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dexseq
•
reset
2
votes
2
replies
1.9k
views
Question: Error when running QoRTs for JunctionSeq
DEXSeq
JunctionSeq
RNAseq
QoRTs
5.0 years ago
n.tear
▴ 20
1
vote
1
reply
1.6k
views
Differential exon usage analysis using DEXSeq for mRNA and lncRNA separately
DEXSeq
updated 5.1 years ago by
Alejandro Reyes
★ 1.9k • written 5.1 years ago by
Anubhav
• 0
0
votes
2
replies
1.8k
views
DEXSeq - what is the best way to filter out low expressed exons / genes?
dexseq
5.7 years ago • updated 5.3 years ago
aleksandar.baburski.g
• 0
1
vote
6
replies
5.0k
views
DEXSeq: question about usage coefficient and splicing plot
dexseq
updated 5.3 years ago by
rohitsatyam102
▴ 20 • written 10.9 years ago by
ywu
• 0
0
votes
2
replies
1.9k
views
Interpreting the EstimateDispersion plot from the DEXSeq package
dexseq
estimatedispersions
updated 5.3 years ago by
rohitsatyam102
▴ 20 • written 8.1 years ago by
brand
• 0
6
votes
7
replies
2.4k
views
Strategy to perform DESeq, DEXSeq workflow
DEXSeq
DESeq2
updated 5.2 years ago by
Michael Love
43k • written 5.3 years ago by
rohitsatyam102
▴ 20
0
votes
2
replies
1.3k
views
DEXSeq : can we plot from the table of results or/and run DEXSeq from a matrix of counts like in DESeq2?
DEXseq
updated 5.6 years ago by
Simon Anders
★ 3.8k • written 5.6 years ago by
lu.la
• 0
0
votes
4
replies
2.4k
views
Calculating per-exon PSI from DEXSeq
DEXSeq
5.6 years ago
Angel Liang
• 0
1
vote
2
replies
1.7k
views
Detailed explanations for DEXSeq output columns
DEXSeq
updated 5.6 years ago by
Alejandro Reyes
★ 1.9k • written 5.6 years ago by
Angel Liang
• 0
0
votes
1
reply
1.2k
views
How to obtain the specific genelists mentioned in the RNASeq DTU workflow?
rnaseqdtu
RNASeq
DEXSeq
DESeq2
updated 5.7 years ago by
Michael Love
43k • written 5.7 years ago by
debatosh das
▴ 10
1
vote
2
replies
1.7k
views
DEXSeq dispersion estimation optimisation for large number of samples
DEXSeq
estimateDispersions
5.7 years ago
aleksandar.baburski.g
• 0
0
votes
2
replies
1.3k
views
DEXSeq HTML report Error
DEXSeq
updated 5.7 years ago by
Kevin Blighe
★ 4.0k • written 5.7 years ago by
aleksandar.baburski.g
• 0
0
votes
0
replies
1.1k
views
Subset samples expressing genes for DEXSeq or DRIMSeq analysis
DEXSeq
DRIMSeq
5.8 years ago
alexis.weinreb
• 0
1
vote
2
replies
2.4k
views
DEXSeq Python script dexseq_prepare_annotation.py unable to process my .gtf file
dexseq
python
gtf
gff3
annotation
5.8 years ago
Raito92
▴ 60
0
votes
1
reply
1.4k
views
DEXseq conversion of GTF to GFF creating incorrect exon coordinates
software error
DEXSeq
5.8 years ago
knuppdav
• 0
1
vote
3
replies
2.2k
views
DEXSeq with large(ish) number of samples
DEXSeq
exon
memory
dispersions
estimateDispersions
5.8 years ago
andreismolnikov00
• 0
0
votes
0
replies
2.1k
views
summarizeOverlaps - (GenomicAlignments) - gives warnings 'package:stats' may not be available when loading
GenomicAlignments
summerizeOverlaps-Method
DEXSeq
updated 5.9 years ago by
Martin Morgan
25k • written 5.9 years ago by
mar.pieraccioli
▴ 10
3
votes
3
replies
2.8k
views
Calculation of Log2 fold change in DEXSeq
DEXSeq
log2foldchange
Tutorial
updated 4.5 years ago by
rohitsatyam102
▴ 20 • written 5.9 years ago by
tmvarsha
▴ 20
1
vote
2
replies
1.0k
views
How to set model formulae in DEXSeq when 2 shRNAs were used to target a same gene
DEXSeq
updated 5.9 years ago by
Alejandro Reyes
★ 1.9k • written 5.9 years ago by
zliu
▴ 10
0
votes
3
replies
1.8k
views
DEXSeq Splicing Result with incomplete lines between exons
DEXSeq
Splicing
Exon Usage
6.0 years ago
gunjan.dikshit
• 0
2
votes
6
replies
3.9k
views
featureCount error - cannot identify gene_id
dexseq
rsubread
featureCount
software error
updated 6.2 years ago by
Yang Liao
▴ 450 • written 6.2 years ago by
seung.ho.steven.choi
• 0
0
votes
2
replies
1.4k
views
JunctionSeq producing strangely large effect sizes for certain exon counting bins
junctionseq
splicing
RNAseq
DEXSeq
written 6.2 years ago by
stuart
▴ 10
0
votes
1
reply
790
views
error in DEXSeq estimateExonFoldChanges
dexseq
6.3 years ago
brown.annaleigh
• 0
0
votes
2
replies
1.1k
views
A question about DEXSeq of estimateDispersions
dexseq
updated 6.4 years ago by
glmazzo
▴ 10 • written 6.5 years ago by
liushang
• 0
0
votes
2
replies
1.6k
views
Issue/Error with DEXSeq design formulae in testForDEU function
deseq2
DEXSeq
BioCParallel
updated 6.5 years ago by
Alejandro Reyes
★ 1.9k • written 6.5 years ago by
acciardo
• 0
1
vote
2
replies
2.6k
views
DEXseq error unable to find an inherited method for function NSBS for signature CompressedIntegerList
Dexseq
updated 3.5 years ago by
ta_awwad
▴ 10 • written 6.6 years ago by
bruce.hayward
▴ 10
0
votes
2
replies
1.2k
views
DEXSeq error in dexseq_count.py. ValueError: need more than 4 values to unpack
DEXSeq
updated 6.7 years ago by
Simon Anders
★ 3.8k • written 6.7 years ago by
Paola Cornejo
• 0
4
votes
1
reply
1.4k
views
Print Differentially Expressed Exons From Dexseq Results
DEXSeq
RNA-Seq
updated 6.7 years ago by
Alejandro Reyes
★ 1.9k • written 6.7 years ago by
justinkablan225
▴ 10
2
votes
3
replies
1.7k
views
exonicParts vs. disjoinExons inconsistency in usage for DEXSeq - bug?
DEXSeq
updated 6.8 years ago by
Hervé Pagès
16k • written 6.8 years ago by
story.benjamin
▴ 20
0
votes
6
replies
2.4k
views
DEXSeq dispersion outlier
DEXSeq
dispersion
pvalue
6.8 years ago
fiona.dick91
▴ 60
2
votes
3
replies
1.6k
views
null model and DEXSeqDataSet object in DEXSEQ
deseq2
dexseq
6.8 years ago
gv
▴ 30
2
votes
6
replies
1.9k
views
estimateDispersions calculation for > 500,000 exons for 2 conditions taking forever
deseq2
dexseq
6.8 years ago
gv
▴ 30
1
vote
6
replies
2.0k
views
How to install DEXSeq on R 3.4.4
DEXSEq
Linux
updated 6.8 years ago by
Alejandro Reyes
★ 1.9k • written 6.8 years ago by
justinkablan225
▴ 10
1
vote
1
reply
1.9k
views
rnaseqDTU log2fold change DEXSeq
DEXSeq
DTU
salmon
rnaseqDTU
foldchange
updated 6.8 years ago by
Michael Love
43k • written 7.1 years ago by
fiona.dick91
▴ 60
0
votes
11
replies
2.4k
views
Issue during transcript variant analysis using rnaseqDTU-DRIMseq-DEXseq.
rnaseqDTU
DRIMseq
DEXseq
rna-seq
6.9 years ago
saddamhusain77
• 0
0
votes
2
replies
1.3k
views
DEXSeq With Reduced Annotations
dexseq
reduced annotation set
6.9 years ago
sumeet460
• 0
1
vote
2
replies
2.2k
views
Normalized transcript/exon counts for network analysis
drimseq
dexseq
wgcna
sva
updated 7.0 years ago by
Gosia Nowicka
▴ 90 • written 7.0 years ago by
maya.kappil
▴ 30
2
votes
4
replies
2.3k
views
stageR: Error in stageWiseAdjustment
stageR
rnaseqDTU
DRIMSeq
DEXSeq
7.1 years ago
d-joester
▴ 20
0
votes
4
replies
2.5k
views
tximport: Error in medianLengthOverIsoform
tximport
deseq2
dexseq
7.1 years ago
d-joester
▴ 20
0
votes
1
reply
1.0k
views
DEXSeq: controlling for cell composition
dexseq
updated 7.1 years ago by
Alejandro Reyes
★ 1.9k • written 7.1 years ago by
reflectedpumice
• 0
0
votes
1
reply
1.3k
views
Can DEXseq be used for splicing QTL analysis?
dexseq
splicing
sqtl
qtl
updated 7.1 years ago by
Alejandro Reyes
★ 1.9k • written 7.1 years ago by
rtunney2
• 0
0
votes
3
replies
1.4k
views
How to get missing columns in DEXSeq analysis (exon usage coefficients)
dexseq
dexseqalt
7.1 years ago
mjrarcher
▴ 10
0
votes
1
reply
1.4k
views
Add interaction term between variables to DEXSeq design
DEXSeq
interaction
7.1 years ago
zhenzuo2
• 0
0
votes
0
replies
1.2k
views
DEXSeq: How to reduce compute time for estimating dispersions for large datasets.
dexseq
estimatedispersions
large dataset
7.1 years ago
mjrarcher
▴ 10
0
votes
5
replies
1.8k
views
DEXSeq 1.26.0 running very slowly (stuck?)
dexseq
7.2 years ago
Lance Parsons
• 0
0
votes
7
replies
3.0k
views
DEXSeqHTML getListElement GRanges error
dexseq
software error
bug
updated 7.3 years ago by
nitesh.turaga
▴ 140 • written 7.3 years ago by
Lance Parsons
• 0
1
vote
5
replies
2.3k
views
Plotting Expression of Differential Transcripts plotDEXseq
DEXSeq
StageR
rnaseqDTU
updated 7.3 years ago by
Michael Love
43k • written 7.4 years ago by
rbenel
▴ 50
0
votes
2
replies
1.4k
views
Preparation of summarizedExperiment for dexSeq
dexseq
genomicalignments
genomicfeatures
genomicranges
7.4 years ago
A
▴ 60
0
votes
0
replies
715
views
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
7.4 years ago
slowsmile820
• 0
6
votes
6
replies
3.3k
views
Kallisto output with DEXSeq
dexseq
kallisto
NH_tag
updated 7.4 years ago by
Alejandro Reyes
★ 1.9k • written 7.4 years ago by
j2h2k2
• 0
364 results • Page
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Recent ...
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Comment: Question on processing compound protein groups in limpa
by
JKim
• 0
Many thanks. I appreciate your advice.
Answer: Question on processing compound protein groups in limpa
by
Gordon Smyth
53k
Different people have different ways of dealing with compound protein groups. You could just leave them in the analysis, in which case limp…
Answer: Correct usage of limpa for protein input
by
Gordon Smyth
53k
limpa can work on protein-level quantifications, but they must be intensity-based and must be on the log scale. From what I read (<https://…
Comment: A problem occurs when running the monocle2
by
a2a2hset32aa
• 0
Troubleshooting monocle2 errors in R 4.5.1 often points to package incompatibilities, particularly with newer versions of igraph. For resea…
Comment: Deadline Extended: EuroBioC2026 Call for Abstracts
by
a2a2hset32aa
• 0
Attending EuroBioC2026 is an excellent way for researchers to explore the intersection of technology and biology. For those seeking high qu…
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Answer: Question on processing compound protein groups in limpa
Answer: Correct usage of limpa for protein input
Answer: Correct usage of limpa for protein input
Answer: Correct usage of limpa for protein input
A: Interpretaion of dendrogram height in WGCNA?
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