User: carlosalfonsogonzalez6

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Posts by carlosalfonsogonzalez6

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Comment: C: scRNA-seq and Chip-seq data integration
... What do you think If I use logistic regression? ...
written 3 months ago by carlosalfonsogonzalez60
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Comment: C: scRNA-seq and Chip-seq data integration
... Hi Kevin, This is a great answer, thank you very much. How many genes would you consider to test for the "Nearby Gene" comparisons? ...
written 6 months ago by carlosalfonsogonzalez60
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scRNA-seq and Chip-seq data integration
... Dear All, I'm currently trying to integrate, a single cell data of the Drosophila embryo, and also Chip-seq experiments from same embryo, same stage. Which statistical framework would you suggest to establish a clear relation between Chip-seq enrichment (of common epigenetics marks e.g. H3k27me2) ...
scrna-seq drop-seq chip-seq rna-seq written 6 months ago by carlosalfonsogonzalez60 • updated 6 months ago by Kevin Blighe33k
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How to annotate peaks inside TADs and annotated with Gene expression?
... Hi I have a dataset of Chip-seq and RNA-seq experiments, there's also available HI-C data from the same stage and condition, I would like to annotate the nearest gene that is within TAD boundaries, Which method would you suggest to do this kind of analysis? I'm doing it just by annotating both coo ...
hi-c chip-seq rna-seq written 9 months ago by carlosalfonsogonzalez60
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Comment: C: complex question cis-regulatory elements chip-seq
... Thank you, Im have already done that, Im looking for something more specific ...
written 9 months ago by carlosalfonsogonzalez60
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Comment: C: FIMO output analysis
... Thank you very much, this is really helpful, I did realize that fimo has a command to give specific regions of the initial bedfile. ...
written 9 months ago by carlosalfonsogonzalez60
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complex question cis-regulatory elements chip-seq
... Hi, I have defined cis-regulatory elements by merging 4TF peaks of chip-seq experiments, I have identified the position of each motif in this cis-regulatory elements, I also have the same data for other 4 related species same coordinates obtained with liftover, so I want to compare like using some ...
chip-seq written 9 months ago by carlosalfonsogonzalez60 • updated 9 months ago by Devon Ryan86k
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FIMO output analysis
... Hi I have use FIMO to find a particular set of 4TF motifs on my chip-seq peaks, the output of FIMO describes coordinates within fasta sequence, does anyone have experience in taking FIMO GFF results and use it to re-annotate peak coordinates to know which one has a particular motif enrichment for ...
chip-seq written 9 months ago by carlosalfonsogonzalez60 • updated 9 months ago by venu5.7k
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Suboptimization in Developmental Enhancers. MOTIF variation
... Hello Everyone, I have a question and I hope some of you have some idea or possible solutions to this problem: It has been publish that enhancers regions undergo suboptimization, which means motifs for certain region have reduced binding affinities, in the paper they test this hypothesis mostly ...
drosophila gene regulation chip-seq written 10 months ago by carlosalfonsogonzalez60 • updated 8 months ago by Biostar ♦♦ 20
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Separate table by diferent string patterns.
... Hello community I hope you can help me with this problem I have the following data frame obtained form StarkLab lines of enhancer construction reporters. Lines <- data.frame(VTID = c("VT0006", "VT0007", "VT0112") , Chr = c("chr2L", "chr3R", "chr3L"), pattern = c("ubitquitous;4", "procephal ...
chip-seq strings written 10 months ago by carlosalfonsogonzalez60 • updated 10 months ago by Alex Reynolds26k

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