Showing : grangeslist • reset
2
votes
3
replies
205
views
S4Vectors, strange metadata behavior
GRangesList S4Vectors
updated 10 weeks ago by 15k • written 10 weeks ago by ▴ 80
4
votes
9
replies
582
views
Using genomic ranges to get counts of non-overlapping (non-redundant) regions
genomicranges granges grangeslist R
updated 2.4 years ago by 58k • written 2.4 years ago by • 0
7
votes
8
replies
5.6k
views
How to remove out of bound rows from granges
Granges grangeslist
updated 2.5 years ago by ▴ 40 • written 6.3 years ago by ▴ 50
1
vote
1
reply
410
views
How to make combined annotation of 5'UTRs and CDS's?
annotation concatenation GRangesList GenomicRanges
2.9 years ago anmej • 0
6
votes
12
replies
784
views
mclapply to loop over a GRangesList object
GenomicRanges GRanges GRangesList parallel mclapply
3.0 years ago foehn ▴ 80
6
votes
5
replies
2.3k
views
summarize scores of GRanges into bins
genomicranges grangeslist bin findoverlaps
updated 3.3 years ago by • 0 • written 4.4 years ago by ★ 1.5k
3
votes
6
replies
1.4k
views
New Version of R cannot coerce "GRanges" to "RangesList"
grangeslist irangeslist
updated 3.5 years ago by 15k • written 3.7 years ago by ▴ 10
0
votes
1
reply
425
views
pintersect using GRangeslist
grangeslist
3.6 years ago rmortenson7 • 0
1
vote
6
replies
723
views
deconvole counts per feature from summerizedOverlaps with GRangesLists
summarizeoverlaps rangedsummarizedexperiment grangeslist summarizedexperiment
3.9 years ago cosmin • 0
2
votes
7
replies
785
views
Splitting lines of a GRanges object based on character list
granges grangeslist
updated 3.9 years ago by 11k • written 3.9 years ago by ▴ 10
0
votes
2
replies
503
views
issue retrieving metadata after psetdiff function
grangeslist granges
4.0 years ago andreag1987 • 0
6
votes
4
replies
1.1k
views
unlist a exons GRangeslist object and add a gene name column
granges grangeslist txdb.hsapiens.ucsc.hg19.knowngene
updated 4.2 years ago by 15k • written 4.2 years ago by ▴ 170
3
votes
6
replies
803
views
Accessing GRangesList rows in Rcpp
Rcpp GRangesList
updated 4.2 years ago by 25k • written 4.2 years ago by ▴ 80
2
votes
5
replies
609
views
Weaknesses with GRanges data type, or just me ?
GRangeslist GRanges makeGrangesFromDataFrame
updated 4.3 years ago by 11k • written 4.3 years ago by ▴ 80
6
votes
6
replies
4.2k
views
converting a GRangesList object with different lengths into a data frame
genomicranges grangeslist dataframe irangeslist lists
updated 4.4 years ago by 11k • written 4.4 years ago by ★ 1.5k
3
votes
15
replies
1.5k
views
(Big)wig file of complete chromosome
bigwig rtracklayer import granges grangeslist
updated 4.5 years ago by 11k • written 4.5 years ago by ★ 1.5k
1
vote
1
reply
524
views
Width in IRanges objects on "+" and "-" strand
iranges granges grangeslist
updated 4.5 years ago by 11k • written 4.5 years ago by ▴ 10
0
votes
1
reply
529
views
qCount with a GRangesList is very slow
QuasR qCount GRangesList
4.6 years ago vakul.mohanty ▴ 10
0
votes
10
replies
1.2k
views
behaviour of findOverlaps on GRangesList object
findOverlaps grangeslist GenomicRanges
4.6 years ago lovro0 ▴ 10
3
votes
1
reply
1.1k
views
Extracting Coordinates of startcodon from Grangeslist
biomart bioconductor grangeslist cds ribosome profiling
updated 4.7 years ago by 15k • written 4.7 years ago by ▴ 10
0
votes
1
reply
512
views
intersect ranges from a GAlignment object with a GRangesList
intersect grangeslist galignment
updated 4.7 years ago by 15k • written 4.7 years ago by • 0
0
votes
4
replies
598
views
Data structure for my dataset
metadata grangeslist granges sample
updated 4.7 years ago by 11k • written 4.7 years ago by • 0
0
votes
3
replies
1.1k
views
genes symbol in RangedSummarizedExperiment object and add GRangesList to DESeqDataSet object in DESeq2
deseq2 rangedsummarizedexperiment grangeslist
4.9 years ago • updated 4.8 years ago layal8785 • 0
2
votes
4
replies
998
views
How to render summary list for `GRangesList` by using `SummarizedExperiment` package?
r summarizedexperiment grangeslist
4.9 years ago Jurat Shahidin ▴ 70
4
votes
3
replies
3.2k
views
Splitting a GRanges object into List of GRange objects by position.
R granges subsett grangeslist group
updated 5.0 years ago by ★ 5.4k • written 5.0 years ago by ▴ 40
0
votes
2
replies
629
views
Why does a `first_time` object appear when showing GRangesList object?
genomicranges grangeslist
updated 5.0 years ago by 58k • written 5.0 years ago by • 0
3
votes
16
replies
2.2k
views
Any way to proceed duplicate removal for list of GRanges object ?
r grangeslist duplicate
updated 5.1 years ago by 25k • written 5.1 years ago by ▴ 70
0
votes
2
replies
726
views
problem with makeGRangesListFromFeatureFragments
genomicranges iranges irangeslist grangeslist
updated 5.1 years ago by 2.9k • written 5.1 years ago by • 0
8
votes
7
replies
4.9k
views
Combining two GRangesLists
GRanges grangeslist
updated 5.2 years ago by 25k • written 5.2 years ago by ▴ 20
5
votes
2
replies
835
views
seeking idea for proper output representation for multiple GRanges overlapping
r grangeslist biocparallel findoverlaps
5.5 years ago • updated 5.2 years ago Jurat Shahidin ▴ 70
2
votes
4
replies
944
views
Any way to combine two GRangesList easily ?
genomicranges grangeslist r
updated 5.3 years ago by 11k • written 5.3 years ago by ▴ 70
3
votes
4
replies
715
views
Any way to detach or simplify nested GRangesList ?
grangeslist filtering r
5.4 years ago • updated 5.3 years ago Jurat Shahidin ▴ 70
3
votes
5
replies
712
views
How to sort set of GRanges object in the list by increasing order?
granges grangeslist genomicranges
5.5 years ago Jurat Shahidin ▴ 70
14
votes
2
replies
6.8k
views
How to convert a GRangesList object into a GRanges object?
genomicranges grangeslist granges s4
5.6 years ago richierocks ▴ 40
6
votes
9
replies
1.1k
views
overlapsAny for elements in GRangesList
granges grangeslist overlapsAny
updated 5.7 years ago by 11k • written 5.7 years ago by ▴ 140
0
votes
3
replies
613
views
replace, merge and delete entries in GRangeList
grangeslist
updated 5.8 years ago by 11k • written 5.8 years ago by • 0
0
votes
5
replies
958
views
how to annotate GenomicRanges objects with genome build
grangeslist rangedsummarizedexperiment parathyroidSE genomicranges granges
5.9 years ago Levi Waldron 1.1k
2
votes
2
replies
844
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
5.9 years ago vinod.acear ▴ 50
0
votes
7
replies
1.0k
views
GRangesList and nearest neighbour search (name-specific)
grangeslist
6.2 years ago • updated 5.9 years ago Maurits • 0
4
votes
5
replies
1.2k
views
GRangesList and `seqlevels<-` with force=TRUE
GRangesList GenomicRanges
updated 6.0 years ago by 15k • written 6.0 years ago by ★ 3.7k
9
votes
11
replies
2.9k
views
looping through a GRangesList object
GenomicRanges GRangesList
updated 6.0 years ago by ★ 1.3k • written 6.0 years ago by ★ 3.7k
4
votes
6
replies
1.1k
views
GenomicRanges mapply to all combinations of GRangesList objects
genomicranges mapply grangeslist
6.3 years ago francesca casalino ▴ 50
0
votes
3
replies
713
views
View of subsequences corresponding granges on +ve strand and rev. complementary of seq on -ve strand.
Views granges grangeslist iranges
updated 6.3 years ago by 15k • written 6.3 years ago by ▴ 50
2
votes
5
replies
1.2k
views
Intersecting a Granges and a GRangesList using within
granges grangeslist findoverlaps
updated 6.4 years ago by 15k • written 6.4 years ago by ▴ 150
2
votes
3
replies
3.3k
views
rtracklayer export GRangesList as gtf and change attributes
grangeslist rtracklayer
updated 6.5 years ago by 11k • written 6.5 years ago by ▴ 90
2
votes
5
replies
1.5k
views
From a GRanges object to a GRangeList
granges grangeslist
updated 6.7 years ago by 58k • written 6.7 years ago by ▴ 20
2
votes
4
replies
1.1k
views
summing integer RLE
rle list irange grangeslist
updated 6.8 years ago by ▴ 80 • written 6.8 years ago by ▴ 30
0
votes
1
reply
754
views
Mean Coverage version of stat_coverage and coverage?
grangeslist granges Genomicfeatures bam
6.8 years ago gen ▴ 30
4
votes
2
replies
1.8k
views
Easy way to sort GRangesList by seqname/start position?
grangeslist sort
updated 7.0 years ago by 15k • written 7.0 years ago by ★ 1.9k
4
votes
2
replies
1.4k
views
Combine two GRanges to a single GRangesList
granges grangeslist GenomicRanges
updated 7.1 years ago by 25k • written 7.1 years ago by 21k
50 results • Page 1 of 1
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Comment: Multi-factor paired RNAseq differential analysis with DEseq2 by Matthew • 0
Thanks for the suggestion, I'll give that a try! Based on the PCA, all three factors do tend to influence the results, so I'll try the colu…
Comment: fgsea not downloading due to new r version. Is there a way around this? by amir.khan • 0
Seems to have done the trick and worked. thanks!
Comment: Multi-factor paired RNAseq differential analysis with DEseq2 by Michael Love 35k
Just to underscore swbarnes2 advice above, I'd also recommend discussing statistical design with a local statistician or someone familiar w…
Answer: Multi-factor paired RNAseq differential analysis with DEseq2 by swbarnes2 ▴ 970
First, I'd start by looking at all your samples in PCA. Does sex have a strong effect? Does it make sense to compare one tissue with anot…
Comment: Unable to install Rhtslib in R-4.1.1 by cf2209 • 0
Thank you for your input I appreciate it. I will revise and make changes to this post as you suggested. Unfortunately I am not able to do t…
Votes
Answer: fgsea not downloading due to new r version. Is there a way around this?
Comment: Unable to install Rhtslib in R-4.1.1
Answer: fgsea not downloading due to new r version. Is there a way around this?
Answer: Swish with more than two conditions. Add support for contrasts?
Answer: ERROR: unable to find an inherited method for function ‘dispersions<-’ for signa
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