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Hello
TFEA is really nice method to explore the motifs in sequencing data. I would like to use TFEA on my ranked gene list. I tried test data and followed these steps :
## With test data which…
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I asked for 10 motifs with -n 10, and found the same exact motif 10 times. Am I missing something here?
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Hi,
Quite impressed with the speed at which mmseq performs pairwise alignments. Have a couple of questions:
1. Can i perform alignments using sequences with degenerate characters? Right now the…
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Hello, it's me again.
I have a question on how you select a threshold for the deepbind score. I see in your example with 4 models and 4 sequences, that the good models have a high, positive value and…
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Hi,
EffectR is a brilliant package for identifying effectors.
I just had a question regarding the identification of proteins with custom motifs. For some reason, when I use a custom pattern, the r…
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### Authors:
> - Saachi Jain - saachi@stanford.edu - Stanford University
> - David Hallac - hallac@stanford.edu - Stanford University
> - Rok Sosic - rok@stanford.edu - Stanford U…
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Hi, I use flanking sequence of D6S477 as 5' and 3' anchors to call this locus, and the sample is 9948 (a standard sample in forensic). To approve the tolerance of sequecing error or SNP variants in t…
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Hello!
Thank you for publishing your work! I'm currently experimenting with your software, and I have some ideas in mind, but I am not sure to what extent they are practical and possible with RFdi…
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https://doi.org/10.1109/BIBM.2016.7822515 (https://arxiv.org/abs/1611.05777)
> Transcription factors (TFs) are macromolecules that bind to \textit{cis}-regulatory specific sub-regions of DNA promot…
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Hi team,
Thank you for the nice explanation about database building. I want to create a database for zebrafish using "create_cistarget_motif_databases.py". I am struggling to get a zebrafish genom…