Showing : Dexseq • reset
0
votes
1
reply
304
views
Make DEXSeq plot normal scale
DEXSeq Dexseq
updated 7 months ago by 68k • written 8 months ago by • 0
4
votes
6
replies
1.6k
views
Surprising behavior for DEXseq dispersion estimate plot?
DESeq2 DEXSeq
updated 8 months ago by ★ 5.0k • written 9 months ago by • 0
0
votes
0
replies
360
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
10 months ago cftattersfield • 0
0
votes
1
reply
567
views
Run DEXSeq successfully but got a result that padj==1 in all genes
DEXSeq
updated 17 months ago by ★ 5.0k • written 17 months ago by • 0
2
votes
1
reply
808
views
How to design DEXSeq formula for multiple variables
DEXSeq
19 months ago • updated 18 months ago Sara • 0
3
votes
1
reply
886
views
How to save the DEXSeq results
DEXSeq
updated 19 months ago by 43k • written 19 months ago by • 0
0
votes
0
replies
565
views
how to do Differential splicing from SGSeq analysis
DEXSeq SGSeq
20 months ago • updated 19 months ago Sara • 0
0
votes
3
replies
892
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 19 months ago by ★ 1.9k • written 20 months ago by • 0
0
votes
1
reply
690
views
Adding columns to DEXSeqResults object
DEXSeq
updated 20 months ago by ★ 1.9k • written 20 months ago by • 0
0
votes
1
reply
1.3k
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 20 months ago by 43k • written 20 months ago by • 0
0
votes
0
replies
503
views
DEXSeq plot error
DEXSeq DEXSeqNAvalues DEXseq
21 months ago jean-christophe.helbling • 0
2
votes
4
replies
1.2k
views
DEXSeq: summarizeOverlaps() crashes Rstudio with too many samples
DEXSeq
22 months ago thomas.heigl.ibk • 0
0
votes
2
replies
874
views
Swimming downstream: transcript fold changes
DEXSeq stageR
2.1 years ago jbono ▴ 10
1
vote
1
reply
955
views
DEXSeq DEXSeqDataSet count matrix duplication
DEXSeq DRIMSeq DEXSeqDataSet columnduplication
2.1 years ago NiKo ▴ 10
0
votes
3
replies
1.4k
views
RNAseq (Deseq2 and Dexseq2) analysis on two time points with expected same effect
DEXSeq RNA-seq DESeq2
updated 2.3 years ago by ★ 1.9k • written 2.3 years ago by • 0
0
votes
3
replies
1.7k
views
Error with makeTxDbFromBiomart
DEXSeq biomaRt
updated 2.4 years ago by 16k • written 2.4 years ago by • 0
0
votes
2
replies
1.3k
views
DEXSeqDataSet object DEXSeqDataSetFromHTSeq Error: line number did not have 3 elements
DEXSeq HTSeq R
2.4 years ago • updated 2.3 years ago yr542 • 0
8
votes
7
replies
3.1k
views
Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2 glmGamPoi DEXSeq
updated 2.5 years ago by ▴ 20 • written 3.2 years ago by ▴ 20
1
vote
5
replies
1.6k
views
DEXSeq output included non-exist exons
DEXSeq exon_definition exon
updated 2.5 years ago by ★ 1.9k • written 2.5 years ago by • 0
0
votes
0
replies
832
views
Recommendation sought for differential exon usage of a single gene
isofor DEXSeq DifferentialSplicing
2.5 years ago nick_brittain55 • 0
0
votes
0
replies
723
views
Error while performing DEXseq
DEXSeq
2.6 years ago vipul14 • 0
0
votes
0
replies
752
views
DEXSeq Subsetting pre or post dispersion calculation?
DEXSeq
2.8 years ago Ben J ▴ 20
2
votes
2
replies
1.9k
views
Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
DEXSeq
2.9 years ago Ben J ▴ 20
0
votes
0
replies
1.0k
views
DESXSEQ warning (Fit for gene/exon ENSG0000002121 threw the next warning(s): the matrix is either rank-deficient or indefinite)?
DEXSeq
updated 3.0 years ago by 43k • written 3.1 years ago by • 0
0
votes
1
reply
1.2k
views
plotDEXSeq error?
DEXSeq dex
3.1 years ago barrypraveen • 0
1
vote
4
replies
1.5k
views
DEXseq batch removal
DEXSeq
updated 3.2 years ago by ★ 1.9k • written 3.2 years ago by ▴ 10
0
votes
0
replies
741
views
DEXSeq: mcols(dxd)$fullBetaConv either contains TRUE or NA
DEXSeq
3.3 years ago Matthias Munz ▴ 20
0
votes
0
replies
844
views
DEXSeq aggregated genes/exons result in NA values
RNASeq R DEXSeq
3.4 years ago osieman52 • 0
1
vote
2
replies
1.4k
views
DEXSeq: Error in reading counts from htseq "Error in FUN(X[[i]], ...) : subscript out of bounds"
DEXSeq
3.4 years ago Delta._.43 ▴ 20
0
votes
1
reply
1.5k
views
DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing Exon featureCounts subread DEXSeq
3.6 years ago NIK • 0
0
votes
4
replies
2.6k
views
DEXSeq: samples$sample_id %in% colnames(counts) is not TRUE
DEXSeq DRIMSeq
updated 3.6 years ago by ▴ 100 • written 3.6 years ago by • 0
0
votes
5
replies
2.6k
views
DEXSeq - counts from paired reads and unpaired singletons
dexseq
written 6.7 years ago by • 0
8
votes
12
replies
5.0k
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 18 months ago by ▴ 30 • written 3.7 years ago by ▴ 390
3
votes
2
replies
1.8k
views
DEX-Seq returns Error in FUN(X[[i]], ...) : subscript out of bounds when I use DEXSeqDatasetFromHTseq()
R DEXSeq SequenceAnnotation RNASeqData
3.7 years ago • updated 3.6 years ago Dakarai ▴ 10
1
vote
1
reply
1.1k
views
Increased number of exons in DEXSeq
DEXSeq exon
updated 3.7 years ago by ★ 1.9k • written 3.7 years ago by • 0
1
vote
2
replies
1.6k
views
Normalizing exonic reads and then log transforming or variance stabilising
DEXSeq
4.1 years ago • updated 3.9 years ago A ▴ 60
3
votes
3
replies
1.7k
views
Joint disperstion estimation for DEXSeq and DESeq2
DESeq2 DEXseq
updated 3.9 years ago by 43k • written 3.9 years ago by ▴ 120
0
votes
1
reply
1.4k
views
DEXSeq prepare annotation script throws "object has no attribute 'next'" for Ensemble GTFs
DEXSeq
updated 3.9 years ago by ★ 1.9k • written 4.2 years ago by • 0
1
vote
1
reply
1.7k
views
DTU using DEXSeq (time series data with condition factor)
DTU DEXSeq RNADTU
updated 3.9 years ago by ★ 1.9k • written 4.3 years ago by ▴ 10
2
votes
7
replies
2.1k
views
Fold Change for rnaseq DTU
DEXSeq rnaseqDTU
4.3 years ago rbenel ▴ 50
0
votes
5
replies
2.0k
views
DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq DRIMSeq DEXSeq rnaseqDTU
4.4 years ago • updated 4.3 years ago bioinformatic_trainee ▴ 10
1
vote
0
replies
1.6k
views
DEXseq: How to do differential exon usage of genes with overlapping exons
GenomicFeatures DEXSeq
4.4 years ago Matthias Munz ▴ 20
0
votes
0
replies
990
views
Disabling aggregation with the option -r no, still combines genes into single “aggregate genes"
DEXSeq
4.4 years ago n.tear ▴ 20
0
votes
0
replies
998
views
DEXSeq: Error in perGeneQValue with a single gene
DEXSeq
4.5 years ago Matthias Munz ▴ 20
1
vote
6
replies
2.4k
views
Differential Transcript Usage: complex factorial design
edgeR DEXSeq IsoformSwitchAnalyzeR DTU
updated 4.5 years ago by ▴ 120 • written 4.7 years ago by ▴ 10
4
votes
5
replies
2.9k
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
4.6 years ago Matthias Munz ▴ 20
0
votes
0
replies
1.3k
views
Error generating counts df for use with DRIMSeq/DEXseq
DRIMSeq DEXSeq
4.7 years ago jbono ▴ 10
0
votes
2
replies
1.6k
views
DRIMSeq + dmFilter
DEXSeq DRIMSeq
4.8 years ago • updated 4.7 years ago Gaia • 0
3
votes
2
replies
1.6k
views
How to better run DEXSeq with a very large number of samples?
DEXSeq
4.8 years ago Angel ▴ 10
2
votes
2
replies
1.8k
views
Question: Error when running QoRTs for JunctionSeq
DEXSeq JunctionSeq RNAseq QoRTs
4.8 years ago n.tear ▴ 20
363 results • Page 1 of 8
Recent ...
Replies
Answer: NUPOP usage by shepherl 4.2k
You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
Comment: How can I correctly use phyloseq with Docker? by fnfgame • 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Awards • All
Scholar to Nikos Ignatiadis ▴ 180
Popular Question to Robert • 0
Popular Question to lamia11me • 0
Popular Question to Gordon Smyth 53k
Popular Question to Michael Love 43k
Locations • All
WEHI, Melbourne, Australia, 24 minutes ago
United States, 35 minutes ago
United States, 1 hour ago
United States, 1 hour ago
United States, 1 hour ago
Traffic: 1017 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