Showing : grangeslist • reset
2
votes
3
replies
1.1k
views
S4Vectors, strange metadata behavior
GRangesList S4Vectors
updated 3.0 years ago by 16k • written 3.0 years ago by ▴ 80
4
votes
9
replies
1.8k
views
Using genomic ranges to get counts of non-overlapping (non-redundant) regions
genomicranges granges grangeslist R
updated 5.2 years ago by 67k • written 5.2 years ago by • 0
8
votes
8
replies
8.7k
views
How to remove out of bound rows from granges
Granges grangeslist
updated 5.3 years ago by ▴ 40 • written 9.1 years ago by ▴ 50
1
vote
1
reply
1.1k
views
How to make combined annotation of 5'UTRs and CDS's?
annotation concatenation GRangesList GenomicRanges
5.6 years ago anmej • 0
6
votes
12
replies
2.2k
views
mclapply to loop over a GRangesList object
GenomicRanges GRanges GRangesList parallel mclapply
5.8 years ago • updated 5.7 years ago foehn ▴ 100
7
votes
5
replies
4.3k
views
summarize scores of GRanges into bins
genomicranges grangeslist bin findoverlaps
updated 6.0 years ago by • 0 • written 7.2 years ago by ★ 1.5k
3
votes
6
replies
2.9k
views
New Version of R cannot coerce "GRanges" to "RangesList"
grangeslist irangeslist
updated 6.3 years ago by 16k • written 6.5 years ago by ▴ 10
0
votes
1
reply
980
views
pintersect using GRangeslist
grangeslist
6.3 years ago rmortenson7 • 0
1
vote
6
replies
1.8k
views
deconvole counts per feature from summerizedOverlaps with GRangesLists
summarizeoverlaps rangedsummarizedexperiment grangeslist summarizedexperiment
6.6 years ago cosmin • 0
2
votes
7
replies
2.0k
views
Splitting lines of a GRanges object based on character list
granges grangeslist
updated 6.7 years ago by ★ 11k • written 6.7 years ago by ▴ 10
0
votes
2
replies
1.2k
views
issue retrieving metadata after psetdiff function
grangeslist granges
6.8 years ago andreag1987 • 0
6
votes
4
replies
2.3k
views
unlist a exons GRangeslist object and add a gene name column
granges grangeslist txdb.hsapiens.ucsc.hg19.knowngene
updated 7.0 years ago by 16k • written 7.0 years ago by ▴ 200
3
votes
6
replies
1.7k
views
Accessing GRangesList rows in Rcpp
Rcpp GRangesList
updated 7.0 years ago by 25k • written 7.0 years ago by ▴ 80
2
votes
5
replies
1.4k
views
Weaknesses with GRanges data type, or just me ?
GRangeslist GRanges makeGrangesFromDataFrame
updated 7.0 years ago by ★ 11k • written 7.0 years ago by ▴ 80
6
votes
6
replies
6.5k
views
converting a GRangesList object with different lengths into a data frame
genomicranges grangeslist dataframe irangeslist lists
updated 7.1 years ago by ★ 11k • written 7.1 years ago by ★ 1.5k
3
votes
15
replies
3.4k
views
(Big)wig file of complete chromosome
bigwig rtracklayer import granges grangeslist
updated 7.3 years ago by ★ 11k • written 7.3 years ago by ★ 1.5k
1
vote
1
reply
1.1k
views
Width in IRanges objects on "+" and "-" strand
iranges granges grangeslist
updated 7.3 years ago by ★ 11k • written 7.3 years ago by ▴ 10
0
votes
1
reply
1.2k
views
qCount with a GRangesList is very slow
QuasR qCount GRangesList
7.3 years ago vakul.mohanty ▴ 20
0
votes
10
replies
2.3k
views
behaviour of findOverlaps on GRangesList object
findOverlaps grangeslist GenomicRanges
7.4 years ago lovro0 ▴ 10
3
votes
1
reply
2.1k
views
Extracting Coordinates of startcodon from Grangeslist
biomart bioconductor grangeslist cds ribosome profiling
updated 7.4 years ago by 16k • written 7.4 years ago by ▴ 10
0
votes
1
reply
1.0k
views
intersect ranges from a GAlignment object with a GRangesList
intersect grangeslist galignment
updated 7.5 years ago by 16k • written 7.5 years ago by • 0
0
votes
4
replies
1.3k
views
Data structure for my dataset
metadata grangeslist granges sample
updated 7.5 years ago by ★ 11k • written 7.5 years ago by • 0
0
votes
3
replies
1.8k
views
genes symbol in RangedSummarizedExperiment object and add GRangesList to DESeqDataSet object in DESeq2
deseq2 rangedsummarizedexperiment grangeslist
7.7 years ago • updated 7.6 years ago layal8785 • 0
2
votes
4
replies
1.9k
views
How to render summary list for `GRangesList` by using `SummarizedExperiment` package?
r summarizedexperiment grangeslist
7.7 years ago Jurat Shahidin ▴ 80
4
votes
3
replies
5.7k
views
Splitting a GRanges object into List of GRange objects by position.
R granges subsett grangeslist group
updated 7.8 years ago by ★ 6.6k • written 7.8 years ago by ▴ 50
0
votes
2
replies
1.2k
views
Why does a `first_time` object appear when showing GRangesList object?
genomicranges grangeslist
updated 7.8 years ago by 67k • written 7.8 years ago by • 0
3
votes
16
replies
4.7k
views
Any way to proceed duplicate removal for list of GRanges object ?
r grangeslist duplicate
updated 7.8 years ago by 25k • written 7.8 years ago by ▴ 80
0
votes
2
replies
1.4k
views
problem with makeGRangesListFromFeatureFragments
genomicranges iranges irangeslist grangeslist
updated 7.9 years ago by 4.1k • written 7.9 years ago by • 0
8
votes
7
replies
8.5k
views
Combining two GRangesLists
GRanges grangeslist
updated 8.0 years ago by 25k • written 8.0 years ago by ▴ 20
5
votes
2
replies
1.5k
views
seeking idea for proper output representation for multiple GRanges overlapping
r grangeslist biocparallel findoverlaps
8.3 years ago • updated 8.0 years ago Jurat Shahidin ▴ 80
2
votes
4
replies
1.7k
views
Any way to combine two GRangesList easily ?
genomicranges grangeslist r
updated 8.1 years ago by ★ 11k • written 8.1 years ago by ▴ 80
3
votes
4
replies
1.5k
views
Any way to detach or simplify nested GRangesList ?
grangeslist filtering r
8.1 years ago Jurat Shahidin ▴ 80
3
votes
5
replies
1.5k
views
How to sort set of GRanges object in the list by increasing order?
granges grangeslist genomicranges
8.3 years ago Jurat Shahidin ▴ 80
15
votes
4
replies
12k
views
How to convert a GRangesList object into a GRanges object?
genomicranges grangeslist granges s4
updated 2.6 years ago by 16k • written 8.4 years ago by ▴ 40
6
votes
10
replies
2.6k
views
overlapsAny for elements in GRangesList
granges grangeslist overlapsAny
updated 6 months ago by • 0 • written 8.5 years ago by ▴ 180
0
votes
3
replies
1.2k
views
replace, merge and delete entries in GRangeList
grangeslist
updated 8.5 years ago by ★ 11k • written 8.5 years ago by • 0
0
votes
5
replies
1.8k
views
how to annotate GenomicRanges objects with genome build
grangeslist rangedsummarizedexperiment parathyroidSE genomicranges granges
8.6 years ago Levi Waldron ★ 1.1k
2
votes
2
replies
1.5k
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
8.7 years ago vinod.acear ▴ 50
0
votes
7
replies
1.8k
views
GRangesList and nearest neighbour search (name-specific)
grangeslist
9.0 years ago • updated 8.7 years ago Maurits • 0
4
votes
5
replies
2.1k
views
GRangesList and `seqlevels<-` with force=TRUE
GRangesList GenomicRanges
updated 8.8 years ago by 16k • written 8.8 years ago by ★ 3.8k
9
votes
11
replies
4.5k
views
looping through a GRangesList object
GenomicRanges GRangesList
updated 8.8 years ago by ★ 1.3k • written 8.8 years ago by ★ 3.8k
4
votes
6
replies
1.8k
views
GenomicRanges mapply to all combinations of GRangesList objects
genomicranges mapply grangeslist
9.0 years ago francesca casalino ▴ 50
0
votes
3
replies
1.3k
views
View of subsequences corresponding granges on +ve strand and rev. complementary of seq on -ve strand.
Views granges grangeslist iranges
updated 9.1 years ago by 16k • written 9.1 years ago by ▴ 50
2
votes
5
replies
2.4k
views
Intersecting a Granges and a GRangesList using within
granges grangeslist findoverlaps
updated 9.1 years ago by 16k • written 9.2 years ago by ▴ 150
2
votes
4
replies
6.7k
views
rtracklayer export GRangesList as gtf and change attributes
grangeslist rtracklayer
updated 2.4 years ago by • 0 • written 9.3 years ago by ▴ 90
2
votes
5
replies
2.4k
views
From a GRanges object to a GRangeList
granges grangeslist
updated 9.5 years ago by 67k • written 9.5 years ago by ▴ 20
2
votes
4
replies
2.1k
views
summing integer RLE
rle list irange grangeslist
updated 9.6 years ago by ▴ 80 • written 9.6 years ago by ▴ 30
0
votes
1
reply
1.3k
views
Mean Coverage version of stat_coverage and coverage?
grangeslist granges Genomicfeatures bam
9.6 years ago gen ▴ 30
4
votes
2
replies
2.6k
views
Easy way to sort GRangesList by seqname/start position?
grangeslist sort
updated 9.8 years ago by 16k • written 9.8 years ago by ★ 2.1k
4
votes
2
replies
2.0k
views
Combine two GRanges to a single GRangesList
granges grangeslist GenomicRanges
updated 9.9 years ago by 25k • written 9.9 years ago by 21k
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Comment: Question about using LRT test for time course experiments with DESeq2 by Denise • 0
Hi James, Yes, I understand that the p-values are with respect to the full versus reduced model comparison. However, the "genes that cha…
Comment: DESeq Input from Salmon + tximport/tximeta by Michael Love 42k
Agree. > for library size and the average transcript length, what additional components will dds <- DESeq(dds) continue to normalize? Will…
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`nec` computes one set of negative control parameters (mu, sigma, alpha) for each sample. For values much larger than the background, the e…
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Thank you to the author for the quick reply. If I use `gene_counts_length_scaled.tsv` as a metric that has already normalized for library s…
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Comment: DESeq Input from Salmon + tximport/tximeta
Comment: DESeq Input from Salmon + tximport/tximeta
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