Showing : dexseq • reset
0
votes
1
reply
244
views
Make DEXSeq plot normal scale
DEXSeq Dexseq
updated 5 months ago by 68k • written 5 months ago by • 0
4
votes
6
replies
1.5k
views
Surprising behavior for DEXseq dispersion estimate plot?
DESeq2 DEXSeq
updated 6 months ago by ★ 5.0k • written 7 months ago by • 0
0
votes
0
replies
305
views
My DEXSeqDataSetFromSE is returning an Error, but all of my checks to seem to indicate that this error is not present
DifferentialSplicing RNASeqData DEXSeq
8 months ago cftattersfield • 0
0
votes
1
reply
527
views
Run DEXSeq successfully but got a result that padj==1 in all genes
DEXSeq
updated 14 months ago by ★ 5.0k • written 14 months ago by • 0
2
votes
1
reply
747
views
How to design DEXSeq formula for multiple variables
DEXSeq
17 months ago • updated 16 months ago Sara • 0
3
votes
1
reply
837
views
How to save the DEXSeq results
DEXSeq
updated 17 months ago by 43k • written 17 months ago by • 0
0
votes
0
replies
486
views
how to do Differential splicing from SGSeq analysis
DEXSeq SGSeq
17 months ago Sara • 0
0
votes
3
replies
807
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 17 months ago by ★ 1.9k • written 17 months ago by • 0
0
votes
1
reply
612
views
Adding columns to DEXSeqResults object
DEXSeq
updated 17 months ago by ★ 1.9k • written 18 months ago by • 0
0
votes
1
reply
1.2k
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 17 months ago by 43k • written 17 months ago by • 0
0
votes
0
replies
462
views
DEXSeq plot error
DEXSeq DEXSeqNAvalues DEXseq
19 months ago jean-christophe.helbling • 0
2
votes
4
replies
1.1k
views
DEXSeq: summarizeOverlaps() crashes Rstudio with too many samples
DEXSeq
20 months ago • updated 19 months ago thomas.heigl.ibk • 0
0
votes
2
replies
819
views
Swimming downstream: transcript fold changes
DEXSeq stageR
23 months ago jbono ▴ 10
1
vote
1
reply
898
views
DEXSeq DEXSeqDataSet count matrix duplication
DEXSeq DRIMSeq DEXSeqDataSet columnduplication
23 months ago NiKo ▴ 10
0
votes
3
replies
1.3k
views
RNAseq (Deseq2 and Dexseq2) analysis on two time points with expected same effect
DEXSeq RNA-seq DESeq2
updated 2.1 years ago by ★ 1.9k • written 2.1 years ago by • 0
0
votes
3
replies
1.6k
views
Error with makeTxDbFromBiomart
DEXSeq biomaRt
updated 2.2 years ago by 16k • written 2.2 years ago by • 0
0
votes
2
replies
1.2k
views
DEXSeqDataSet object DEXSeqDataSetFromHTSeq Error: line number did not have 3 elements
DEXSeq HTSeq R
2.2 years ago • updated 2.1 years ago yr542 • 0
8
votes
7
replies
3.0k
views
Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2 glmGamPoi DEXSeq
updated 2.3 years ago by ▴ 20 • written 3.0 years ago by ▴ 20
1
vote
5
replies
1.5k
views
DEXSeq output included non-exist exons
DEXSeq exon_definition exon
updated 2.3 years ago by ★ 1.9k • written 2.3 years ago by • 0
0
votes
0
replies
773
views
Recommendation sought for differential exon usage of a single gene
isofor DEXSeq DifferentialSplicing
2.3 years ago nick_brittain55 • 0
0
votes
0
replies
694
views
Error while performing DEXseq
DEXSeq
2.4 years ago vipul14 • 0
0
votes
0
replies
717
views
DEXSeq Subsetting pre or post dispersion calculation?
DEXSeq
2.6 years ago Ben J ▴ 20
2
votes
2
replies
1.8k
views
Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
DEXSeq
2.7 years ago Ben J ▴ 20
0
votes
0
replies
968
views
DESXSEQ warning (Fit for gene/exon ENSG0000002121 threw the next warning(s): the matrix is either rank-deficient or indefinite)?
DEXSeq
updated 2.9 years ago by 43k • written 2.9 years ago by • 0
0
votes
1
reply
1.2k
views
plotDEXSeq error?
DEXSeq dex
2.9 years ago barrypraveen • 0
1
vote
4
replies
1.5k
views
DEXseq batch removal
DEXSeq
updated 3.0 years ago by ★ 1.9k • written 3.0 years ago by ▴ 10
0
votes
0
replies
699
views
DEXSeq: mcols(dxd)$fullBetaConv either contains TRUE or NA
DEXSeq
3.1 years ago Matthias Munz ▴ 20
0
votes
0
replies
790
views
DEXSeq aggregated genes/exons result in NA values
RNASeq R DEXSeq
3.2 years ago osieman52 • 0
1
vote
2
replies
1.3k
views
DEXSeq: Error in reading counts from htseq "Error in FUN(X[[i]], ...) : subscript out of bounds"
DEXSeq
3.2 years ago Delta._.43 ▴ 20
0
votes
1
reply
1.3k
views
DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing Exon featureCounts subread DEXSeq
3.4 years ago NIK • 0
0
votes
4
replies
2.5k
views
DEXSeq: samples$sample_id %in% colnames(counts) is not TRUE
DEXSeq DRIMSeq
updated 3.4 years ago by ▴ 100 • written 3.4 years ago by • 0
0
votes
5
replies
2.6k
views
DEXSeq - counts from paired reads and unpaired singletons
dexseq
written 6.5 years ago by • 0
8
votes
12
replies
4.8k
views
DEXSeq errors "Error in scan( line ... did not have 3 elements" and "Error in FUN(X[[i]], ...) : subscript out of bounds" (DEXSeqDataSetFromHTSeq)
DEXSeq
updated 16 months ago by ▴ 30 • written 3.5 years ago by ▴ 380
3
votes
2
replies
1.7k
views
DEX-Seq returns Error in FUN(X[[i]], ...) : subscript out of bounds when I use DEXSeqDatasetFromHTseq()
R DEXSeq SequenceAnnotation RNASeqData
3.5 years ago • updated 3.4 years ago Dakarai ▴ 10
1
vote
1
reply
1.0k
views
Increased number of exons in DEXSeq
DEXSeq exon
updated 3.6 years ago by ★ 1.9k • written 3.6 years ago by • 0
1
vote
2
replies
1.5k
views
Normalizing exonic reads and then log transforming or variance stabilising
DEXSeq
3.9 years ago • updated 3.7 years ago A ▴ 60
3
votes
3
replies
1.6k
views
Joint disperstion estimation for DEXSeq and DESeq2
DESeq2 DEXseq
updated 3.7 years ago by 43k • written 3.7 years ago by ▴ 120
0
votes
1
reply
1.3k
views
DEXSeq prepare annotation script throws "object has no attribute 'next'" for Ensemble GTFs
DEXSeq
updated 3.7 years ago by ★ 1.9k • written 4.0 years ago by • 0
1
vote
1
reply
1.6k
views
DTU using DEXSeq (time series data with condition factor)
DTU DEXSeq RNADTU
updated 3.7 years ago by ★ 1.9k • written 4.1 years ago by ▴ 10
2
votes
7
replies
2.0k
views
Fold Change for rnaseq DTU
DEXSeq rnaseqDTU
4.1 years ago rbenel ▴ 50
0
votes
5
replies
1.9k
views
DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq DRIMSeq DEXSeq rnaseqDTU
4.2 years ago bioinformatic_trainee ▴ 10
1
vote
0
replies
1.5k
views
DEXseq: How to do differential exon usage of genes with overlapping exons
GenomicFeatures DEXSeq
4.2 years ago Matthias Munz ▴ 20
0
votes
0
replies
953
views
Disabling aggregation with the option -r no, still combines genes into single “aggregate genes"
DEXSeq
4.2 years ago n.tear ▴ 20
0
votes
0
replies
962
views
DEXSeq: Error in perGeneQValue with a single gene
DEXSeq
4.3 years ago Matthias Munz ▴ 20
1
vote
6
replies
2.3k
views
Differential Transcript Usage: complex factorial design
edgeR DEXSeq IsoformSwitchAnalyzeR DTU
updated 4.3 years ago by ▴ 120 • written 4.5 years ago by ▴ 10
4
votes
5
replies
2.8k
views
DEXSeq: What's the best way to map an exon counting bin, e.g. E002 to exon(s) or position in transcript(s)
DEXSeq
4.4 years ago Matthias Munz ▴ 20
0
votes
0
replies
1.3k
views
Error generating counts df for use with DRIMSeq/DEXseq
DRIMSeq DEXSeq
4.5 years ago jbono ▴ 10
0
votes
2
replies
1.5k
views
DRIMSeq + dmFilter
DEXSeq DRIMSeq
4.6 years ago Gaia • 0
3
votes
2
replies
1.5k
views
How to better run DEXSeq with a very large number of samples?
DEXSeq
4.6 years ago Angel ▴ 10
2
votes
2
replies
1.7k
views
Question: Error when running QoRTs for JunctionSeq
DEXSeq JunctionSeq RNAseq QoRTs
4.6 years ago n.tear ▴ 20
363 results • Page 1 of 8
Recent ...
Replies
Comment: Help with defining groups by Phinney, Brett ▴ 10
I got it working , thank you!!!
Comment: Check removeBatchEffect effectiveness by massimo • 0
I would kindly ask for additional support. When not including the design_timepoint argument in removeBatchEffect and thus keeping the inter…
Comment: Error Loading Experiment from SimBenchData Package by ksankaran • 0
Aha, that was it! The object was class Seurat, but I didn't have it installed. After installing, everything works as expected.
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset? by ATpoint ★ 5.0k
Is a method that is so computationally expensive really beneficial and necessary? You seem to have biological replication, don't you, so ps…
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes by ATpoint ★ 5.0k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
Votes
Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
Answer: Error Loading Experiment from SimBenchData Package
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
Awards • All
Popular Question to Peter • 0
Popular Question to Travis • 0
Popular Question to James W. MacDonald 68k
Popular Question to Gordon Smyth 53k
Popular Question to shepherl 4.2k
Locations • All
United States, 27 minutes ago
WEHI, Melbourne, Australia, 30 minutes ago
The city by the bay, 59 minutes ago
United States, 1 hour ago
United States, 3 hours ago
Traffic: 583 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6