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salmon rna seq
•
reset
3
votes
3
replies
2.5k
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Using sluth with Salmon data, error while sleuth_prep
sleuth
R
salmon rna seq
salmon
6.5 years ago
Walter F. Baumann
▴ 10
2
votes
9
replies
1.8k
views
stageR NA in getAdjustedPValues() (method=dtu)
drimseq
stageR
dtu
salmon rna seq
updated 5.8 years ago by
Koen Van den Berge
▴ 180 • written 5.8 years ago by
fiona.dick91
▴ 60
0
votes
5
replies
1.7k
views
salmon output file for differential expression analysis
salmon rna seq
deseq2
updated 5.5 years ago by
Michael Love
42k • written 5.5 years ago by
Bob
• 0
3
votes
4
replies
1.4k
views
tximport and de novo transcriptome
tximport
salmon rna seq
de novo
updated 5.6 years ago by
James W. MacDonald
65k • written 5.6 years ago by
RMRG
▴ 10
0
votes
1
reply
1.2k
views
Using TPM of a specific isoform as a phenotype for gene set enrichment analysis
deseq2
gsea
tpm
rnaseq
salmon rna seq
updated 5.6 years ago by
Michael Love
42k • written 5.6 years ago by
leo_CD
• 0
0
votes
1
reply
1.1k
views
Salmon RNA Seq
salmon rna seq
updated 6.6 years ago by
Michael Love
42k • written 6.6 years ago by
tanyabioinfo
▴ 20
1
vote
1
reply
910
views
Post-processing RNA-Seq after tximport
salmon rna seq
tximport
ruv-seq
deseq2
updated 6.0 years ago by
Michael Love
42k • written 6.0 years ago by
mad6kj
• 0
1
vote
1
reply
896
views
DEseq2 with different fastq read numbers after salmon
deseq2
salmon rna seq
salmon
updated 5.5 years ago by
Michael Love
42k • written 5.5 years ago by
danalvoronov
▴ 10
8 results • Page
1 of 1
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Replies
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?
Comment: DESeq2- Mysterious interaction suppresses DEGs
by
shaunpeterson
• 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
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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