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motif analysis
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Plotting motif enrichment vs background - Jaspar core vertebrates
pwm
motifs
jaspar
meme
motif analysis
5.3 years ago
rbronste
▴ 60
2
votes
5
replies
2.4k
views
Error with R package motifbreakR while trying to read a vcf file with snps.from.file function
motifbreakR
vcf
snps
motif analysis
updated 5.7 years ago by
Valerie Obenchain
★ 6.8k • written 5.8 years ago by
svlachavas
▴ 830
0
votes
1
reply
1.1k
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Identification of Overrepresented Transcription Factor Binding Motifs in the Promoters of a List of DE Genes
HOMER
Motif Analysis
updated 6.2 years ago by
Ou, Jianhong
★ 1.3k • written 6.2 years ago by
JMallory
• 0
3 results • Page
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Comment: DEG Filtering
by
Gordon Smyth
50k
RMA normalization is good but batch correction using NOISeq isn't right. Data shouldn't be batch corrected before the limma analysis and NO…
Answer: maftools: Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicat
by
snijesh
▴ 20
You can try: using `read.delim` or `fread`. ``` my_maf = data.table::fread("path/to/maf/sample.maf") my_maf = read.maf(maf = my_maf) …
Comment: DEG Filtering
by
Amit
• 0
Hi Gordon, Thank you for your response and advice. I want to analyze Dataset GSE18090 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi) whic…
Comment: edgeR, 3 x 2 design with a batch effect and contrasts
by
Gordon Smyth
50k
Yes, that is a quote from [A guide to creating design matrices for gene expression experiments](https://bioconductor.org/packages/release/w…
Comment: edgeR, 3 x 2 design with a batch effect and contrasts
by
JKim
• 0
Thank you. I think I found why the order matters. > Although an intercept-free design matrix has been coded using the 0+ notation, the in…
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Answer: edgeR, 3 x 2 design with a batch effect and contrasts
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