Showing : DEXseq • reset
0
votes
0
replies
58
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 days ago cftattersfield • 0
0
votes
1
reply
358
views
Run DEXSeq successfully but got a result that padj==1 in all genes
DEXSeq
updated 6 months ago by ★ 4.6k • written 6 months ago by • 0
2
votes
1
reply
474
views
How to design DEXSeq formula for multiple variables
DEXSeq
9 months ago • updated 8 months ago Sara • 0
3
votes
1
reply
568
views
How to save the DEXSeq results
DEXSeq
updated 9 months ago by 43k • written 9 months ago by • 0
0
votes
0
replies
316
views
how to do Differential splicing from SGSeq analysis
DEXSeq SGSeq
9 months ago Sara • 0
0
votes
3
replies
544
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 9 months ago by ★ 1.9k • written 9 months ago by • 0
0
votes
1
reply
424
views
Adding columns to DEXSeqResults object
DEXSeq
updated 9 months ago by ★ 1.9k • written 9 months ago by • 0
0
votes
1
reply
712
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 9 months ago by 43k • written 9 months ago by • 0
0
votes
0
replies
363
views
DEXSeq plot error
DEXSeq DEXSeqNAvalues DEXseq
11 months ago jean-christophe.helbling • 0
2
votes
4
replies
807
views
DEXSeq: summarizeOverlaps() crashes Rstudio with too many samples
DEXSeq
12 months ago • updated 11 months ago thomas.heigl.ibk • 0
0
votes
2
replies
648
views
Swimming downstream: transcript fold changes
DEXSeq stageR
15 months ago jbono ▴ 10
1
vote
1
reply
691
views
DEXSeq DEXSeqDataSet count matrix duplication
DEXSeq DRIMSeq DEXSeqDataSet columnduplication
15 months ago NiKo ▴ 10
0
votes
3
replies
1.0k
views
RNAseq (Deseq2 and Dexseq2) analysis on two time points with expected same effect
DEXSeq RNA-seq DESeq2
updated 17 months ago by ★ 1.9k • written 17 months ago by • 0
0
votes
3
replies
1.3k
views
Error with makeTxDbFromBiomart
DEXSeq biomaRt
updated 18 months ago by 16k • written 18 months ago by • 0
0
votes
2
replies
925
views
DEXSeqDataSet object DEXSeqDataSetFromHTSeq Error: line number did not have 3 elements
DEXSeq HTSeq R
18 months ago • updated 17 months ago yr542 • 0
8
votes
7
replies
2.5k
views
Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2 glmGamPoi DEXSeq
updated 19 months ago by ▴ 20 • written 2.3 years ago by ▴ 20
1
vote
5
replies
1.2k
views
DEXSeq output included non-exist exons
DEXSeq exon_definition exon
updated 19 months ago by ★ 1.9k • written 19 months ago by • 0
0
votes
0
replies
651
views
Recommendation sought for differential exon usage of a single gene
isofor DEXSeq DifferentialSplicing
20 months ago nick_brittain55 • 0
0
votes
0
replies
582
views
Error while performing DEXseq
DEXSeq
20 months ago vipul14 • 0
0
votes
0
replies
578
views
DEXSeq Subsetting pre or post dispersion calculation?
DEXSeq
23 months ago Ben J ▴ 20
2
votes
2
replies
1.5k
views
Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
DEXSeq
2.0 years ago Ben J ▴ 20
0
votes
0
replies
812
views
DESXSEQ warning (Fit for gene/exon ENSG0000002121 threw the next warning(s): the matrix is either rank-deficient or indefinite)?
DEXSeq
updated 2.2 years ago by 43k • written 2.2 years ago by • 0
0
votes
1
reply
1.0k
views
plotDEXSeq error?
DEXSeq dex
2.2 years ago barrypraveen • 0
1
vote
4
replies
1.2k
views
DEXseq batch removal
DEXSeq
updated 2.3 years ago by ★ 1.9k • written 2.3 years ago by ▴ 10
0
votes
0
replies
561
views
DEXSeq: mcols(dxd)$fullBetaConv either contains TRUE or NA
DEXSeq
2.4 years ago Matthias Munz ▴ 20
0
votes
0
replies
678
views
DEXSeq aggregated genes/exons result in NA values
RNASeq R DEXSeq
2.5 years ago osieman52 • 0
1
vote
2
replies
1.1k
views
DEXSeq: Error in reading counts from htseq "Error in FUN(X[[i]], ...) : subscript out of bounds"
DEXSeq
2.5 years ago Delta._.43 ▴ 20
0
votes
1
reply
1.1k
views
DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing Exon featureCounts subread DEXSeq
2.7 years ago NIK • 0
0
votes
4
replies
2.1k
views
DEXSeq: samples$sample_id %in% colnames(counts) is not TRUE
DEXSeq DRIMSeq
updated 2.7 years ago by ▴ 90 • written 2.8 years ago by • 0
0
votes
5
replies
2.3k
views
DEXSeq - counts from paired reads and unpaired singletons
dexseq
written 5.8 years ago by • 0
8
votes
12
replies
4.1k
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 8 months ago by ▴ 30 • written 2.8 years ago by ▴ 380
3
votes
2
replies
1.3k
views
DEX-Seq returns Error in FUN(X[[i]], ...) : subscript out of bounds when I use DEXSeqDatasetFromHTseq()
R DEXSeq SequenceAnnotation RNASeqData
2.8 years ago Dakarai ▴ 10
1
vote
1
reply
883
views
Increased number of exons in DEXSeq
DEXSeq exon
updated 2.9 years ago by ★ 1.9k • written 2.9 years ago by • 0
1
vote
2
replies
1.2k
views
Normalizing exonic reads and then log transforming or variance stabilising
DEXSeq
3.2 years ago • updated 3.0 years ago A ▴ 40
3
votes
3
replies
1.4k
views
Joint disperstion estimation for DEXSeq and DESeq2
DESeq2 DEXseq
updated 3.1 years ago by 43k • written 3.1 years ago by ▴ 120
0
votes
1
reply
1.1k
views
DEXSeq prepare annotation script throws "object has no attribute 'next'" for Ensemble GTFs
DEXSeq
updated 3.0 years ago by ★ 1.9k • written 3.3 years ago by • 0
1
vote
1
reply
1.4k
views
DTU using DEXSeq (time series data with condition factor)
DTU DEXSeq RNADTU
updated 3.0 years ago by ★ 1.9k • written 3.5 years ago by ▴ 10
2
votes
7
replies
1.7k
views
Fold Change for rnaseq DTU
DEXSeq rnaseqDTU
3.5 years ago • updated 3.4 years ago rbenel ▴ 40
0
votes
5
replies
1.6k
views
DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq DRIMSeq DEXSeq rnaseqDTU
3.5 years ago bioinformatic_trainee ▴ 10
1
vote
0
replies
1.3k
views
DEXseq: How to do differential exon usage of genes with overlapping exons
GenomicFeatures DEXSeq
3.5 years ago Matthias Munz ▴ 20
0
votes
0
replies
838
views
Disabling aggregation with the option -r no, still combines genes into single “aggregate genes"
DEXSeq
3.6 years ago n.tear ▴ 20
0
votes
0
replies
810
views
DEXSeq: Error in perGeneQValue with a single gene
DEXSeq
3.6 years ago Matthias Munz ▴ 20
1
vote
6
replies
1.9k
views
Differential Transcript Usage: complex factorial design
edgeR DEXSeq IsoformSwitchAnalyzeR DTU
updated 3.7 years ago by ▴ 120 • written 3.8 years ago by ▴ 10
4
votes
5
replies
2.5k
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
3.8 years ago Matthias Munz ▴ 20
0
votes
0
replies
1.1k
views
Error generating counts df for use with DRIMSeq/DEXseq
DRIMSeq DEXSeq
3.8 years ago jbono ▴ 10
0
votes
2
replies
1.3k
views
DRIMSeq + dmFilter
DEXSeq DRIMSeq
3.9 years ago Gaia • 0
3
votes
2
replies
1.3k
views
How to better run DEXSeq with a very large number of samples?
DEXSeq
3.9 years ago Angel ▴ 10
2
votes
2
replies
1.4k
views
Question: Error when running QoRTs for JunctionSeq
DEXSeq JunctionSeq RNAseq QoRTs
4.0 years ago • updated 3.9 years ago n.tear ▴ 20
1
vote
1
reply
1.3k
views
Differential exon usage analysis using DEXSeq for mRNA and lncRNA separately
DEXSeq
updated 4.1 years ago by ★ 1.9k • written 4.1 years ago by • 0
0
votes
2
replies
1.6k
views
DEXSeq - what is the best way to filter out low expressed exons / genes?
dexseq
4.6 years ago • updated 4.2 years ago aleksandar.baburski.g • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: accounting for vs. removing batch effects with DESeq2 in RNAseq analysis by Blair • 0
@[Sprunki][1] wrote: Please read the vignette and think about adhering to the author's best practice, which discusses batch impacts. [1…
Comment: error in ChAMP loading file by 81becky • 0
hi Giulia, it sounds like you're facing a frustating issue with your chAMP import. One common suggestion is to double-check your CSV fomat…
Answer: DESeq2 adujsted p-value cutoff seemingly not working by James W. MacDonald 68k
From `?results' ``` On p-values: By default, independent filtering is performed to select a set of genes for multiple tes…
Comment: Issue with assigning transcript IDs to reads when using summarizeOverlaps(mode = by SofieK • 0
Thank you, I will try this and see.
Comment: DiffBind - question on the use of filtered or unfiltered input data by deltaexploitss • 0
Data input is the adding of data into a computer. This can take place through an input device such as a keyboard. A user inputs data, which…
Votes
A: Effect of lfcThreshold on p-value in DESeq2
Answer: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
Answer: Issue with assigning transcript IDs to reads when using summarizeOverlaps(mode =
Comment: Unused arguments error without used arguments in GSVA?
Awards • All
Popular Question to Vincent J. Carey, Jr. 6.7k
Teacher to Gordon Smyth 52k
Scholar to James W. MacDonald 68k
Popular Question to Sara ▴ 20
Scholar to Michael Love 43k
Locations • All
United States, just now
United States, 2 minutes ago
Switzerland, 1 hour ago
United States, 1 hour ago
India, 2 hours ago
Traffic: 625 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