.py issue
dexseq dexseq_count genomicfeatures
updated 5.1 years ago by • 0 • written 5.2 years ago by • 0
2
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2
replies
2.2k
views
DEXSeq prepare annotation on Stringtie outputGTF - KeyError: 'gene_id'
dexseq
6.0 years ago craigmonger ▴ 10
0
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2
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2.2k
views
DESeq vs DEXSeq
RNASeq Annotation DESeq DEXSeq RNASeq Annotation DESeq DEXSeq
updated 11.2 years ago by ★ 3.7k • written 11.2 years ago by ▴ 280
0
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5
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2.2k
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NA in padj in the DEXSeq package
dexseq padj
7.4 years ago gil.hornung • 0
4
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4
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2.1k
views
DEXSeq and Independent filtering
dexseq deseq2 genefilter
updated 7.5 years ago by 13k • written 7.5 years ago by ▴ 20
0
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1
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2.1k
views
Making a gff file for introns to be used with DEXSEQ
dexseq
updated 6.2 years ago by 16k • written 6.2 years ago by ▴ 40
2
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10
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2.1k
views
Undefined log2Foldchanges within DEXSeq for significantly regulated exons
DEXSeq
8.3 years ago n.kreim ▴ 20
0
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3
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2.1k
views
DEXSeq Issue
Alignment Annotation GO Homo sapiens TranscriptDb PROcess GenomicFeatures DEXSeq Alignment
updated 10.0 years ago by 40k • written 10.0 years ago by ▴ 150
0
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12
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2.0k
views
problem with loading DESeq after upgrading from R 2.14 to R 2.15
GUI DESeq DEXSeq GUI DESeq DEXSeq
updated 11.1 years ago by ▴ 60 • written 11.1 years ago by ▴ 370
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3
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2.0k
views
interpreting DEXSeq output
DEXSeq DEXSeq
updated 11.0 years ago by ★ 1.8k • written 11.0 years ago by ▴ 150
0
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4
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1.9k
views
Error for plotDEXSeq and warning for estimateDispersions
graph DEXSeq
updated 8.7 years ago by ★ 1.8k • written 8.7 years ago by ▴ 20
0
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8
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1.9k
views
DEXSeq - too many exons in gene
Sequencing Annotation DEXSeq Sequencing Annotation DEXSeq
updated 9.3 years ago by 13k • written 9.3 years ago by ▴ 490
0
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1
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1.9k
views
Detecting differential usage of introns from RNA-seq data.
Preprocessing DEXSeq Preprocessing DEXSeq
updated 10.0 years ago by ★ 1.8k • written 10.0 years ago by ▴ 70
5
votes
6
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1.9k
views
Translating model formula from DESeq to DEXSeq
dexseq linear model formula
updated 7.6 years ago by ★ 1.8k • written 7.6 years ago by ▴ 110
0
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3
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1.9k
views
DEXSeq on introns but exon overlap and error message
dexseq intron retention prepare annotation
7.9 years ago mat.lesche ▴ 90
3
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4
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1.9k
views
having trouble with dexseq_prepare_annotation.py
dexseq gtf
updated 7.6 years ago by ★ 1.8k • written 7.6 years ago by ▴ 10
0
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7
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1.9k
views
htseq and dexseq
DEXSeq DEXSeq
updated 9.9 years ago by 13k • written 9.9 years ago by ▴ 810
2
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3
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1.8k
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DEXSeqDataSetFromHTSeq object creation error
dexseq
8.7 years ago guffanti.alessandro • 0
0
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2
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1.8k
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DEXSeq-Error in FUN(X[[i]], ...) : subscript out of bounds
dexseq
6.6 years ago Mthabisi Moyo ▴ 30
0
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5
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1.8k
views
DEXSeq - Error in estimateSizeFactorsForMatrix(featureCounts(object)
DEXSeq DESeq2 dexseq deseq2 alternative splicing
7.7 years ago Fahmi Nazarie • 0
2
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3
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1.8k
views
dexseq_count.py 'SAM optional field tag NH not found'
dexseq
updated 7.2 years ago by • 0 • written 7.5 years ago by ▴ 30
1
vote
4
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1.8k
views
DEXSeq continous variable in model
RNASeq TimeCourse timecourse DEXSeq DESeq2 RNASeq TimeCourse timecourse DEXSeq DESeq2
updated 8.8 years ago by ★ 1.8k • written 8.8 years ago by ▴ 650
0
votes
1
reply
1.8k
views
illegal operand when I run DEXSeq
DEXSeq DEXSeq
updated 10.3 years ago by ★ 1.3k • written 10.3 years ago by 13k
0
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2
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1.8k
views
DEXSeq without replicates?
DEXSeq DEXSeq
updated 11.5 years ago by ★ 3.7k • written 11.5 years ago by ▴ 210
0
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3
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1.8k
views
dexseq read.HTSeqCounts error
DEXSeq DEXSeq
updated 9.1 years ago by ★ 1.8k • written 9.1 years ago by ▴ 550
6
votes
4
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1.8k
views
Problem running dexseq in parallel using BiocParallel
dexseq
updated 6.2 years ago by ▴ 30 • written 6.2 years ago by ▴ 20
50 results • Page 1 of 1
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Comment: Diffbind "No genome detected" by kyliecode • 0
Hi James, Thanks for your reply! For the blacklist, I just used the one provided by DiffBind, which is "DBA_BLACKLIST_MM10". For the grey…
Answer: DESeq2 on multilevel design variable by ATpoint ★ 2.9k
You can make your life simply and use a contrast for each, for example: ```r library(DESeq2) dds <- makeExampleDESeqDataSet() diagnosis <…
Answer: Diffbind "No genome detected" by James W. MacDonald 63k
You can specify the greylist in the same manner as the blacklist, which should fix your problem.
Answer: Generate false reads for testing by James W. MacDonald 63k
https://www.bioconductor.org/packages/release/bioc/html/polyester.html
Comment: Adjusting for baseline when having longitudinal data, mixed model and no treat by Anna ▴ 20
Yes. But still I prefer using the covariance matrix over fixed effects for power issues. Or at least I wanted to use it as such before our …
Votes
Answer: Annotation with org.Hs.eg.db Genome Build 38
Comment: Adjusting for baseline when having longitudinal data, mixed model and no treat
A: overlap GRangesList and vcf
A: Ranges from a fasta file
Answer: NA transcript values in my Txdb
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