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reactome.db
•
reset
3
votes
4
replies
1.7k
views
Download of package ‘reactome.db’ failed (Ubuntu, not for Windows)
reactome.db
ReactomePA
2.6 years ago
florianjt
• 0
5
votes
6
replies
2.0k
views
Download errors during Bioconductor 3.12 update
reactome.db
Bioconductor
BiocManager
updated 2.9 years ago by
Martin Morgan
25k • written 2.9 years ago by
Michael Steinbaugh
▴ 90
0
votes
5
replies
1.6k
views
ReactomePA / Reactome: Crash when plotting
reactomepa
reactomepa reactome bioconductor viewpathway
reactome.db
reactome
5.3 years ago
martin.busch
• 0
3
votes
4
replies
1.5k
views
Enrichment Analysis for Shot-gun proteomics data using the ReactomePA package: problem with identities loss
reactomepa
reactome.db
reactome
proteomics
uniprot accessions
updated 5.9 years ago by
willem.ligtenberg
▴ 150 • written 5.9 years ago by
Miguel.Cosenza
▴ 10
0
votes
1
reply
903
views
Retrieve the reactome ID of a protein
reactome.db
updated 6.2 years ago by
alserg
▴ 240 • written 6.2 years ago by
Lluís Revilla Sancho
▴ 720
0
votes
5
replies
2.3k
views
reactome.db installation problem
reactome.db
bioclite
6.4 years ago
Jan-Jaap
• 0
6
votes
15
replies
2.5k
views
Change in pathway IDs scheme in reactome.db
reactome.db
fgsea
updated 6.4 years ago by
willem.ligtenberg
▴ 150 • written 6.4 years ago by
alserg
▴ 240
3
votes
7
replies
1.9k
views
Misleading information in reactome.db
reactome.db
6.6 years ago
Lluís Revilla Sancho
▴ 720
1
vote
1
reply
1.2k
views
Unable to see reactome.db dbschema
reactome.db
rsqlite
updated 6.7 years ago by
willem.ligtenberg
▴ 150 • written 6.7 years ago by
Lluís Revilla Sancho
▴ 720
3
votes
5
replies
1.4k
views
Selecting few ids from reactome.db
annotationdbi
reactome.db
bug
updated 6.8 years ago by
Martin Morgan
25k • written 6.8 years ago by
Lluís Revilla Sancho
▴ 720
0
votes
6
replies
1.3k
views
Is reactome.db still updated?
reactome.db
annotation
pathways
6.9 years ago
Guido Hooiveld
★ 3.7k
5
votes
6
replies
2.1k
views
Reactome pathway names from IDs?
biomart
reactome
reactome.db
id
updated 7.9 years ago by
James W. MacDonald
63k • written 7.9 years ago by
enricoferrero
▴ 660
0
votes
1
reply
1.1k
views
Reactome's bug of feature?
reactome.db
updated 8.1 years ago by
willem.ligtenberg
▴ 150 • written 8.1 years ago by
petyuk
▴ 70
8
votes
14
replies
3.3k
views
reactome.db is not updated?
genesetenrichment
pathways
reactome.db
updated 8.5 years ago by
willem.ligtenberg
▴ 150 • written 8.9 years ago by
Guangchuang Yu
★ 1.2k
14 results • Page
1 of 1
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Replies
Comment: Suggested package missing from Development version of Bioconductor
by
shepherl
3.5k
Have you tried reaching out to the maintainers? If they do not fix the package it will remain unavailable and cause ERROR in your package.…
Answer: Batch effect adjust in model matrix
by
ATpoint
★ 3.4k
Each sample is a different day, that is called "nested", so there is nothing you can do here. Next time do a better experimental design, he…
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
by
Michael Love
40k
Oh, I see. If you can't use counts + offset then I prefer lengthScaledTPM to DESeq2, i.e. `txi$counts` to `DESeqDataSetFromMatrix()`. So …
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
by
Christian
• 0
I´m sorry causing confusion here, but the gene matrices I refer to are actually obtained via https://nf-co.re/rnaseq. The problem with the…
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
by
Michael Love
40k
For the reasons outlined in the Soneson paper, I'd prefer this pipeline: https://nf-co.re/rnaseq You cannot use these scaled TPM approach…
Votes
Comment: Batch correction and repeated measures
batch effect : comBat or blocking in limma ?
Batch correction and repeated measures
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
Comment: Phenotype effect - building a contrast matrix - grouping vs interaction
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