Showing : grangeslist • reset
2
votes
3
replies
956
views
S4Vectors, strange metadata behavior
GRangesList S4Vectors
updated 2.6 years ago by 16k • written 2.6 years ago by ▴ 80
4
votes
9
replies
1.6k
views
Using genomic ranges to get counts of non-overlapping (non-redundant) regions
genomicranges granges grangeslist R
updated 4.8 years ago by 66k • written 4.8 years ago by • 0
8
votes
8
replies
8.3k
views
How to remove out of bound rows from granges
Granges grangeslist
updated 4.9 years ago by ▴ 40 • written 8.7 years ago by ▴ 50
1
vote
1
reply
967
views
How to make combined annotation of 5'UTRs and CDS's?
annotation concatenation GRangesList GenomicRanges
5.2 years ago anmej • 0
6
votes
12
replies
1.9k
views
mclapply to loop over a GRangesList object
GenomicRanges GRanges GRangesList parallel mclapply
5.4 years ago foehn ▴ 100
7
votes
5
replies
4.0k
views
summarize scores of GRanges into bins
genomicranges grangeslist bin findoverlaps
updated 5.6 years ago by • 0 • written 6.8 years ago by ★ 1.5k
3
votes
6
replies
2.6k
views
New Version of R cannot coerce "GRanges" to "RangesList"
grangeslist irangeslist
updated 5.9 years ago by 16k • written 6.1 years ago by ▴ 10
0
votes
1
reply
875
views
pintersect using GRangeslist
grangeslist
5.9 years ago rmortenson7 • 0
1
vote
6
replies
1.6k
views
deconvole counts per feature from summerizedOverlaps with GRangesLists
summarizeoverlaps rangedsummarizedexperiment grangeslist summarizedexperiment
6.2 years ago cosmin • 0
2
votes
7
replies
1.8k
views
Splitting lines of a GRanges object based on character list
granges grangeslist
updated 6.3 years ago by ★ 11k • written 6.3 years ago by ▴ 10
0
votes
2
replies
1.1k
views
issue retrieving metadata after psetdiff function
grangeslist granges
6.4 years ago andreag1987 • 0
6
votes
4
replies
2.1k
views
unlist a exons GRangeslist object and add a gene name column
granges grangeslist txdb.hsapiens.ucsc.hg19.knowngene
updated 6.6 years ago by 16k • written 6.6 years ago by ▴ 190
3
votes
6
replies
1.5k
views
Accessing GRangesList rows in Rcpp
Rcpp GRangesList
updated 6.6 years ago by 25k • written 6.6 years ago by ▴ 80
2
votes
5
replies
1.3k
views
Weaknesses with GRanges data type, or just me ?
GRangeslist GRanges makeGrangesFromDataFrame
updated 6.6 years ago by ★ 11k • written 6.6 years ago by ▴ 80
6
votes
6
replies
6.1k
views
converting a GRangesList object with different lengths into a data frame
genomicranges grangeslist dataframe irangeslist lists
updated 6.8 years ago by ★ 11k • written 6.8 years ago by ★ 1.5k
3
votes
15
replies
3.1k
views
(Big)wig file of complete chromosome
bigwig rtracklayer import granges grangeslist
updated 6.9 years ago by ★ 11k • written 6.9 years ago by ★ 1.5k
1
vote
1
reply
974
views
Width in IRanges objects on "+" and "-" strand
iranges granges grangeslist
updated 6.9 years ago by ★ 11k • written 6.9 years ago by ▴ 10
0
votes
1
reply
1.1k
views
qCount with a GRangesList is very slow
QuasR qCount GRangesList
6.9 years ago vakul.mohanty ▴ 20
0
votes
10
replies
2.1k
views
behaviour of findOverlaps on GRangesList object
findOverlaps grangeslist GenomicRanges
7.0 years ago lovro0 ▴ 10
3
votes
1
reply
1.9k
views
Extracting Coordinates of startcodon from Grangeslist
biomart bioconductor grangeslist cds ribosome profiling
updated 7.0 years ago by 16k • written 7.1 years ago by ▴ 10
0
votes
1
reply
915
views
intersect ranges from a GAlignment object with a GRangesList
intersect grangeslist galignment
updated 7.1 years ago by 16k • written 7.1 years ago by • 0
0
votes
4
replies
1.2k
views
Data structure for my dataset
metadata grangeslist granges sample
updated 7.1 years ago by ★ 11k • written 7.1 years ago by • 0
0
votes
3
replies
1.6k
views
genes symbol in RangedSummarizedExperiment object and add GRangesList to DESeqDataSet object in DESeq2
deseq2 rangedsummarizedexperiment grangeslist
7.3 years ago • updated 7.2 years ago layal8785 • 0
2
votes
4
replies
1.8k
views
How to render summary list for `GRangesList` by using `SummarizedExperiment` package?
r summarizedexperiment grangeslist
7.3 years ago Jurat Shahidin ▴ 80
4
votes
3
replies
5.3k
views
Splitting a GRanges object into List of GRange objects by position.
R granges subsett grangeslist group
updated 7.4 years ago by ★ 6.5k • written 7.4 years ago by ▴ 50
0
votes
2
replies
1.1k
views
Why does a `first_time` object appear when showing GRangesList object?
genomicranges grangeslist
updated 7.4 years ago by 66k • written 7.4 years ago by • 0
3
votes
16
replies
4.2k
views
Any way to proceed duplicate removal for list of GRanges object ?
r grangeslist duplicate
updated 7.4 years ago by 25k • written 7.4 years ago by ▴ 80
0
votes
2
replies
1.2k
views
problem with makeGRangesListFromFeatureFragments
genomicranges iranges irangeslist grangeslist
updated 7.5 years ago by 3.9k • written 7.5 years ago by • 0
8
votes
7
replies
8.0k
views
Combining two GRangesLists
GRanges grangeslist
updated 7.6 years ago by 25k • written 7.6 years ago by ▴ 20
5
votes
2
replies
1.4k
views
seeking idea for proper output representation for multiple GRanges overlapping
r grangeslist biocparallel findoverlaps
7.9 years ago • updated 7.6 years ago Jurat Shahidin ▴ 80
2
votes
4
replies
1.5k
views
Any way to combine two GRangesList easily ?
genomicranges grangeslist r
updated 7.7 years ago by ★ 11k • written 7.7 years ago by ▴ 80
3
votes
4
replies
1.3k
views
Any way to detach or simplify nested GRangesList ?
grangeslist filtering r
7.7 years ago Jurat Shahidin ▴ 80
3
votes
5
replies
1.3k
views
How to sort set of GRanges object in the list by increasing order?
granges grangeslist genomicranges
7.9 years ago Jurat Shahidin ▴ 80
15
votes
4
replies
11k
views
How to convert a GRangesList object into a GRanges object?
genomicranges grangeslist granges s4
updated 2.2 years ago by 16k • written 8.0 years ago by ▴ 40
6
votes
10
replies
2.3k
views
overlapsAny for elements in GRangesList
granges grangeslist overlapsAny
updated 8 weeks ago by • 0 • written 8.1 years ago by ▴ 180
0
votes
3
replies
1.1k
views
replace, merge and delete entries in GRangeList
grangeslist
updated 8.1 years ago by ★ 11k • written 8.1 years ago by • 0
0
votes
5
replies
1.6k
views
how to annotate GenomicRanges objects with genome build
grangeslist rangedsummarizedexperiment parathyroidSE genomicranges granges
8.2 years ago Levi Waldron ★ 1.1k
2
votes
2
replies
1.4k
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
8.3 years ago vinod.acear ▴ 50
0
votes
7
replies
1.6k
views
GRangesList and nearest neighbour search (name-specific)
grangeslist
8.6 years ago • updated 8.3 years ago Maurits • 0
4
votes
5
replies
1.9k
views
GRangesList and `seqlevels<-` with force=TRUE
GRangesList GenomicRanges
updated 8.4 years ago by 16k • written 8.4 years ago by ★ 3.7k
9
votes
11
replies
4.3k
views
looping through a GRangesList object
GenomicRanges GRangesList
updated 8.4 years ago by ★ 1.3k • written 8.4 years ago by ★ 3.7k
4
votes
6
replies
1.7k
views
GenomicRanges mapply to all combinations of GRangesList objects
genomicranges mapply grangeslist
8.7 years ago francesca casalino ▴ 50
0
votes
3
replies
1.2k
views
View of subsequences corresponding granges on +ve strand and rev. complementary of seq on -ve strand.
Views granges grangeslist iranges
updated 8.7 years ago by 16k • written 8.7 years ago by ▴ 50
2
votes
5
replies
2.2k
views
Intersecting a Granges and a GRangesList using within
granges grangeslist findoverlaps
updated 8.8 years ago by 16k • written 8.8 years ago by ▴ 150
2
votes
4
replies
6.1k
views
rtracklayer export GRangesList as gtf and change attributes
grangeslist rtracklayer
updated 23 months ago by • 0 • written 8.9 years ago by ▴ 90
2
votes
5
replies
2.2k
views
From a GRanges object to a GRangeList
granges grangeslist
updated 9.1 years ago by 66k • written 9.1 years ago by ▴ 20
2
votes
4
replies
1.9k
views
summing integer RLE
rle list irange grangeslist
updated 9.2 years ago by ▴ 80 • written 9.2 years ago by ▴ 30
0
votes
1
reply
1.2k
views
Mean Coverage version of stat_coverage and coverage?
grangeslist granges Genomicfeatures bam
9.2 years ago gen ▴ 30
4
votes
2
replies
2.5k
views
Easy way to sort GRangesList by seqname/start position?
grangeslist sort
updated 9.4 years ago by 16k • written 9.4 years ago by ★ 2.1k
4
votes
2
replies
1.9k
views
Combine two GRanges to a single GRangesList
granges grangeslist GenomicRanges
updated 9.5 years ago by 25k • written 9.5 years ago by 21k
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Comment: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0` by isaac.vock • 0
Thank you for looking into this and for your explanation! As a follow-up, would it be possible in future releases of featureCounts to pro…
Comment: error loading collectTRI regulon by silvaesilva.da • 0
Fantastic. Thank you very much. Everything has been sorted out
Answer: DESeq2 returns results for group with just one replicate by James W. MacDonald 66k
There is no problem having only one replicate per group, so long as you have replicates for other groups. The degrees of freedom are based …
Answer: Limma model.matrix design with batch effect and different life stages proportion by Masongeorge • 0
Thanks for this post. i found it helpful for my own issue that was occurring on the backend of this page.
Comment: error loading collectTRI regulon by deeenes ▴ 50
I fixed the original, Ensembl HTTP 403 error only now, [see here][1]. If you've seen it gone earlier today, only shows that this error appe…
Votes
Answer: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
Answer: DESeq2 returns results for group with just one replicate
Answer: DESeq2 returns results for group with just one replicate
Comment: error loading collectTRI regulon
A: Scaling option in fastMNN
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