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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
1.7k
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
5.7k
views
StringTie + Ballgown: handling biological replicates
ballgown
stringtie
updated 7.1 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 6.4 years ago by
k.vitting.seerup
▴ 120 • written 6.4 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
41k • written 5.6 years ago by
Nancy
▴ 10
0
votes
4
replies
1.3k
views
tximport and its version
tximport
stringtie
RNA-seq analysis
updated 5.4 years ago by
James W. MacDonald
65k • written 5.4 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
41k • 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 22 months ago by
Kevin Blighe
★ 3.9k • written 3.7 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
274
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
723
views
How to make the data compatible for DESeq2?
DESeq2
TPM
rawcounts
StringTie
updated 20 months ago by
Michael Love
41k • written 20 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 6.4 years ago by
Alyssa Frazee
▴ 210 • written 7.1 years ago by
linda.boshans
• 0
0
votes
0
replies
1.8k
views
RNA-seq with hisat2+stringtie+ballgown
hisat2
stringtie
ballgown
RNAseq
6.2 years ago • updated 6.0 years ago
Nancy
▴ 10
0
votes
0
replies
1.3k
views
Ballgown data processing error
Ballgown
Stringtie
DEG
rnaseq
6.0 years ago
vharshavardhanan
• 0
16 results • Page
1 of 1
Recent ...
Replies
Comment: Why p value inconsistent when using different number of pathway score?
by
Chris
• 0
Hi Robert, if two conditions don't have hundreds of differential express genes ( in some conditions such as peripheral blood Alzheimer vs n…
Answer: Dominance Index for Shotgun Metagenomics Data
by
Leo Lahti
▴ 40
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
pl23
• 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions
by
Michael Love
41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
by
ussarizona
▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Votes
Answer: Dominance Index for Shotgun Metagenomics Data
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
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