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isoforms
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5
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18
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3.2k
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Incongruencies between DEXSeq and BitSeq/Cuffdiff
dexseq
bitseq
cuffdiff
Differential exon usage
isoforms
8.9 years ago • updated 8.8 years ago
elle
▴ 10
5
votes
3
replies
2.5k
views
edgeR: annotation and isoform analysis alternatives
edgeR
ruvseq
rnaseq
isoforms
8.9 years ago
sergio.espeso-gil
• 0
1
vote
2
replies
1.4k
views
DEXSeq transcripts per condition
DEXSeq
transcripts
isoforms
updated 8.9 years ago by
Alejandro Reyes
★ 1.9k • written 9.0 years ago by
peter_venhuizen
• 0
1
vote
9
replies
1.9k
views
Difference between gene-level test and transcript-level test with RATs (Relative Abundance of Transcrits)
RATs
RNA-Seq
Isoforms
DTU
expression
updated 4.8 years ago by
fruce_ki
▴ 20 • written 4.8 years ago by
UserAnonyme
• 0
2
votes
2
replies
785
views
Confounding DE results with DESeq2
isoforms
DESeq2
2.1 years ago
arfranco
▴ 130
0
votes
3
replies
1.4k
views
Downstream analysis for Salmon output: IsoformSwitchAnalyzeR or TSIS?
isoforms
diffrential expression
noncoding rna
TSIS
isoformswitchanalyzeR
5.9 years ago
rbenel
▴ 40
0
votes
0
replies
1.5k
views
cummeRbund heatmap for specific isoforms (not genes)
cummerbund
heatmap
isoforms
transcript_id
7.1 years ago
domenico.somma
• 0
0
votes
0
replies
962
views
Metadata sheet for DEXSeq analysis
dexseq
differential isoform usage
isoforms
summarizeoverlaps
granges
6.1 years ago
A
▴ 40
8 results • Page
1 of 1
Recent ...
Replies
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…
Answer: Deseq2. decontXcounts not integers. Useful alternative?
by
Michael Love
41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks
by
ATpoint
★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
camp
▴ 10
Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…
Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
ATpoint
★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Votes
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)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
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