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keggorthology
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7
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1.8k
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Problem with universe argument in enrichKEGG
KEGG
clusterProfiler
keggorthology
updated 13 months ago by
Basti
▴ 770 • written 13 months ago by
ruiqi.li
▴ 10
0
votes
2
replies
837
views
How do we get genes involved in all immune system pathways?
keggorthology
KEGG
updated 20 months ago by
sandmann.t
▴ 70 • written 21 months ago by
Recep
▴ 20
0
votes
0
replies
975
views
How to compute the "completeness" of a KEGG module using a set of KEGG orthologs? (Module Completion Ratio)
KEGG
KEGGREST
keggorthology
Metagenomics
3.1 years ago
jol.espinoz
▴ 40
0
votes
7
replies
2.2k
views
Bioconductor 2.6 is released
Sequencing
Microarray
Visualization
Infrastructure
PROcess
beadarray
keggorthology
eisa
updated 7.7 years ago by
wangyizhusss
• 0 • written 14.0 years ago by
Patrick Aboyoun
★ 1.6k
0
votes
2
replies
7.3k
views
Using Keggrest to convert ncbi gene IDs to kegg orthology and pathway
keggrest
kegg
keggorthology
updated 9.4 years ago by
James W. MacDonald
65k • written 9.4 years ago by
francesca.defilippis
▴ 100
1
vote
5
replies
2.0k
views
About the state of KEGG-related packages
KEGGSOAP
KEGGgraph
keggorthology
clusterProfiler
KEGGprofile
PathNet
KEGGSOAP
KEGGgraph
updated 10.7 years ago by
Luo Weijun
★ 1.6k • written 10.7 years ago by
enricoferrero
▴ 660
6 results • Page
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Comment: Which input file is used for DGEList in EgdeR?
by
Michael Love
41k
"gene_counts_length_scaled.tsv file generated by the nf-core be exactly that?" No that is the counts scaled by the length. Counts + offset…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa
by
Michael Love
41k
These genes are fine. They are just the ones where, by chance, the sample variance is below the sample mean. It happens. DESeq2 brings thes…
Comment: DEG with low counts
by
Michael Love
41k
These counts are too low, only a few samples above a count of 10. So for typical RNA-seq data that is underpowered to call differences. It…
Comment: DESeq filtering specific to contrasts
by
Michael Love
41k
If the counts are too low it in one group then you can't make the comparison either way (whether they are filtered out or just under-powere…
Comment: Estimating Cell Counts for EPIC V2 array data
by
normawiedman059
• 0
0 [103] spam_2.9-1 doParallel_1.0.17 iterators_1.0.14 [106] foreach_1.5.2 beeswarm_0.4.0 tgp_2.4-20 [109] beanplot_1.3.1 fpc_2.2-9 dbscan_1…
Votes
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Comment: DEXSeq DEXSeqDataSet count matrix duplication
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