Showing : grangeslist • reset
2
votes
3
replies
504
views
S4Vectors, strange metadata behavior
GRangesList S4Vectors
updated 14 months ago by 16k • written 14 months ago by ▴ 80
4
votes
9
replies
1.0k
views
Using genomic ranges to get counts of non-overlapping (non-redundant) regions
genomicranges granges grangeslist R
updated 3.4 years ago by 62k • written 3.4 years ago by • 0
7
votes
8
replies
6.7k
views
How to remove out of bound rows from granges
Granges grangeslist
updated 3.5 years ago by ▴ 40 • written 7.3 years ago by ▴ 50
1
vote
1
reply
580
views
How to make combined annotation of 5'UTRs and CDS's?
annotation concatenation GRangesList GenomicRanges
3.9 years ago anmej • 0
6
votes
12
replies
1.1k
views
mclapply to loop over a GRangesList object
GenomicRanges GRanges GRangesList parallel mclapply
4.0 years ago foehn ▴ 80
7
votes
5
replies
2.9k
views
summarize scores of GRanges into bins
genomicranges grangeslist bin findoverlaps
updated 4.3 years ago by • 0 • written 5.4 years ago by ★ 1.5k
3
votes
6
replies
1.9k
views
New Version of R cannot coerce "GRanges" to "RangesList"
grangeslist irangeslist
updated 4.6 years ago by 16k • written 4.7 years ago by ▴ 10
0
votes
1
reply
585
views
pintersect using GRangeslist
grangeslist
4.6 years ago rmortenson7 • 0
1
vote
6
replies
917
views
deconvole counts per feature from summerizedOverlaps with GRangesLists
summarizeoverlaps rangedsummarizedexperiment grangeslist summarizedexperiment
4.9 years ago cosmin • 0
2
votes
7
replies
1.1k
views
Splitting lines of a GRanges object based on character list
granges grangeslist
updated 4.9 years ago by 11k • written 4.9 years ago by ▴ 10
0
votes
2
replies
646
views
issue retrieving metadata after psetdiff function
grangeslist granges
5.0 years ago andreag1987 • 0
6
votes
4
replies
1.4k
views
unlist a exons GRangeslist object and add a gene name column
granges grangeslist txdb.hsapiens.ucsc.hg19.knowngene
updated 5.3 years ago by 16k • written 5.3 years ago by ▴ 190
3
votes
6
replies
1.0k
views
Accessing GRangesList rows in Rcpp
Rcpp GRangesList
updated 5.3 years ago by 25k • written 5.3 years ago by ▴ 80
2
votes
5
replies
810
views
Weaknesses with GRanges data type, or just me ?
GRangeslist GRanges makeGrangesFromDataFrame
updated 5.3 years ago by 11k • written 5.3 years ago by ▴ 80
6
votes
6
replies
4.8k
views
converting a GRangesList object with different lengths into a data frame
genomicranges grangeslist dataframe irangeslist lists
updated 5.4 years ago by 11k • written 5.4 years ago by ★ 1.5k
3
votes
15
replies
1.9k
views
(Big)wig file of complete chromosome
bigwig rtracklayer import granges grangeslist
updated 5.5 years ago by 11k • written 5.5 years ago by ★ 1.5k
1
vote
1
reply
645
views
Width in IRanges objects on "+" and "-" strand
iranges granges grangeslist
updated 5.6 years ago by 11k • written 5.6 years ago by ▴ 10
0
votes
1
reply
694
views
qCount with a GRangesList is very slow
QuasR qCount GRangesList
5.6 years ago vakul.mohanty ▴ 10
0
votes
10
replies
1.5k
views
behaviour of findOverlaps on GRangesList object
findOverlaps grangeslist GenomicRanges
5.6 years ago lovro0 ▴ 10
3
votes
1
reply
1.3k
views
Extracting Coordinates of startcodon from Grangeslist
biomart bioconductor grangeslist cds ribosome profiling
updated 5.7 years ago by 16k • written 5.7 years ago by ▴ 10
0
votes
1
reply
630
views
intersect ranges from a GAlignment object with a GRangesList
intersect grangeslist galignment
updated 5.7 years ago by 16k • written 5.7 years ago by • 0
0
votes
4
replies
720
views
Data structure for my dataset
metadata grangeslist granges sample
updated 5.8 years ago by 11k • written 5.8 years ago by • 0
0
votes
3
replies
1.3k
views
genes symbol in RangedSummarizedExperiment object and add GRangesList to DESeqDataSet object in DESeq2
deseq2 rangedsummarizedexperiment grangeslist
5.9 years ago layal8785 • 0
2
votes
4
replies
1.2k
views
How to render summary list for `GRangesList` by using `SummarizedExperiment` package?
r summarizedexperiment grangeslist
5.9 years ago Jurat Shahidin ▴ 70
4
votes
3
replies
4.0k
views
Splitting a GRanges object into List of GRange objects by position.
R granges subsett grangeslist group
updated 6.0 years ago by ★ 5.9k • written 6.0 years ago by ▴ 50
0
votes
2
replies
750
views
Why does a `first_time` object appear when showing GRangesList object?
genomicranges grangeslist
updated 6.1 years ago by 62k • written 6.1 years ago by • 0
3
votes
16
replies
2.8k
views
Any way to proceed duplicate removal for list of GRanges object ?
r grangeslist duplicate
updated 6.1 years ago by 25k • written 6.1 years ago by ▴ 70
0
votes
2
replies
847
views
problem with makeGRangesListFromFeatureFragments
genomicranges iranges irangeslist grangeslist
updated 6.1 years ago by 3.4k • written 6.2 years ago by • 0
8
votes
7
replies
6.2k
views
Combining two GRangesLists
GRanges grangeslist
updated 6.2 years ago by 25k • written 6.2 years ago by ▴ 20
5
votes
2
replies
1.0k
views
seeking idea for proper output representation for multiple GRanges overlapping
r grangeslist biocparallel findoverlaps
6.6 years ago • updated 6.2 years ago Jurat Shahidin ▴ 70
2
votes
4
replies
1.1k
views
Any way to combine two GRangesList easily ?
genomicranges grangeslist r
updated 6.4 years ago by 11k • written 6.4 years ago by ▴ 70
3
votes
4
replies
861
views
Any way to detach or simplify nested GRangesList ?
grangeslist filtering r
6.4 years ago Jurat Shahidin ▴ 70
3
votes
5
replies
854
views
How to sort set of GRanges object in the list by increasing order?
granges grangeslist genomicranges
6.5 years ago Jurat Shahidin ▴ 70
15
votes
4
replies
8.5k
views
How to convert a GRangesList object into a GRanges object?
genomicranges grangeslist granges s4
updated 10 months ago by 16k • written 6.7 years ago by ▴ 40
6
votes
9
replies
1.5k
views
overlapsAny for elements in GRangesList
granges grangeslist overlapsAny
updated 6.8 years ago by 11k • written 6.8 years ago by ▴ 140
0
votes
3
replies
716
views
replace, merge and delete entries in GRangeList
grangeslist
updated 6.8 years ago by 11k • written 6.8 years ago by • 0
0
votes
5
replies
1.1k
views
how to annotate GenomicRanges objects with genome build
grangeslist rangedsummarizedexperiment parathyroidSE genomicranges granges
6.9 years ago Levi Waldron 1.1k
2
votes
2
replies
989
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
6.9 years ago vinod.acear ▴ 50
0
votes
7
replies
1.2k
views
GRangesList and nearest neighbour search (name-specific)
grangeslist
7.2 years ago • updated 7.0 years ago Maurits • 0
4
votes
5
replies
1.4k
views
GRangesList and `seqlevels<-` with force=TRUE
GRangesList GenomicRanges
updated 7.0 years ago by 16k • written 7.1 years ago by ★ 3.7k
9
votes
11
replies
3.3k
views
looping through a GRangesList object
GenomicRanges GRangesList
updated 7.1 years ago by ★ 1.3k • written 7.1 years ago by ★ 3.7k
4
votes
6
replies
1.3k
views
GenomicRanges mapply to all combinations of GRangesList objects
genomicranges mapply grangeslist
7.3 years ago francesca casalino ▴ 50
0
votes
3
replies
815
views
View of subsequences corresponding granges on +ve strand and rev. complementary of seq on -ve strand.
Views granges grangeslist iranges
updated 7.3 years ago by 16k • written 7.3 years ago by ▴ 50
2
votes
5
replies
1.5k
views
Intersecting a Granges and a GRangesList using within
granges grangeslist findoverlaps
updated 7.4 years ago by 16k • written 7.4 years ago by ▴ 150
2
votes
4
replies
4.3k
views
rtracklayer export GRangesList as gtf and change attributes
grangeslist rtracklayer
updated 7 months ago by • 0 • written 7.6 years ago by ▴ 90
2
votes
5
replies
1.7k
views
From a GRanges object to a GRangeList
granges grangeslist
updated 7.7 years ago by 62k • written 7.7 years ago by ▴ 20
2
votes
4
replies
1.3k
views
summing integer RLE
rle list irange grangeslist
updated 7.9 years ago by ▴ 80 • written 7.9 years ago by ▴ 30
0
votes
1
reply
862
views
Mean Coverage version of stat_coverage and coverage?
grangeslist granges Genomicfeatures bam
7.9 years ago gen ▴ 30
4
votes
2
replies
2.1k
views
Easy way to sort GRangesList by seqname/start position?
grangeslist sort
updated 8.1 years ago by 16k • written 8.1 years ago by ★ 2.0k
4
votes
2
replies
1.6k
views
Combine two GRanges to a single GRangesList
granges grangeslist GenomicRanges
updated 8.2 years ago by 25k • written 8.2 years ago by 21k
50 results • Page 1 of 1
Recent ...
Replies
Comment: DESeq2 and heatmap for multiple comparisons by artem.vorobyev • 0
this I already did. My question is how to visualize differentially expressed genes on the heatmap for all 3 groups (healty->lesion->treat…
Comment: athPkgBuilder data source :missing probesets by nicklesteele532 • 0
> >>> > >>> How to handle the one probeset to multiple locus mappings? I can > >think 3 > >>> possible solutions: > >>> 1. pick the "best" …
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
> sum(width(gr_toexclude)) [1] 2713499861 I excluded everything which was not locus. If small rna locus is from 2000 to 4000 and next locu…
Comment: Why in Bioconductor community people rarely upvote questions? by Hervé Pagès 16k
BTW I fail to see how the lack of upvotes to a question would be discouraging as long as you get a good answer. OTOH I can see how failing …
Answer: DESeq2 and heatmap for multiple comparisons by swbarnes2 ★ 1.2k
If you want to know what genes are different between lesion and treated, compare them to each other.
Votes
Comment: recount 3 protect read length metadata
Answer: Doubts about manipulation and annotation of microarray files deposited at GEO
C: Batch correction in DESeq2
Comment: Strand information in a GAlignmentsList object derived from strand-specific pair
Comment: Strand information in a GAlignmentsList object derived from strand-specific pair
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