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STRINGTIE
•
reset
2
votes
3
replies
1.5k
views
how to get the lastest version of tximport
tximport
stringtie
6.2 years ago • updated 6.0 years ago
matrs
▴ 10
2
votes
1
reply
1.8k
views
How to change stringtie gene_id names with ref_gene_id when performing featureCount
featureCount
rna-seq
gene_id
re_gene_id
stringtie
updated 5.3 years ago by
Wei Shi
★ 3.6k • written 5.3 years ago by
IRAIA.MAIALEN
• 0
2
votes
8
replies
5.8k
views
StringTie + Ballgown: handling biological replicates
ballgown
stringtie
updated 7.2 years ago by
linda.boshans
• 0 • written 8.2 years ago by
bhawley1991
▴ 10
1
vote
1
reply
1.4k
views
RNA-seq for DGE
stringtie
illumina
hisat2
ballgown
updated 6.5 years ago by
k.vitting.seerup
▴ 120 • written 6.5 years ago by
amy16
• 0
1
vote
3
replies
1.4k
views
Interaction term analysis using ballgown
ballgown
stringtie
voom limma
differential gene expression
rnaseq
updated 7.6 years ago by
Alyssa Frazee
▴ 210 • written 7.6 years ago by
jcalis
▴ 10
0
votes
1
reply
4.4k
views
Usage of prepDE.py with stringtie and deseq2
prepDE
STRINGTIE
deseq2
updated 5.6 years ago by
Michael Love
42k • written 5.6 years ago by
Nancy
▴ 10
0
votes
4
replies
1.4k
views
tximport and its version
tximport
stringtie
RNA-seq analysis
updated 5.5 years ago by
James W. MacDonald
65k • written 5.5 years ago by
Mithil Gaikwad
• 0
0
votes
3
replies
3.5k
views
Normalisation - Deseq2 vs StingTie-Ballgown
deseq2
StringTie
RNA-seq
normalisation
updated 4.4 years ago by
Michael Love
42k • written 4.4 years ago by
JindrichK
• 0
0
votes
3
replies
1.4k
views
StringTie output as Ballgown input
ballgown
StringTie
galaxy
rnaseq
updated 23 months ago by
Kevin Blighe
★ 3.9k • written 3.8 years ago by
lakshmi9c
• 0
0
votes
0
replies
1.3k
views
HISAT2/StringTie/Ballgown for Novel Transcript Isoform Differential Expression
isoform
RNA-seq
hisat2
stringtie
ballgown
3.6 years ago
ra711
• 0
0
votes
0
replies
306
views
help with converting MSTRG tags with isoformswictanalyzer
stringtie
IsoformSwitchAnalyzeR
pfamAnalyzeR
gtf
updated 5 months ago by
James W. MacDonald
65k • written 5 months ago by
sumitra.20
• 0
0
votes
1
reply
731
views
How to make the data compatible for DESeq2?
DESeq2
TPM
rawcounts
StringTie
updated 21 months ago by
Michael Love
42k • written 21 months ago by
snijesh
▴ 20
0
votes
4
replies
1.8k
views
Ballgown from StringTie results transcripts which are not expressed in both conditions as Differentially expressed ones
ballgown
stringtie
updated 7.8 years ago by
Jeff Leek
▴ 650 • written 7.8 years ago by
alva.james
• 0
0
votes
7
replies
2.5k
views
Handling both technical and biological replicates in Ballgown
ballgown
biologicalreplicates
technical replicates
stringtie
updated 6.5 years ago by
Alyssa Frazee
▴ 210 • written 7.2 years ago by
linda.boshans
• 0
0
votes
0
replies
1.8k
views
RNA-seq with hisat2+stringtie+ballgown
hisat2
stringtie
ballgown
RNAseq
6.3 years ago • updated 6.0 years ago
Nancy
▴ 10
0
votes
0
replies
1.4k
views
Ballgown data processing error
Ballgown
Stringtie
DEG
rnaseq
6.0 years ago
vharshavardhanan
• 0
16 results • Page
1 of 1
Recent ...
Replies
Answer: Subsetting RNAseq data | voomaByGroup()
by
Gordon Smyth
50k
Judging from your MDS plot, cell types 1 and 2 look radically different, so it would make perfect sense to analyse them separately. There's…
Answer: Numerical differences in DESeq2 output depending on different design matrix cons
by
Michael Love
42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs
by
Michael Love
42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
swbarnes2
★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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Dario Strbenac
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Vincent J. Carey, Jr.
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