Showing : GenomicRanges • reset
9
votes
21
replies
13k
views
annotate GRanges with upstream or downstream nearest gene
GRange genomicranges genomicfeatures
updated 9.3 years ago by ★ 1.3k • written 9.3 years ago by ▴ 200
3
votes
21
replies
3.6k
views
`precede` does not perform as expected
genomicranges precede ph525.5x
8.3 years ago wcstcyx ▴ 30
5
votes
14
replies
3.2k
views
Subsetting a GenomicRanges::GRanges with "%in%" fails
genomicranges
5.7 years ago Aditya ▴ 160
1
vote
14
replies
2.5k
views
DistanceToNearest() error: 'nLnode' and 'nRnode' must be single integers
genomicranges DistanceToNearest
updated 8.6 years ago by ★ 6.8k • written 8.7 years ago by ▴ 20
3
votes
13
replies
3.1k
views
IRanges error from derfinder analyzeChr with custom TxDb?
derfinder genomicfeatures genomicranges
updated 7.7 years ago by ★ 1.1k • written 7.7 years ago by ▴ 20
11
votes
13
replies
5.8k
views
How to retrieve genomic coordinates for a list of entrezID and their respective gene names
genomic AnnotationHub GenomicRanges org.Hs.eg.db
4.4 years ago • updated 4.2 years ago rohitsatyam102 ▴ 20
8
votes
12
replies
6.6k
views
Intergenic coordinates with Genomic Feaures
genomicranges genomicfeatures iranges
updated 2.8 years ago by • 0 • written 10.1 years ago by ▴ 20
2
votes
12
replies
2.5k
views
nearest without overlapping
genomicranges
updated 6.8 years ago by 16k • written 6.8 years ago by ▴ 40
2
votes
12
replies
2.2k
views
remove set number of nucleotides from each gene's cds region in GRangesList
genomicranges genomicfeatures
updated 9.7 years ago by ★ 11k • written 9.7 years ago by ▴ 90
7
votes
12
replies
2.9k
views
Extract isoform-specific ranges
bioconductor genomicranges
updated 7.7 years ago by ★ 1.6k • written 7.7 years ago by ▴ 10
6
votes
12
replies
2.5k
views
mclapply to loop over a GRangesList object
GenomicRanges GRanges GRangesList parallel mclapply
6.2 years ago foehn ▴ 100
0
votes
12
replies
2.9k
views
more stupid *Ranges questions...
Transcription ChIPpeakAnno GenomicRanges Transcription ChIPpeakAnno GenomicRanges
updated 13.6 years ago by ★ 11k • written 13.6 years ago by ★ 4.2k
9
votes
11
replies
4.9k
views
looping through a GRangesList object
GenomicRanges GRangesList
updated 9.3 years ago by ★ 1.3k • written 9.3 years ago by ★ 3.8k
1
vote
11
replies
2.8k
views
Had to remove duplicated() in order to install GenomicRanges 1.22 on top of 1.20 on linux
installation genomicranges summarizedexperiment
9.5 years ago • updated 9.4 years ago knb • 0
2
votes
10
replies
2.2k
views
Reorder exons on negative strand in GRanges list
genomicranges
updated 9.0 years ago by ★ 11k • written 9.0 years ago by ▴ 90
5
votes
10
replies
3.8k
views
tileGenome for overlapping ranges?
genomicranges
updated 9.7 years ago by • 0 • written 10.2 years ago by ▴ 740
20
votes
10
replies
21k
views
How do I merge a list of GRanges?
GenomicRanges
updated 3.2 years ago by ▴ 40 • written 8.9 years ago by ▴ 40
1
vote
10
replies
3.0k
views
GenomicRanges bug in follow?
genomicranges
9.6 years ago • updated 9.5 years ago Janet Young ▴ 740
0
votes
10
replies
1.9k
views
Calculate Outer Positions of GappedAlignmentPairs
Coverage GenomicRanges Coverage GenomicRanges
updated 12.1 years ago by ★ 11k • written 12.1 years ago by ★ 1.6k
4
votes
10
replies
3.8k
views
mapCoords for converting genomic coordinates to cDNA coordinates?
genomicranges
updated 10.5 years ago by ★ 6.8k • written 10.5 years ago by ▴ 10
0
votes
10
replies
2.5k
views
behaviour of findOverlaps on GRangesList object
findOverlaps grangeslist GenomicRanges
7.9 years ago lovro0 ▴ 10
2
votes
10
replies
2.7k
views
How to find the amino acid codons corresponding to a subset of a range of genomic positions
genomicfeatures genomicranges cds overlap
updated 9.4 years ago by ★ 11k • written 9.4 years ago by ▴ 10
3
votes
10
replies
8.6k
views
Extract metadata from GRanges object for every genomic coordinate
GenomicRanges GRanges
5.8 years ago Robert ▴ 10
9
votes
9
replies
4.7k
views
Subset GRanges by intersection
findOverlaps GPos GenomicRanges subsetByOverlaps
updated 3.3 years ago by 68k • written 3.3 years ago by ▴ 10
4
votes
9
replies
2.0k
views
Using genomic ranges to get counts of non-overlapping (non-redundant) regions
genomicranges granges grangeslist R
updated 5.6 years ago by 68k • written 5.6 years ago by • 0
0
votes
9
replies
2.6k
views
using a gtf file to map reads
GenomicRanges DESeq2 GenomicRanges DESeq2
updated 11.9 years ago by ★ 11k • written 11.9 years ago by ▴ 300
0
votes
9
replies
1.7k
views
ReportingTools - trouble incorporating annotations
Annotation edgeR GenomicRanges Annotation edgeR GenomicRanges
updated 11.9 years ago by 68k • written 11.9 years ago by ▴ 300
8
votes
9
replies
6.5k
views
could not find symbol "keepNA" in environment of the generic function
R function genomicalignments genomicranges summarizeoverlaps
updated 9.8 years ago by • 0 • written 9.8 years ago by ★ 1.5k
5
votes
8
replies
10k
views
Non overlapping granges (or opposite of subsetByOverlaps)
granges genomicranges iranges subsetByOverlaps
updated 3.2 years ago by • 0 • written 9.6 years ago by ▴ 50
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 10.2 years ago by ★ 13k • written 10.2 years ago by ▴ 30
5
votes
8
replies
2.9k
views
closest-features equivalent in Bioconductor for finding closest gene(s)
genomicranges granges iranges annotatepeak
updated 9.0 years ago by ★ 11k • written 9.0 years ago by ▴ 80
2
votes
8
replies
6.1k
views
GenomicRanges: identify overlapping regions, get intersection between each overlapping pair and add gene coordinates (start, end, strand and ids)
genomicranges overlap intersect findoverlaps
7.3 years ago Caroline Grisbach Meissner ▴ 10
0
votes
8
replies
2.3k
views
good news and bad news
Infrastructure Cancer IRanges GenomicRanges Infrastructure Cancer IRanges GenomicRanges
updated 12.7 years ago by ★ 13k • written 12.7 years ago by 16k
1
vote
8
replies
1.8k
views
Aggregating scores of multiple metadata columns from one GRanges object on another
GenomicRanges
updated 6.1 years ago by ★ 11k • written 6.1 years ago by • 0
0
votes
8
replies
2.8k
views
Confusion over inconsistencies with showMethods('Rle') when loaded via GenomicRanges
GenomicRanges GenomicRanges
updated 12.3 years ago by ★ 13k • written 12.3 years ago by ▴ 750
6
votes
8
replies
3.6k
views
Ranges from a fasta file
biostrings fasta genomicranges granges
updated 6.2 years ago by 25k • written 6.2 years ago by ▴ 80
0
votes
7
replies
2.5k
views
VariantTools installation problem: dependencies not available
IRanges GenomicRanges VariantTools XVector IRanges GenomicRanges VariantTools XVector
updated 11.5 years ago by ★ 11k • written 11.5 years ago by ▴ 360
0
votes
7
replies
1.6k
views
rtracklayer cannot export empty BED file
rtracklayer bed genomicranges
updated 6.4 years ago by ★ 11k • written 6.4 years ago by ▴ 100
0
votes
7
replies
2.1k
views
Probe ID to Sequence
SNPlocs GenomicRanges SNPlocs GenomicRanges
updated 13.8 years ago by ★ 4.2k • written 13.8 years ago by ▴ 400
2
votes
7
replies
4.9k
views
coverage over specific GenomicRanges
genomicranges
updated 9.8 years ago by 16k • written 9.8 years ago by ▴ 90
3
votes
7
replies
2.5k
views
Intersecting a Granges and a GRangesList elementwise
findoverlaps genomicranges
updated 9.7 years ago by 16k • written 9.7 years ago by ▴ 150
0
votes
7
replies
2.7k
views
regionMatrix for derfinder crashes with seqnames issue on non-human data
derfinder GenomeInfoDb GenomicRanges
8.0 years ago Wayne • 0
0
votes
7
replies
3.9k
views
GenomicRanges requires S4Vectors 0.23.19 when 0.22.1 installs from BiocManager
S4Vectors GenomicRanges BiocManager
5.6 years ago james.dalgleish ▴ 30
0
votes
7
replies
2.2k
views
multicore and GRangesList
GenomicRanges GenomicRanges
updated 14.3 years ago by 25k • written 14.3 years ago by ▴ 200
0
votes
7
replies
1.5k
views
distanceToNearest for GRanges?
Cancer GenomicRanges Cancer GenomicRanges
updated 13.0 years ago by ▴ 420 • written 13.1 years ago by ★ 6.8k
0
votes
7
replies
2.2k
views
Speeding up or replacing Loops to process Bam Reads
genomicranges reads genomicfeatures Bam
10.1 years ago gen ▴ 30
3
votes
7
replies
1.9k
views
GRanges/GFeatures: Retain all parent columns in cdsByOverlaps output
GRanges GenomicRanges GenomicFeatures cdsByOverlaps DiffBind
updated 4.7 years ago by 68k • written 4.7 years ago by ▴ 30
4
votes
6
replies
2.0k
views
GenomicRanges mapply to all combinations of GRangesList objects
genomicranges mapply grangeslist
9.5 years ago francesca casalino ▴ 50
0
votes
6
replies
1.5k
views
wishlist for readGappedAlignments
GenomicRanges Rsamtools GenomicRanges Rsamtools
updated 13.7 years ago by 25k • written 13.7 years ago by ▴ 420
3
votes
6
replies
3.0k
views
Assign genes to CpG islands
annotation genomicranges bsgenome
updated 9.5 years ago by ★ 1.3k • written 9.5 years ago by ▴ 10
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Comment: Cannot extract size factor from DESeq2 analysis by s.malik • 0
Dear Mike, using tximeta and following code, is this fine to extract normalized counts after `sizeFactors(dds)` gives NULL? `dds <- DESeq…
Comment: Design formula for circadian time-course data for vst() function by Vishnu • 0
Thank you so much for your reply.
Comment: Analyzing TnSeq data with DESeq2 by Tom • 0
[Doncaster Locksmith][1] delivers trusted, efficient security services tailored to your needs. Analyzing TnSeq data with DESeq2 may uncover…
Answer: Design formula for circadian time-course data for vst() function by ATpoint ★ 4.8k
This was asked before: https://support.bioconductor.org/p/9148734/#9148812 Take-home message is that influence is minor, as you see your…
Comment: Filtering after DESeq by caroline.zanchi • 0
... I did it. It does filter out quite a bit of genes : ``` keep <- filterByExpr(dds, group="host_treatment_generation",min.count = 10, mi…
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Comment: Filtering after DESeq
A: Normalized counts from DESeq2 results in similar but not equal total read count?
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