Questions tagged [genomicranges]

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Assign score to PyRanges from another PyRanges object

I have two PyRanges objects. PR1 is a set of regions of interest across a chromosome, PR2 tiles the genome and has a score associated with each range. I need a way to get for each range in PR1 its ...
Whitehot's user avatar
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3 votes
1 answer

Find a genomic coordinates for a protein aminoacid position

Is there a function that can map genomic position (hg19) back from a protein position? I can have name of a particular transcript, and exon number. For example, I have KRAS gene for which I would like ...
lizaveta's user avatar
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3 votes
2 answers

How to subset a GRanges object based on a specific genomic window of interest?

Goal: To keep only rows of a GRanges object if their start coordinate is within 1 Mb of the start coordinate of a gene of interest. I am aware of some functions that come close: ...
Gawain's user avatar
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1 vote
2 answers

Pulling a numbered chromosome range file given a gene location from a lookup table ideally from command line or R

have a folder with roughly 1000 vcf files which have divided the human genome into chunks, the folder looks like this: ...
tacrolimus's user avatar
1 vote
1 answer

Retrieve overlap widths with Bioconductor

I want to retrieve all overlaps between two sets of genomic intervals (GRanges) using Bioconductor. I am interested in the widths of the resulting overlapping ranges. In cases with discontinuous ...
cmdoret's user avatar
  • 595
-1 votes
2 answers

Calculating the number of probes for a given genomic range

I have a big data frame like this for copy number (exome seq) ...
Exhausted's user avatar
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2 votes
0 answers

What Cellbase resources are 0-indexed, and which are 1-indexed?

The UCSC Genome Browser Team is clear about that the genome browser GUI indexing which is 1-based, closed interval. Genomic sequence retrieval via the UCSC REST API is 1-based, closed interval. All ...
mRotten's user avatar
  • 192
0 votes
2 answers

GenomicRanges: get nearest neighbor distances for random genes using a for loop

I want to compute the nearest neighbour distances using a for loop. I can do this with a random subset by doing this: ...
R-MASHup's user avatar
  • 105
4 votes
1 answer

Find intervals that genes fall within their range

I am trying to run some frequency based stats to identify selective sweep in my study system using Rpackage "PopGenome". To proceed with it I have split my genome data (whole genome sequencing) into ...
Anna1364's user avatar
  • 496
2 votes
3 answers

Getting a stretch of genomic ranges from a dataframe/granges object based on metadata column

I have a "test" data.frame object in R, which is basically a small subset of a 66000 row dataframe, which looks as follows: ...
rishi's user avatar
  • 353
4 votes
1 answer

How to find genomic overlaps faster?

I was trying to find a way to find overlaps between two genomic ranges. I found a post at Biostars but it couldn't consider the chromosome information. For example: ...
satyanarayan rao's user avatar
1 vote
1 answer

Expand granges object different amounts upstream vs. downstream

I am attempting to get gene regions and their immediate neighborhoods using Bioconductor GenomicRanges packages. It is very easy for me to extend the regions around genes if I want to extend it the ...
Reilstein's user avatar
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6 votes
3 answers

How to subset a GRanges via an argument passed into a function?

Let's say I have following example GRanges: ...
EB2127's user avatar
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