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pwm
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765
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universalmotif, question about enrich_motifs function and number of hits returned
universalmotif
scanning
enrich_motifs
PWM
2.2 years ago
alexandre.blais
▴ 50
2
votes
0
replies
1.5k
views
motifDb PFM vs JASPAR database PFM: conversion to PWM
pwm
pfm
jaspar
motifdb
updated 5.2 years ago by
Bioconductor Community
0 • written 5.3 years ago by
chrisclarkson100
▴ 50
0
votes
0
replies
747
views
Plotting motif enrichment vs background - Jaspar core vertebrates
pwm
motifs
jaspar
meme
motif analysis
5.3 years ago
rbronste
▴ 60
2
votes
1
reply
2.2k
views
Error: unable to find an inherited method for function searchSeq for signature matrix
pwm
tfbstools
jaspar
updated 6.5 years ago by
Ge Tan
▴ 20 • written 6.5 years ago by
chrisclarkson100
▴ 50
0
votes
1
reply
1.2k
views
PWM with columns that add up to 1
biostrings
seqlogo
pwm
updated 7.3 years ago by
Marcel Ramos
680 • written 7.4 years ago by
clausdkuhn
• 0
0
votes
0
replies
829
views
maxScore calculation for 'log2probratio' and 'prob' type PWMs
biostrings
pwm
7.5 years ago
Stefanie Tauber
▴ 40
0
votes
3
replies
1.4k
views
motif scanning using position frequncy matrix of motif in a given set of DNAstringset sequnces?.
motifdb
matchpwm
motif
pwmenrich
pwm
8.3 years ago
vinod.acear
▴ 50
7 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…
Votes
Answer: edgeR, 3 x 2 design with a batch effect and contrasts
Answer: padj-based gradient scale from barplot (clusterProfiler results) does not work p
C: How to check that the reads in two fastq files are in the same order
Answer: Need help with creating and plotting temporal clustering analysis of DEGs
Answer: Problem converting msigdb Human symbols to Zebrafish in gmt format
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