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motifdb
•
reset
2
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6
replies
2.2k
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Identifying TF binding sites (Motifdb + TxDb.Hsapiens.UCSC.hg19.knownGene)
motifdb
JASPAR
transcription factor binding site
9.2 years ago
Lisa Hopcroft
▴ 40
0
votes
1
reply
1.4k
views
ChIPpeakAnno "examplePattern.fa" file
rGADEM
MotifDb
rGADEM
MotifDb
updated 11.9 years ago by
José Luis Lavín
▴ 80 • written 11.9 years ago by
Paul Shannon
▴ 750
2
votes
16
replies
2.9k
views
MotifDb missing some FlyFactor Motifs
Motifdb
updated 2.9 years ago by
gunjan.dikshit
• 0 • written 4.7 years ago by
snystrom
▴ 10
0
votes
1
reply
1.5k
views
problem installing biocLite, MotifDb.
motifdb
bioclite
updated 8.6 years ago by
Hervé Pagès
16k • written 8.6 years ago by
mirzabiotech2000
• 0
3
votes
3
replies
1.8k
views
Fail to load "MotifDb" package
MotifDb
library
load
updated 7.9 years ago by
Paul Shannon
▴ 470 • written 7.9 years ago by
Pengcheng Yang
▴ 60
0
votes
2
replies
1.8k
views
How to make a MotifDb object from pwm/pfm files?
motifdb
updated 7.4 years ago by
Paul Shannon
▴ 470 • written 7.4 years ago by
Yiwei Niu
▴ 20
1
vote
1
reply
1.3k
views
total number of unique transcription factors in MotifDB
motifdb
updated 7.3 years ago by
Paul Shannon
▴ 470 • written 7.3 years ago by
scotronq
• 0
0
votes
1
reply
1.9k
views
promoter prediction
Transcription
MotIV
MotifDb
Transcription
MotIV
MotifDb
updated 12.2 years ago by
Jing Huang
▴ 380 • written 12.2 years ago by
Paul Shannon
▴ 750
0
votes
5
replies
2.8k
views
Motif enrichment analysis: Error in transfac format and background frequencies from BSGenome
BSgenome
convert
BSgenome
PWMEnrich
MotifDb
updated 10.4 years ago by
Robert Stojnic
▴ 80 • written 10.4 years ago by
deepti anand
▴ 50
0
votes
1
reply
2.4k
views
non-numeric argument to binary operator error with makeBackground() in PWMEnrich
pwmenrich
MotifDB
updated 9.2 years ago by
Robert Stojnic
▴ 50 • written 9.2 years ago by
elliott77
• 0
2
votes
1
reply
4.5k
views
Please suggest any good motif Discovery tool in R-Bioconductor.
motif
motifdb
meme
updated 9.2 years ago by
Hervé Pagès
16k • written 9.2 years ago by
vinod.acear
▴ 50
0
votes
0
replies
1.6k
views
ChIPpeakAnno
rGADEM
MotIV
MotifDb
rGADEM
MotIV
MotifDb
10.9 years ago
Bahar
▴ 10
1
vote
0
replies
1.5k
views
question on MotifDb package
Transcription
MotifDb
Transcription
MotifDb
10.9 years ago
Paul Shannon
▴ 470
2
votes
0
replies
2.1k
views
motifDb PFM vs JASPAR database PFM: conversion to PWM
pwm
pfm
jaspar
motifdb
updated 6.0 years ago by
Bioconductor Community
0 • written 6.2 years ago by
chrisclarkson100
▴ 50
0
votes
0
replies
910
views
Research questions that are answered using MotifDb
MotifDb
MotifDb
11.0 years ago
T M
▴ 10
0
votes
3
replies
1.7k
views
motif scanning using position frequncy matrix of motif in a given set of DNAstringset sequnces?.
motifdb
matchpwm
motif
pwmenrich
pwm
9.2 years ago
vinod.acear
▴ 50
16 results • Page
1 of 1
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Answer: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
by
Robert Castelo
★ 3.4k
Following the discussion of this post, the package [gDNAx](https://bioconductor.org/packages/gDNAx) has been fixed in devel and release 1.4…
Answer: Selection of correct coefficients or contrasts in DESeq2
by
James W. MacDonald
67k
Using R's model formulation for three-way interactions is probably not the way to go here. Or at least I wouldn't do it that way. An easier…
Comment: How to generate circular cnetplot and color nodes and edges in the same plot ?
by
Blandine
• 0
Thank you so much ! It's working !
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
by
James W. MacDonald
67k
Yes. If you have the Illumina IDs, then all the annotation data that `cpg.annotate` uses will be based on hg19. It doesn't matter if TCGA l…
Comment: Recount3 data correspond to TCGA data
by
Leonardo Collado Torres
★ 1.1k
Thanks @fep29! ^^
Votes
A: DESeq2 interaction term
Comment: Recount3 data correspond to TCGA data
Answer: DESeq2- merging technical vs biological replicates
Answer: SingleCellExperiment convenience function for metadata+expression?
How to correct for tumor purity using DESeq2 to analyze TCGA tumor sample expression.
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