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bacteria
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RNA-seq bacterial transcriptome analysis in EdgeR with unusual dispersion trend
RNA-seq
edgeR
estimatedispersions
bacteria
9.2 years ago
Mauve
• 0
2
votes
4
replies
1.4k
views
GO/KEEG enrichment for non-model bacteria - help for beginner
bacteria
GO
KEEG
RNAseq
4.0 years ago
liz.marjory
• 0
0
votes
1
reply
601
views
Syntenet application to bacterial genome and file processing
syntenet
Bacteria
synteny
updated 4 months ago by
Fabricio Almeida-Silva
▴ 40 • written 6 months ago by
kluongni
• 0
0
votes
1
reply
1.5k
views
Using summarizeOverlaps for bacterial genomes
summarizeoverlaps
bacteria
e coli
unique reads
updated 8.2 years ago by
Valerie Obenchain
★ 6.8k • written 8.2 years ago by
as9309
• 0
3
votes
1
reply
2.1k
views
Tools for GO term enrichment in prokaryotes
bacteria
GO enrichment
updated 8.7 years ago by
Marc Carlson
★ 7.2k • written 8.7 years ago by
ksw
▴ 20
3
votes
2
replies
1.4k
views
Job:
Hunting for Human Infectious Agents in Cancer using data from Genomics England's 100,000 genome project : PhD Studentship @ UEA, Norwich
PhD
cancer genomics
bacteria
pathogens
Job
7.2 years ago
Daniel Brewer
▴ 100
0
votes
0
replies
1.2k
views
Job:
postdoc 3yrs bioinformatics bacterial population genomics: Wellington, New Zealand
bacteria
evolution
population
genomics
Job
6.8 years ago
una.ren
• 0
7 results • Page
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Comment: How to retrieve gene ontology GO class from gene list?
by
bandconductor
• 0
Thanks, this is potentially a much faster way than parsing BiomRt. However, it is only returning one GO term right now (biomaRt returns a f…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
James W. MacDonald
65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
Alexandre
• 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Comment: PCA plot suggestions
by
JKim
• 0
cross post: https://www.biostars.org/p/9593486/
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
James W. MacDonald
65k
You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
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James W. MacDonald
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Gordon Smyth
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