User: alessandro.pastore

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Posts by alessandro.pastore

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Rsubread Read Bam and filter reads by TAG field
... I have multi samples BAM files (from 10x Experiments). My aim is to count reads on genomic region.  I am using the  tagFilter parameter of  ScanBamParam with  summarizeOverlaps to import each single cells. It would be nice if also something like this would be possible with featurecounts() . Thanks ...
rsubread featurecounts featurerequest written 6 months ago by alessandro.pastore20
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Comment: C: how to get intron with ensembldb. package?
...   Thanks ! I thought it would be nice to keep some kind of mcols information...   ...
written 6 months ago by alessandro.pastore20
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Answer: A: how to get intron with ensembldb. package?
... I can generate a GRangesList of introns but the name are lost . intron.Grange <- transcripts(edb, columns = c(listColumns(edb , "tx"), "gene_name"), filter = list(GeneBiotypeFilter("protein_coding") )) intron.Grange <- setdiff(intron.Grange, exons.Grange) int ...
written 6 months ago by alessandro.pastore20
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how to get intron with ensembldb. package?
... I would like to generate a  GRangesList of all gene introns with names. I can make the exon list but I do not see a elegant way do get the introns. any suggestion?   Thanks!   library(AnnotationHub)​ edb <- query(AnnotationHub(), c("Ensembl 90 EnsDb", "Homo sapiens"))[[1]] exons.Grange < ...
genomicfeatures granges ensembldb written 6 months ago by alessandro.pastore20
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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 13 months ago by alessandro.pastore20
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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 21 months ago by alessandro.pastore20 • updated 21 months ago by Mike Smith2.8k
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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 23 months ago by alessandro.pastore20
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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 23 months ago by alessandro.pastore20 • updated 23 months ago by Michael Lawrence10k
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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 2.2 years ago by alessandro.pastore20 • updated 2.2 years ago by Michael Lawrence10k

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