Showing : grangeslist • reset
4
votes
9
replies
375
views
Using genomic ranges to get counts of non-overlapping (non-redundant) regions
genomicranges granges grangeslist R
updated 22 months ago by 57k • written 22 months ago by • 0
7
votes
8
replies
5.1k
views
How to remove out of bound rows from granges
Granges grangeslist
updated 2.0 years ago by ▴ 40 • written 5.8 years ago by ▴ 50
1
vote
1
reply
338
views
How to make combined annotation of 5'UTRs and CDS's?
annotation concatenation GRangesList GenomicRanges
2.4 years ago anmej • 0
3
votes
12
replies
554
views
mclapply to loop over a GRangesList object
GenomicRanges GRanges GRangesList parallel mclapply
2.5 years ago foehn ▴ 60
5
votes
5
replies
2.0k
views
summarize scores of GRanges into bins
genomicranges grangeslist bin findoverlaps
updated 2.8 years ago by • 0 • written 3.9 years ago by ★ 1.5k
3
votes
6
replies
1.3k
views
New Version of R cannot coerce "GRanges" to "RangesList"
grangeslist irangeslist
updated 3.0 years ago by 15k • written 3.2 years ago by ▴ 10
0
votes
1
reply
357
views
pintersect using GRangeslist
grangeslist
3.1 years ago rmortenson7 • 0
1
vote
6
replies
600
views
deconvole counts per feature from summerizedOverlaps with GRangesLists
summarizeoverlaps rangedsummarizedexperiment grangeslist summarizedexperiment
3.4 years ago cosmin • 0
2
votes
7
replies
652
views
Splitting lines of a GRanges object based on character list
granges grangeslist
updated 3.4 years ago by 11k • written 3.4 years ago by ▴ 10
0
votes
2
replies
412
views
issue retrieving metadata after psetdiff function
grangeslist granges
3.5 years ago andreag1987 • 0
6
votes
4
replies
960
views
unlist a exons GRangeslist object and add a gene name column
granges grangeslist txdb.hsapiens.ucsc.hg19.knowngene
updated 3.7 years ago by 15k • written 3.7 years ago by ▴ 170
3
votes
6
replies
705
views
Accessing GRangesList rows in Rcpp
Rcpp GRangesList
updated 3.7 years ago by 25k • written 3.8 years ago by ▴ 80
2
votes
5
replies
533
views
Weaknesses with GRanges data type, or just me ?
GRangeslist GRanges makeGrangesFromDataFrame
updated 3.8 years ago by 11k • written 3.8 years ago by ▴ 80
6
votes
6
replies
3.8k
views
converting a GRangesList object with different lengths into a data frame
genomicranges grangeslist dataframe irangeslist lists
updated 3.9 years ago by 11k • written 3.9 years ago by ★ 1.5k
3
votes
15
replies
1.3k
views
(Big)wig file of complete chromosome
bigwig rtracklayer import granges grangeslist
updated 4.0 years ago by 11k • written 4.0 years ago by ★ 1.5k
1
vote
1
reply
469
views
Width in IRanges objects on "+" and "-" strand
iranges granges grangeslist
updated 4.0 years ago by 11k • written 4.0 years ago by ▴ 10
0
votes
1
reply
444
views
qCount with a GRangesList is very slow
QuasR qCount GRangesList
4.1 years ago vakul.mohanty ▴ 10
0
votes
10
replies
1.1k
views
behaviour of findOverlaps on GRangesList object
findOverlaps grangeslist GenomicRanges
4.1 years ago lovro0 ▴ 10
3
votes
1
reply
919
views
Extracting Coordinates of startcodon from Grangeslist
biomart bioconductor grangeslist cds ribosome profiling
updated 4.2 years ago by 15k • written 4.2 years ago by ▴ 10
0
votes
1
reply
454
views
intersect ranges from a GAlignment object with a GRangesList
intersect grangeslist galignment
updated 4.2 years ago by 15k • written 4.2 years ago by • 0
0
votes
4
replies
531
views
Data structure for my dataset
metadata grangeslist granges sample
updated 4.2 years ago by 11k • written 4.2 years ago by • 0
0
votes
3
replies
979
views
genes symbol in RangedSummarizedExperiment object and add GRangesList to DESeqDataSet object in DESeq2
deseq2 rangedsummarizedexperiment grangeslist
4.4 years ago • updated 4.3 years ago layal8785 • 0
2
votes
4
replies
903
views
How to render summary list for `GRangesList` by using `SummarizedExperiment` package?
r summarizedexperiment grangeslist
4.4 years ago Jurat Shahidin ▴ 70
2
votes
3
replies
2.7k
views
Splitting a GRanges object into List of GRange objects by position.
R granges subsett grangeslist group
updated 4.5 years ago by ★ 5.0k • written 4.5 years ago by ▴ 30
0
votes
2
replies
581
views
Why does a `first_time` object appear when showing GRangesList object?
genomicranges grangeslist
updated 4.5 years ago by 57k • written 4.5 years ago by • 0
3
votes
16
replies
1.9k
views
Any way to proceed duplicate removal for list of GRanges object ?
r grangeslist duplicate
updated 4.6 years ago by 25k • written 4.6 years ago by ▴ 70
0
votes
2
replies
677
views
problem with makeGRangesListFromFeatureFragments
genomicranges iranges irangeslist grangeslist
updated 4.6 years ago by 2.8k • written 4.6 years ago by • 0
8
votes
7
replies
4.1k
views
Combining two GRangesLists
GRanges grangeslist
updated 4.7 years ago by 25k • written 4.7 years ago by ▴ 20
5
votes
2
replies
774
views
seeking idea for proper output representation for multiple GRanges overlapping
r grangeslist biocparallel findoverlaps
5.0 years ago • updated 4.7 years ago Jurat Shahidin ▴ 70
2
votes
4
replies
880
views
Any way to combine two GRangesList easily ?
genomicranges grangeslist r
updated 4.8 years ago by 11k • written 4.8 years ago by ▴ 70
3
votes
4
replies
632
views
Any way to detach or simplify nested GRangesList ?
grangeslist filtering r
4.9 years ago • updated 4.8 years ago Jurat Shahidin ▴ 70
3
votes
5
replies
654
views
How to sort set of GRanges object in the list by increasing order?
granges grangeslist genomicranges
5.0 years ago Jurat Shahidin ▴ 70
14
votes
2
replies
6.2k
views
How to convert a GRangesList object into a GRanges object?
genomicranges grangeslist granges s4
5.1 years ago richierocks ▴ 40
6
votes
9
replies
1.1k
views
overlapsAny for elements in GRangesList
granges grangeslist overlapsAny
updated 5.2 years ago by 11k • written 5.2 years ago by ▴ 140
0
votes
3
replies
561
views
replace, merge and delete entries in GRangeList
grangeslist
updated 5.3 years ago by 11k • written 5.3 years ago by • 0
0
votes
5
replies
872
views
how to annotate GenomicRanges objects with genome build
grangeslist rangedsummarizedexperiment parathyroidSE genomicranges granges
5.4 years ago Levi Waldron 1.1k
2
votes
2
replies
777
views
How to rename seqlevels style (I, II, III, ...,XVI, Mito to 1,2,3,...16, 17.) in txdb granges?
renameSeqlevels mapSeqlevels grangeslist granges txdb
5.4 years ago vinod.acear ▴ 50
0
votes
7
replies
907
views
GRangesList and nearest neighbour search (name-specific)
grangeslist
5.7 years ago • updated 5.4 years ago Maurits • 0
4
votes
5
replies
1.1k
views
GRangesList and `seqlevels<-` with force=TRUE
GRangesList GenomicRanges
updated 5.5 years ago by 15k • written 5.5 years ago by ★ 3.7k
9
votes
11
replies
2.7k
views
looping through a GRangesList object
GenomicRanges GRangesList
updated 5.5 years ago by ★ 1.3k • written 5.5 years ago by ★ 3.7k
4
votes
6
replies
968
views
GenomicRanges mapply to all combinations of GRangesList objects
genomicranges mapply grangeslist
5.8 years ago francesca casalino ▴ 50
0
votes
3
replies
654
views
View of subsequences corresponding granges on +ve strand and rev. complementary of seq on -ve strand.
Views granges grangeslist iranges
updated 5.8 years ago by 15k • written 5.8 years ago by ▴ 50
2
votes
5
replies
1.1k
views
Intersecting a Granges and a GRangesList using within
granges grangeslist findoverlaps
updated 5.9 years ago by 15k • written 5.9 years ago by ▴ 150
2
votes
3
replies
3.0k
views
rtracklayer export GRangesList as gtf and change attributes
grangeslist rtracklayer
updated 6.0 years ago by 11k • written 6.0 years ago by ▴ 90
2
votes
5
replies
1.4k
views
From a GRanges object to a GRangeList
granges grangeslist
updated 6.2 years ago by 57k • written 6.2 years ago by ▴ 20
1
vote
4
replies
955
views
summing integer RLE
rle list irange grangeslist
updated 6.3 years ago by ▴ 80 • written 6.3 years ago by ▴ 30
0
votes
1
reply
705
views
Mean Coverage version of stat_coverage and coverage?
grangeslist granges Genomicfeatures bam
6.3 years ago gen ▴ 30
4
votes
2
replies
1.7k
views
Easy way to sort GRangesList by seqname/start position?
grangeslist sort
updated 6.5 years ago by 15k • written 6.5 years ago by ★ 1.9k
4
votes
2
replies
1.4k
views
Combine two GRanges to a single GRangesList
granges grangeslist GenomicRanges
updated 6.6 years ago by 25k • written 6.6 years ago by 21k
1
vote
3
replies
1.1k
views
Fast way to access metadata for GRangesList?
grangeslist metadata
6.7 years ago Robert K. Bradley ▴ 40
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