Showing : GenomicRanges • reset
20
votes
10
replies
21k
views
How do I merge a list of GRanges?
GenomicRanges
updated 3.1 years ago by ▴ 40 • written 8.8 years ago by ▴ 40
17
votes
4
replies
18k
views
How to properly sort GRanges?
granges genomicranges sort seqnames order
updated 9.9 years ago by ▴ 30 • written 10.4 years ago by ▴ 680
17
votes
4
replies
12k
views
How to use GenomicRanges to find overlaps by percentage covered of interval
genomicranges
updated 9.5 years ago by ★ 11k • written 9.5 years ago by ▴ 50
15
votes
4
replies
12k
views
How to convert a GRangesList object into a GRanges object?
genomicranges grangeslist granges s4
updated 3.0 years ago by 16k • written 8.8 years ago by ▴ 40
11
votes
0
replies
6.2k
views
Tutorial: Introduction to Bioconductor for high-throughput sequence analysis
GenomicRanges Annotation RNAseq visualization Tutorial
9.7 years ago Martin Morgan 25k
11
votes
13
replies
5.6k
views
How to retrieve genomic coordinates for a list of entrezID and their respective gene names
genomic AnnotationHub GenomicRanges org.Hs.eg.db
4.3 years ago • updated 4.1 years ago rohitsatyam102 ▴ 20
10
votes
3
replies
11k
views
resize (shrink/expand) GenomicRanges
GenomicRanges IRanges
updated 9.1 years ago by 16k • written 9.1 years ago by ▴ 40
9
votes
9
replies
4.5k
views
Subset GRanges by intersection
findOverlaps GPos GenomicRanges subsetByOverlaps
updated 3.2 years ago by 68k • written 3.2 years ago by ▴ 10
9
votes
11
replies
4.8k
views
looping through a GRangesList object
GenomicRanges GRangesList
updated 9.2 years ago by ★ 1.3k • written 9.2 years ago by ★ 3.8k
9
votes
21
replies
12k
views
annotate GRanges with upstream or downstream nearest gene
GRange genomicranges genomicfeatures
updated 9.2 years ago by ★ 1.3k • written 9.2 years ago by ▴ 200
8
votes
12
replies
6.4k
views
Intergenic coordinates with Genomic Feaures
genomicranges genomicfeatures iranges
updated 2.7 years ago by • 0 • written 10.0 years ago by ▴ 20
8
votes
3
replies
1.8k
views
Counting ambiguously mapped reads per feature
rnaseq bam genomicranges GenomicAlignments Rsamtools
updated 8.7 years ago by 52k • written 8.7 years ago by ▴ 110
8
votes
9
replies
6.5k
views
could not find symbol "keepNA" in environment of the generic function
R function genomicalignments genomicranges summarizeoverlaps
updated 9.7 years ago by • 0 • written 9.7 years ago by ★ 1.5k
7
votes
4
replies
2.0k
views
seqlengths is not an exported object from namespace GenomicRanges
GenomicRanges
updated 5.6 years ago by ★ 11k • written 5.6 years ago by ▴ 160
7
votes
5
replies
4.6k
views
summarize scores of GRanges into bins
genomicranges grangeslist bin findoverlaps
updated 6.4 years ago by • 0 • written 7.5 years ago by ★ 1.5k
7
votes
5
replies
2.2k
views
Strange error in bsseq when trying to assign seqinfo
bsseq genomeinfodb genomicranges seqinfo
written 6.9 years ago by ▴ 140
7
votes
0
replies
4.1k
views
Tutorial: New edX "Data analysis for Life Sciences" module: High performance computing for reproducible genomics
annotation genomicranges visualization docker shiny Tutorial
9.0 years ago Vincent J. Carey, Jr. 6.7k
7
votes
12
replies
2.8k
views
Extract isoform-specific ranges
bioconductor genomicranges
updated 7.6 years ago by ★ 1.6k • written 7.6 years ago by ▴ 10
6
votes
2
replies
5.2k
views
How to get the intersect and get the difference of a grange object while keeping meta data
genomicranges intersect
updated 8.8 years ago by 4.1k • written 8.9 years ago by ▴ 30
6
votes
8
replies
3.5k
views
Ranges from a fasta file
biostrings fasta genomicranges granges
updated 6.1 years ago by 25k • written 6.1 years ago by ▴ 80
6
votes
2
replies
1.6k
views
strand-aware GRanges shift
GenomicRanges
updated 3.1 years ago by ★ 1.6k • written 3.1 years ago by ▴ 10
6
votes
6
replies
1.9k
views
Implementing fast mathematical and statistical operations on genomic variables in bioconductor
genomicranges biocgenerics rlelist genomicvars iranges
updated 7.5 years ago by 16k • written 7.5 years ago by ▴ 20
6
votes
6
replies
6.9k
views
converting a GRangesList object with different lengths into a data frame
genomicranges grangeslist dataframe irangeslist lists
updated 7.5 years ago by ★ 11k • written 7.5 years ago by ★ 1.5k
6
votes
12
replies
2.4k
views
mclapply to loop over a GRangesList object
GenomicRanges GRanges GRangesList parallel mclapply
6.1 years ago foehn ▴ 100
6
votes
4
replies
1.5k
views
Aggregate read counts by non-uniform overlapping sliding windows
granges genomicranges featurecounts
updated 8.2 years ago by ★ 11k • written 8.2 years ago by ▴ 20
5
votes
14
replies
3.1k
views
Subsetting a GenomicRanges::GRanges with "%in%" fails
genomicranges
5.6 years ago Aditya ▴ 160
5
votes
8
replies
10k
views
Non overlapping granges (or opposite of subsetByOverlaps)
granges genomicranges iranges subsetByOverlaps
updated 3.1 years ago by • 0 • written 9.5 years ago by ▴ 50
5
votes
3
replies
1.3k
views
countOverlaps with weights
genomicranges countoverlaps
updated 8.5 years ago by 25k • written 8.5 years ago by ▴ 180
5
votes
8
replies
2.8k
views
closest-features equivalent in Bioconductor for finding closest gene(s)
genomicranges granges iranges annotatepeak
updated 8.9 years ago by ★ 11k • written 8.9 years ago by ▴ 80
5
votes
3
replies
1.5k
views
How to avoid repeated overlap pair for GRanges object in grid?
r genomicranges
8.6 years ago • updated 8.4 years ago Jurat Shahidin ▴ 80
5
votes
8
replies
3.7k
views
Large disk images of DESeqDataSet / SummarizedExperiment objects when using the save function
SummarizedExperiment DESeqDataSet GenomicRanges DESeq2 save
updated 10.1 years ago by ★ 13k • written 10.1 years ago by ▴ 30
5
votes
6
replies
10k
views
Merge multiple genomic intervals if overlapping more than xx percents
genomicranges
written 9.8 years ago by ▴ 140
5
votes
2
replies
1.4k
views
How to build a GRangesList where each GRanges element is a CDS coordinate of gene transcripts?
GenomicRanges sesame sesameData GenomicFeatures
3.5 years ago Pratik Mehta ▴ 10
5
votes
2
replies
2.5k
views
How to extract positions present in one genomic ranges object and not the other?
genomicranges r overlap
updated 4.9 years ago by ★ 4.0k • written 4.9 years ago by • 0
5
votes
10
replies
3.7k
views
tileGenome for overlapping ranges?
genomicranges
updated 9.6 years ago by • 0 • written 10.1 years ago by ▴ 740
5
votes
4
replies
2.4k
views
How do I do a bedtools like intersection in GenomicRanges?
genomicranges
updated 6.7 years ago by ★ 11k • written 6.7 years ago by ▴ 40
5
votes
2
replies
6.1k
views
setdiff for GenomicRanges
genomicranges
updated 8.5 years ago by ★ 11k • written 8.5 years ago by ★ 4.3k
4
votes
5
replies
3.8k
views
How to find the amino acid codon corresponding to a translated genomic position
genomicranges genomicfeatures translation
updated 14 months ago by ▴ 10 • written 9.3 years ago by ▴ 10
4
votes
2
replies
1.8k
views
How to find particular types of overlap with GenomicRanges
r genomicranges iranges
updated 9.5 years ago by ★ 11k • written 9.5 years ago by ▴ 50
4
votes
6
replies
2.0k
views
GenomicRanges mapply to all combinations of GRangesList objects
genomicranges mapply grangeslist
9.4 years ago francesca casalino ▴ 50
4
votes
2
replies
1.3k
views
Build GPos from IPos
genomicranges granges gpos
updated 5.8 years ago by 16k • written 6.5 years ago by ▴ 180
4
votes
2
replies
1.3k
views
Speed efficient way to select the n-th element from GRangsList
R GenomicRanges IRanges
6.3 years ago foehn ▴ 100
4
votes
9
replies
2.0k
views
Using genomic ranges to get counts of non-overlapping (non-redundant) regions
genomicranges granges grangeslist R
updated 5.5 years ago by 68k • written 5.5 years ago by • 0
4
votes
1
reply
1.4k
views
Select from Overlapping Genomic Ranges based on Score or other Metadata
genomicranges
updated 9.1 years ago by ★ 11k • written 9.1 years ago by ▴ 30
4
votes
5
replies
1.4k
views
Write multiple UTRs for a gene to a fasta file
genomicranges genomicfeatures
updated 9.1 years ago by ★ 11k • written 9.1 years ago by ▴ 90
4
votes
2
replies
1.5k
views
Split Genome into 2kb bins GenomicRanges
genomicranges
updated 7.5 years ago by 16k • written 7.5 years ago by ▴ 10
4
votes
2
replies
3.5k
views
extracting distance from Hits object
genomicranges iranges
updated 10.2 years ago by 16k • written 10.2 years ago by ▴ 140
4
votes
1
reply
7.6k
views
how to get genomic coordinates for a list of genes
genomicranges
updated 10.1 years ago by 21k • written 10.1 years ago by ▴ 50
4
votes
2
replies
2.1k
views
Combine two GRanges to a single GRangesList
granges grangeslist GenomicRanges
updated 10.3 years ago by 25k • written 10.3 years ago by 21k
4
votes
10
replies
3.7k
views
mapCoords for converting genomic coordinates to cDNA coordinates?
genomicranges
updated 10.4 years ago by ★ 6.8k • written 10.4 years ago by ▴ 10
50 results • Page 1 of 1
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Comment: DiffBind custom normalization factor by Abbie • 0
Hello! Thanks so much for adding dba.normalize and all the documentation in the manual! I'm hoping I can ask a follow-up question here. I…
Answer: CpGs with genomic positions greater than the chromosome size in EPICv2? by James W. MacDonald 68k
All of the annotation packages provided by Bioconductor are simply repackaging of existing data from one or more sources. In this case, the…
Comment: Using TPM from tximport of Salmon output for singscore by Kent • 0
Thank you for the suggestions Michael. Would you say that after filtering out the low count genes, `rlog(counts, blind = T)` is doing the s…
Comment: Using TPM from tximport of Salmon output for singscore by Michael Love 43k
For clustering generally we recommend `vst()` see the workflow for example. For working with individual samples, I can see how a scaling/t…
Comment: DESeq2 model - How to test case/control time course model when taking account wi by Michael Love 43k
I'd recommend working with a local statistician or someone familiar with linear models in R. I have to reserve my time on the support site …
Votes
clusterProfiler-GO enrichment Error
A: Machine learning in R book
Data preparation and Machine learning on time course RNAseq data
Data preparation and Machine learning on time course RNAseq data
Answer: Use of org.Rn.eg.db with GRCr8 reference genome
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