Showing : dexseq • reset
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Differential exon usage analysis using DEXSeq for mRNA and lncRNA separately
DEXSeq
updated 4.7 years ago by ★ 1.9k • written 4.7 years ago by • 0
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2
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DEXSeq - what is the best way to filter out low expressed exons / genes?
dexseq
5.2 years ago • updated 4.8 years ago aleksandar.baburski.g • 0
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6
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4.8k
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DEXSeq: question about usage coefficient and splicing plot
dexseq
updated 4.8 years ago by ▴ 20 • written 10.5 years ago by • 0
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2
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1.8k
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Interpreting the EstimateDispersion plot from the DEXSeq package
dexseq estimatedispersions
updated 4.8 years ago by ▴ 20 • written 7.7 years ago by • 0
6
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7
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2.2k
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Strategy to perform DESeq, DEXSeq workflow
DEXSeq DESeq2
updated 4.7 years ago by 43k • written 4.8 years ago by ▴ 20
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2
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1.2k
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DEXSeq : can we plot from the table of results or/and run DEXSeq from a matrix of counts like in DESeq2?
DEXseq
updated 5.1 years ago by ★ 3.8k • written 5.2 years ago by • 0
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4
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2.2k
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Calculating per-exon PSI from DEXSeq
DEXSeq
5.1 years ago Angel Liang • 0
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2
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1.6k
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Detailed explanations for DEXSeq output columns
DEXSeq
updated 5.2 years ago by ★ 1.9k • written 5.2 years ago by • 0
0
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1
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1.0k
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How to obtain the specific genelists mentioned in the RNASeq DTU workflow?
rnaseqdtu RNASeq DEXSeq DESeq2
updated 5.2 years ago by 43k • written 5.2 years ago by ▴ 10
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2
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1.6k
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DEXSeq dispersion estimation optimisation for large number of samples
DEXSeq estimateDispersions
5.2 years ago aleksandar.baburski.g • 0
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2
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1.2k
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DEXSeq HTML report Error
DEXSeq
updated 5.2 years ago by ★ 4.0k • written 5.2 years ago by • 0
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0
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978
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Subset samples expressing genes for DEXSeq or DRIMSeq analysis
DEXSeq DRIMSeq
5.3 years ago alexis.weinreb • 0
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2
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2.2k
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DEXSeq Python script dexseq_prepare_annotation.py unable to process my .gtf file
dexseq python gtf gff3 annotation
5.4 years ago • updated 5.3 years ago Raito92 ▴ 60
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1.3k
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DEXseq conversion of GTF to GFF creating incorrect exon coordinates
software error DEXSeq
5.4 years ago knuppdav • 0
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3
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1.9k
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DEXSeq with large(ish) number of samples
DEXSeq exon memory dispersions estimateDispersions
5.4 years ago andreismolnikov00 • 0
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0
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2.0k
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summarizeOverlaps - (GenomicAlignments) - gives warnings 'package:stats' may not be available when loading
GenomicAlignments summerizeOverlaps-Method DEXSeq
updated 5.4 years ago by 25k • written 5.4 years ago by ▴ 10
3
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3
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2.5k
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Calculation of Log2 fold change in DEXSeq
DEXSeq log2foldchange Tutorial
updated 4.0 years ago by ▴ 20 • written 5.4 years ago by ▴ 20
1
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2
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930
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How to set model formulae in DEXSeq when 2 shRNAs were used to target a same gene
DEXSeq
updated 5.4 years ago by ★ 1.9k • written 5.4 years ago by ▴ 10
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3
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1.6k
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DEXSeq Splicing Result with incomplete lines between exons
DEXSeq Splicing Exon Usage
5.6 years ago gunjan.dikshit • 0
2
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6
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3.6k
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featureCount error - cannot identify gene_id
dexseq rsubread featureCount software error
updated 5.8 years ago by ▴ 450 • written 5.8 years ago by • 0
0
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1
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1.2k
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JunctionSeq producing strangely large effect sizes for certain exon counting bins
junctionseq splicing RNAseq DEXSeq
5.8 years ago stuart ▴ 10
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1
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720
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error in DEXSeq estimateExonFoldChanges
dexseq
5.8 years ago brown.annaleigh • 0
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2
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1.0k
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A question about DEXSeq of estimateDispersions
dexseq
updated 5.9 years ago by ▴ 10 • written 6.1 years ago by • 0
0
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2
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1.5k
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Issue/Error with DEXSeq design formulae in testForDEU function
deseq2 DEXSeq BioCParallel
updated 6.0 years ago by ★ 1.9k • written 6.0 years ago by • 0
1
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2
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2.4k
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DEXseq error unable to find an inherited method for function NSBS for signature CompressedIntegerList
Dexseq
updated 3.1 years ago by ▴ 10 • written 6.1 years ago by ▴ 10
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2
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1.1k
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DEXSeq error in dexseq_count.py. ValueError: need more than 4 values to unpack
DEXSeq
updated 6.2 years ago by ★ 3.8k • written 6.2 years ago by • 0
4
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1
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1.3k
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Print Differentially Expressed Exons From Dexseq Results
DEXSeq RNA-Seq
updated 6.3 years ago by ★ 1.9k • written 6.3 years ago by ▴ 10
2
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3
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1.5k
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exonicParts vs. disjoinExons inconsistency in usage for DEXSeq - bug?
DEXSeq
updated 6.3 years ago by 16k • written 6.3 years ago by ▴ 20
0
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6
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2.2k
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DEXSeq dispersion outlier
DEXSeq dispersion pvalue
6.4 years ago • updated 6.3 years ago fiona.dick91 ▴ 60
2
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3
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1.5k
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null model and DEXSeqDataSet object in DEXSEQ
deseq2 dexseq
6.3 years ago gv ▴ 40
2
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6
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1.7k
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estimateDispersions calculation for > 500,000 exons for 2 conditions taking forever
deseq2 dexseq
6.4 years ago gv ▴ 40
1
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6
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1.8k
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How to install DEXSeq on R 3.4.4
DEXSEq Linux
updated 6.4 years ago by ★ 1.9k • written 6.4 years ago by ▴ 10
1
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1
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1.8k
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rnaseqDTU log2fold change DEXSeq
DEXSeq DTU salmon rnaseqDTU foldchange
updated 6.4 years ago by 43k • written 6.7 years ago by ▴ 60
0
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11
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2.2k
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Issue during transcript variant analysis using rnaseqDTU-DRIMseq-DEXseq.
rnaseqDTU DRIMseq DEXseq rna-seq
6.4 years ago saddamhusain77 • 0
0
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2
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1.1k
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DEXSeq With Reduced Annotations
dexseq reduced annotation set
6.5 years ago sumeet460 • 0
1
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2
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1.9k
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Normalized transcript/exon counts for network analysis
drimseq dexseq wgcna sva
updated 6.6 years ago by ▴ 90 • written 6.6 years ago by ▴ 30
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4
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2.1k
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stageR: Error in stageWiseAdjustment
stageR rnaseqDTU DRIMSeq DEXSeq
6.6 years ago d-joester ▴ 20
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4
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2.4k
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tximport: Error in medianLengthOverIsoform
tximport deseq2 dexseq
6.6 years ago d-joester ▴ 20
0
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1
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951
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DEXSeq: controlling for cell composition
dexseq
updated 6.6 years ago by ★ 1.9k • written 6.7 years ago by • 0
0
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1
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1.2k
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Can DEXseq be used for splicing QTL analysis?
dexseq splicing sqtl qtl
updated 6.6 years ago by ★ 1.9k • written 6.6 years ago by • 0
0
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3
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1.3k
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How to get missing columns in DEXSeq analysis (exon usage coefficients)
dexseq dexseqalt
6.6 years ago mjrarcher ▴ 10
0
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1
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1.2k
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Add interaction term between variables to DEXSeq design
DEXSeq interaction
6.7 years ago zhenzuo2 • 0
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0
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994
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DEXSeq: How to reduce compute time for estimating dispersions for large datasets.
dexseq estimatedispersions large dataset
6.7 years ago mjrarcher ▴ 10
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5
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1.7k
views
DEXSeq 1.26.0 running very slowly (stuck?)
dexseq
6.7 years ago Lance Parsons • 0
0
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7
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2.8k
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DEXSeqHTML getListElement GRanges error
dexseq software error bug
updated 6.8 years ago by ▴ 140 • written 6.8 years ago by • 0
1
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5
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2.1k
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Plotting Expression of Differential Transcripts plotDEXseq
DEXSeq StageR rnaseqDTU
updated 6.9 years ago by 43k • written 6.9 years ago by ▴ 50
0
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2
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1.3k
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Preparation of summarizedExperiment for dexSeq
dexseq genomicalignments genomicfeatures genomicranges
6.9 years ago A ▴ 60
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0
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633
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How to use DEXSeq processing whole genome (~650k exons/counting bins) and many samples? Can I process per 100 genes (or more) a batch until it covers…
dexseq
6.9 years ago slowsmile820 • 0
6
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6
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3.1k
views
Kallisto output with DEXSeq
dexseq kallisto NH_tag
updated 6.9 years ago by ★ 1.9k • written 6.9 years ago by • 0
4
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3
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1.9k
views
DEXSeq and DRIMSeq on paired samples?
DRIMSeq DEXSeq
updated 7.0 years ago by ▴ 90 • written 7.0 years ago by • 0
363 results • Page 2 of 8
Recent ...
Replies
Answer: Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg? by Michael Love 43k
I'm not familiar with this usage, or code here ``` normFactors <- exp(-1 * offst(set2)) ``` In the RNA-seq gene-level workflow, we …
Answer: Which of apeglm and ashr may be more appropriate for pseudobulked DESeq2 analysi by Michael Love 43k
> apeglm appears much more aggressive in shrinkage, pushing many genes toward logFC = 0 > ashr maintains a gradient of shrinkage val…
Comment: voomLmFit fitted log-CPM values by Gordon Smyth 53k
The fitted values are on the log2CPM scale. I would have told you if they were not! I think you may be getting confused by the differences…
Comment: voomLmFit fitted log-CPM values by Lina ▴ 10
Is the output from fitted(v) in the log2 CPM scale? or CPM scale?
Answer: voomLmFit fitted log-CPM values by Gordon Smyth 53k
Fitted values are obtained from limma MArrayLM objects by ``` fitted(v) ```
Votes
A: How barcode-plot enrichment is calculated?
A: How barcode-plot enrichment is calculated?
Answer: ROAST compare results with complex design
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
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