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ALPINE
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Bias correction in single end experiment for DEG and DET
tximport
alpine
7.9 years ago
yohann.nedelec
• 0
2
votes
7
replies
1.6k
views
Transcript abundance estimation for time-course RNA-seq data
rna-seq
salmon
alpine
transcript expression
updated 5.9 years ago by
Michael Love
42k • written 5.9 years ago by
relathman
▴ 20
2
votes
1
reply
2.3k
views
Should I use alpine and can I convert the output back to counts?
alpine
deseq2
updated 5.8 years ago by
Michael Love
42k • written 5.8 years ago by
harry.smith
▴ 20
0
votes
3
replies
777
views
Error in alpine::fitBiasModels shows as "offset needs to be finite"
Alpine
jcc
4.7 years ago
bioinagesh
• 0
5
votes
11
replies
1.5k
views
Visualization tool for GC-bias in SE data?
GC-bias
ALPINE
visualization
updated 3.9 years ago by
Michael Love
42k • written 3.9 years ago by
AKSR
▴ 20
5 results • Page
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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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