Showing : grangeslist • reset
2
votes
3
replies
1.2k
views
S4Vectors, strange metadata behavior
GRangesList S4Vectors
updated 3.1 years ago by 16k • written 3.1 years ago by ▴ 80
4
votes
9
replies
1.9k
views
Using genomic ranges to get counts of non-overlapping (non-redundant) regions
genomicranges granges grangeslist R
updated 5.3 years ago by 67k • written 5.3 years ago by • 0
8
votes
8
replies
8.8k
views
How to remove out of bound rows from granges
Granges grangeslist
updated 5.4 years ago by ▴ 40 • written 9.2 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
5.8 years ago anmej • 0
6
votes
12
replies
2.2k
views
mclapply to loop over a GRangesList object
GenomicRanges GRanges GRangesList parallel mclapply
5.9 years ago foehn ▴ 100
7
votes
5
replies
4.4k
views
summarize scores of GRanges into bins
genomicranges grangeslist bin findoverlaps
updated 6.2 years ago by • 0 • written 7.3 years ago by ★ 1.5k
3
votes
6
replies
3.0k
views
New Version of R cannot coerce "GRanges" to "RangesList"
grangeslist irangeslist
updated 6.4 years ago by 16k • written 6.6 years ago by ▴ 10
0
votes
1
reply
1.0k
views
pintersect using GRangeslist
grangeslist
6.5 years ago rmortenson7 • 0
1
vote
6
replies
1.8k
views
deconvole counts per feature from summerizedOverlaps with GRangesLists
summarizeoverlaps rangedsummarizedexperiment grangeslist summarizedexperiment
6.8 years ago cosmin • 0
2
votes
7
replies
2.1k
views
Splitting lines of a GRanges object based on character list
granges grangeslist
updated 6.8 years ago by ★ 11k • written 6.8 years ago by ▴ 10
0
votes
2
replies
1.3k
views
issue retrieving metadata after psetdiff function
grangeslist granges
6.9 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 7.1 years ago by 16k • written 7.1 years ago by ▴ 200
3
votes
6
replies
1.8k
views
Accessing GRangesList rows in Rcpp
Rcpp GRangesList
updated 7.1 years ago by 25k • written 7.1 years ago by ▴ 80
2
votes
5
replies
1.4k
views
Weaknesses with GRanges data type, or just me ?
GRangeslist GRanges makeGrangesFromDataFrame
updated 7.2 years ago by ★ 11k • written 7.2 years ago by ▴ 80
6
votes
6
replies
6.6k
views
converting a GRangesList object with different lengths into a data frame
genomicranges grangeslist dataframe irangeslist lists
updated 7.3 years ago by ★ 11k • written 7.3 years ago by ★ 1.5k
3
votes
15
replies
3.5k
views
(Big)wig file of complete chromosome
bigwig rtracklayer import granges grangeslist
updated 7.4 years ago by ★ 11k • written 7.4 years ago by ★ 1.5k
1
vote
1
reply
1.1k
views
Width in IRanges objects on "+" and "-" strand
iranges granges grangeslist
updated 7.4 years ago by ★ 11k • written 7.4 years ago by ▴ 10
0
votes
1
reply
1.3k
views
qCount with a GRangesList is very slow
QuasR qCount GRangesList
7.5 years ago vakul.mohanty ▴ 20
0
votes
10
replies
2.3k
views
behaviour of findOverlaps on GRangesList object
findOverlaps grangeslist GenomicRanges
7.5 years ago lovro0 ▴ 10
3
votes
1
reply
2.2k
views
Extracting Coordinates of startcodon from Grangeslist
biomart bioconductor grangeslist cds ribosome profiling
updated 7.6 years ago by 16k • written 7.6 years ago by ▴ 10
0
votes
1
reply
1.0k
views
intersect ranges from a GAlignment object with a GRangesList
intersect grangeslist galignment
updated 7.6 years ago by 16k • written 7.6 years ago by • 0
0
votes
4
replies
1.4k
views
Data structure for my dataset
metadata grangeslist granges sample
updated 7.6 years ago by ★ 11k • written 7.6 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
7.8 years ago • updated 7.7 years ago layal8785 • 0
2
votes
4
replies
2.0k
views
How to render summary list for `GRangesList` by using `SummarizedExperiment` package?
r summarizedexperiment grangeslist
7.8 years ago Jurat Shahidin ▴ 80
4
votes
3
replies
5.8k
views
Splitting a GRanges object into List of GRange objects by position.
R granges subsett grangeslist group
updated 7.9 years ago by ★ 6.6k • written 7.9 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 7.9 years ago by 67k • written 7.9 years ago by • 0
3
votes
16
replies
4.8k
views
Any way to proceed duplicate removal for list of GRanges object ?
r grangeslist duplicate
updated 8.0 years ago by 25k • written 8.0 years ago by ▴ 80
0
votes
2
replies
1.4k
views
problem with makeGRangesListFromFeatureFragments
genomicranges iranges irangeslist grangeslist
updated 8.0 years ago by 4.1k • written 8.0 years ago by • 0
8
votes
7
replies
8.7k
views
Combining two GRangesLists
GRanges grangeslist
updated 8.1 years ago by 25k • written 8.1 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
8.4 years ago • updated 8.1 years ago Jurat Shahidin ▴ 80
2
votes
4
replies
1.7k
views
Any way to combine two GRangesList easily ?
genomicranges grangeslist r
updated 8.2 years ago by ★ 11k • written 8.2 years ago by ▴ 80
3
votes
4
replies
1.5k
views
Any way to detach or simplify nested GRangesList ?
grangeslist filtering r
8.2 years ago Jurat Shahidin ▴ 80
3
votes
5
replies
1.6k
views
How to sort set of GRanges object in the list by increasing order?
granges grangeslist genomicranges
8.4 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 2.7 years ago by 16k • written 8.5 years ago by ▴ 40
6
votes
10
replies
2.7k
views
overlapsAny for elements in GRangesList
granges grangeslist overlapsAny
updated 8 months ago by • 0 • written 8.6 years ago by ▴ 180
0
votes
3
replies
1.3k
views
replace, merge and delete entries in GRangeList
grangeslist
updated 8.6 years ago by ★ 11k • written 8.6 years ago by • 0
0
votes
5
replies
1.8k
views
how to annotate GenomicRanges objects with genome build
grangeslist rangedsummarizedexperiment parathyroidSE genomicranges granges
8.8 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
8.8 years ago vinod.acear ▴ 50
0
votes
7
replies
1.8k
views
GRangesList and nearest neighbour search (name-specific)
grangeslist
9.1 years ago • updated 8.8 years ago Maurits • 0
4
votes
5
replies
2.2k
views
GRangesList and `seqlevels<-` with force=TRUE
GRangesList GenomicRanges
updated 8.9 years ago by 16k • written 8.9 years ago by ★ 3.8k
9
votes
11
replies
4.6k
views
looping through a GRangesList object
GenomicRanges GRangesList
updated 8.9 years ago by ★ 1.3k • written 8.9 years ago by ★ 3.8k
4
votes
6
replies
1.9k
views
GenomicRanges mapply to all combinations of GRangesList objects
genomicranges mapply grangeslist
9.2 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 9.2 years ago by 16k • written 9.2 years ago by ▴ 50
2
votes
5
replies
2.4k
views
Intersecting a Granges and a GRangesList using within
granges grangeslist findoverlaps
updated 9.3 years ago by 16k • written 9.3 years ago by ▴ 150
2
votes
4
replies
6.9k
views
rtracklayer export GRangesList as gtf and change attributes
grangeslist rtracklayer
updated 2.5 years ago by • 0 • written 9.4 years ago by ▴ 90
2
votes
5
replies
2.4k
views
From a GRanges object to a GRangeList
granges grangeslist
updated 9.6 years ago by 67k • written 9.6 years ago by ▴ 20
2
votes
4
replies
2.1k
views
summing integer RLE
rle list irange grangeslist
updated 9.7 years ago by ▴ 80 • written 9.7 years ago by ▴ 30
0
votes
1
reply
1.3k
views
Mean Coverage version of stat_coverage and coverage?
grangeslist granges Genomicfeatures bam
9.7 years ago gen ▴ 30
4
votes
2
replies
2.7k
views
Easy way to sort GRangesList by seqname/start position?
grangeslist sort
updated 9.9 years ago by 16k • written 9.9 years ago by ★ 2.1k
4
votes
2
replies
2.0k
views
Combine two GRanges to a single GRangesList
granges grangeslist GenomicRanges
updated 10.0 years ago by 25k • written 10.0 years ago by 21k
50 results • Page 1 of 1
Recent ...
Replies
Comment: Cross-validation with multiple control subgroups in limma by Ali Barry ▴ 40
Thanks so much for taking the time here, the insights are much appreciated. I suspected I'd have to ad hoc compare results if I did repeat …
Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Votes
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
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