User: alessandro.pastore

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Posts by alessandro.pastore

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reduce granges if mcols value are ideitical with the next intervals
... Is possible to reduce a granges if the mcols value are idetical with the ones of the following intervals ?   Thanks! ...
granges reduce written 4 months ago by alessandro.pastore10
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Biomart getLDS do not retrive all mouse / human genes
... I want to obtain all human homologous gene from a Ensembl.Gene.ID vector of all Mouse genes. The df i obtain is missing many entries. Also if I use gene names instead of the Ensemble ID I have the same Issues. the getBM work fine  What is wrong? Thanks! mart <- useMart(biomart = "ensembl", da ...
biomart written 12 months ago by alessandro.pastore10 • updated 12 months ago by Mike Smith2.1k
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Comment: C: aggregate bins in large SummarizedExperiment efficiently
... Thanks this is nice, but it only list the first and last occurrence of a state pair, not if a state pair occur more than one time. the pair 1,1 occurs at the begin and at the end of the GRanges but in you case is listed as occurring in a interval that span the whole GRanges. I need both interval on ...
written 14 months ago by alessandro.pastore10
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aggregate bins in large SummarizedExperiment efficiently
... I have a SummarizedExperiment (but we can consider it a GRanges). What I want is to reduce the number of intervals, keeping only one row for every identical adjacent mcol(gr), important is to also keep track of the new extend interval. if a state pair is present also in non adjacent intervals (this ...
granges summarizedexperiment reduce written 14 months ago by alessandro.pastore10 • updated 14 months ago by Michael Lawrence9.8k
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find next non-overlapping nth elements of a given region
...   I have the following problem: I want to find the next 5 gene in (chr1_gene) on both side of a interval give from the GRanges (gr3) and generate a dataframe containing chr start end (from gr3) of the interval and i column for each ensembl_transcript_id with eventually NA. Thanks a lot for suggest ...
biomart granges findoverlaps written 17 months ago by alessandro.pastore10 • updated 17 months ago by Michael Lawrence9.8k

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