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batch correction
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3
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3
replies
1.6k
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fastMNN based correction for large multi-run experiment requires a similar population set in all the individual datasets?
scrna-seq
integration
batch correction
updated 4.4 years ago by
Aaron Lun
★ 28k • written 4.4 years ago by
p.joshi
▴ 40
0
votes
1
reply
1.0k
views
Batch correction in Linear Models for methylation data
methylation
ComBat
Linear models
batch correction
AIC
updated 4.5 years ago by
Kevin Blighe
★ 3.9k • written 4.5 years ago by
lucasmiranda42
• 0
5
votes
3
replies
624
views
batch correction in DESeq2 > matrix not full rank > mitigate
DESeq2
batch correction
updated 4.5 years ago by
James W. MacDonald
66k • written 4.5 years ago by
MT
▴ 10
0
votes
3
replies
965
views
Diffbind batch effect blocking error
Diffbind
ATAC
batch correction
blocking factor
updated 4.8 years ago by
Rory Stark
★ 5.2k • written 4.8 years ago by
rm1238
• 0
1
vote
1
reply
1.0k
views
All Pairwise Comparisons with DESeq2 While Controlling for Batch Effects: Does Reference Level Matter?
deseq2
differential expression
batch correction
design
updated 5.0 years ago by
Michael Love
42k • written 5.0 years ago by
wunderl
▴ 40
4
votes
4
replies
1.4k
views
Batch Correction: DESeq2 Linear Model vs Batch-Correction-Specific Algorithms (RUV, ComBat, ect.)
deseq2
differential expression
batch correction
updated 5.0 years ago by
Michael Love
42k • written 5.0 years ago by
wunderl
▴ 40
4
votes
5
replies
1.8k
views
Using SC3 with batch corrected MNN values
SC3
Scater
Scran
scRNA-Seq
Batch Correction
updated 5.2 years ago by
Vladimir Kiselev
▴ 150 • written 5.2 years ago by
hamza_karakurt
▴ 60
7 results • Page
1 of 1
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Replies
Comment: How to compare subset of samples from VCF files
by
Gordon Smyth
50k
Welcome to Bioconductor support. Did you know that you can delete your old postings if they haven't received an answer yet? Instead of ap…
Comment: How to compare subset of samples from VCF files
by
Marco
• 0
Here's the vcf file as code block ``` ##fileformat=VCFv4.2 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth"> ##FOR…
Comment: Gviz and custom database
by
James W. MacDonald
66k
The vignette for `Gviz` says you can use a `DNAStringSet`, generated using `Biostrings`. Have you tried that?
Comment: Gviz and custom database
by
luigi.faino
• 0
Dear, this is not what I need. I need to transform a fasta sequence in a genome track usable in Gviz. L
Answer: Gviz and custom database
by
James W. MacDonald
66k
https://bioconductor.org/packages/release/bioc/vignettes/txdbmaker/inst/doc/txdbmaker.html
Votes
Answer: makeExampleDESeqDataSet using pilot data
Answer: Checking/updating package versions
Answer: Why is longestConsecutive() depreceated in version 2.72 (BioC version 3.19)?
convert data frame of Entrez IDs to Gene Symbols
Answer: LRT, pairwise comparisons and p-value adjustment
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