Showing : Iranges • reset
0
votes
28
replies
2.4k
views
countMatches() (was: table for GenomicRanges)
Cancer IRanges Cancer IRanges
updated 11.3 years ago by ★ 11k • written 11.3 years ago by 16k
4
votes
17
replies
3.2k
views
How to construct a valid GRanges object from RCPP and pass back to R
GRanges IRanges RCPP Constructor
updated 6.5 years ago by ▴ 10 • written 6.6 years ago by ▴ 80
0
votes
16
replies
1.6k
views
IRanges is broken in Cygwin (mingw/math.h)
IRanges IRanges
updated 10.8 years ago by ★ 11k • written 10.8 years ago by ▴ 660
0
votes
16
replies
4.1k
views
subset a RleList using GRanges object?
Coverage Cancer IRanges Coverage Cancer IRanges
updated 10.4 years ago by 16k • written 10.4 years ago by ▴ 740
0
votes
15
replies
2.0k
views
Looking for the source for IRanges 2.8.1, S4Vectors 0.12.1 and XVector 0.14.0
bioconductor iranges s4vectors xvector r 3.3.2
updated 5.7 years ago by ▴ 10 • written 5.7 years ago by • 0
1
vote
13
replies
2.5k
views
Rsamtools memory leak
rsamtools scanbam bam granges iranges
8.5 years ago mhills ▴ 10
1
vote
12
replies
2.1k
views
How can I integrate set of compressedList in multiple list into one without duplication?
r iranges findoverlaps IntegerList List
7.7 years ago • updated 7.4 years ago jian_liangli • 0
8
votes
12
replies
5.4k
views
Intergenic coordinates with Genomic Feaures
genomicranges genomicfeatures iranges
updated 21 months ago by • 0 • written 9.1 years ago by ▴ 20
0
votes
11
replies
2.3k
views
NucleR: processReads/solveUserSEW0 - Error
IRanges ShortRead nucleR IRanges ShortRead nucleR
12.5 years ago Stefanie Ververs ▴ 70
0
votes
11
replies
1.9k
views
nearest() for GRanges
IRanges IRanges
updated 11.8 years ago by 25k • written 11.8 years ago by ▴ 20
8
votes
10
replies
1.9k
views
Compare ranges from two GRanges and check if the ranges from the first GRanges is contained in another.
GRanges IRanges
updated 3.9 years ago by 65k • written 3.9 years ago by ▴ 50
0
votes
10
replies
1.8k
views
How to convert from IRanges(List) to Rle(List)
convert IRanges convert IRanges
updated 12.0 years ago by 25k • written 12.0 years ago by ★ 1.2k
2
votes
10
replies
3.5k
views
Extract three types of intergenic regions
granges views annotation iranges
updated 8.5 years ago by ★ 1.7k • written 8.5 years ago by ▴ 50
1
vote
9
replies
1.6k
views
Big data for IRanges: Combining reduce and gaps with dplyr functions
r iranges reduce gaps
8.4 years ago pesquivel • 0
0
votes
9
replies
2.7k
views
IRanges: reduce(), findOverlaps(), and intersect() by group
iranges findoverlaps intersect group
8.3 years ago pesquivel • 0
0
votes
8
replies
2.0k
views
IRanges/List oddity: do.call of `c` on a list of IRangesList returns "list" only when the list is named
Cancer IRanges BiocGenerics Cancer IRanges BiocGenerics
updated 11.4 years ago by ★ 11k • written 11.4 years ago by 16k
0
votes
8
replies
1.8k
views
CIGAR-aware coverage
Coverage IRanges Coverage IRanges
updated 10.1 years ago by ★ 11k • written 10.1 years ago by ▴ 30
5
votes
8
replies
2.2k
views
closest-features equivalent in Bioconductor for finding closest gene(s)
genomicranges granges iranges annotatepeak
updated 8.0 years ago by ★ 11k • written 8.0 years ago by ▴ 80
0
votes
8
replies
1.7k
views
IRanges problem: findOverlaps
IRanges IRanges
updated 11.8 years ago by ▴ 50 • written 11.8 years ago by ▴ 20
5
votes
8
replies
8.7k
views
Non overlapping granges (or opposite of subsetByOverlaps)
granges genomicranges iranges subsetByOverlaps
updated 2.2 years ago by • 0 • written 8.6 years ago by ▴ 50
0
votes
8
replies
1.9k
views
good news and bad news
Infrastructure Cancer IRanges GenomicRanges Infrastructure Cancer IRanges GenomicRanges
updated 11.7 years ago by ★ 13k • written 11.7 years ago by 16k
0
votes
8
replies
1.2k
views
stranded findOverlaps
IRanges IRanges
updated 14.2 years ago by ▴ 50 • written 14.2 years ago by ★ 3.2k
0
votes
7
replies
1.3k
views
IRanges: interaction with model fitting
Regression IRanges Regression IRanges
updated 13.7 years ago by 25k • written 13.7 years ago by ★ 6.5k
0
votes
7
replies
2.1k
views
VariantTools installation problem: dependencies not available
IRanges GenomicRanges VariantTools XVector IRanges GenomicRanges VariantTools XVector
updated 10.4 years ago by ★ 11k • written 10.4 years ago by ▴ 360
4
votes
7
replies
2.1k
views
IRanges/ShortRead causing crash?
iranges shortread Biostrings
updated 8.4 years ago by 25k • written 8.4 years ago by ▴ 20
0
votes
7
replies
1.6k
views
Best way to subset one IRanges by list of IRanges
iranges
4.6 years ago Robert M. Flight ▴ 280
0
votes
6
replies
1.4k
views
IRanges: Trying to cut overlapping intervals into pieces
IRanges IRanges
updated 15.2 years ago by ▴ 620 • written 15.2 years ago by ▴ 210
0
votes
6
replies
1.5k
views
IRanges coverage integer limit?
Coverage IRanges Coverage IRanges
updated 11.8 years ago by 16k • written 11.8 years ago by ★ 1.2k
2
votes
6
replies
2.8k
views
Shrink or Expand RLE
RLE iranges granges coverage
updated 9.0 years ago by 25k • written 9.1 years ago by ▴ 30
6
votes
6
replies
1.5k
views
Implementing fast mathematical and statistical operations on genomic variables in bioconductor
genomicranges biocgenerics rlelist genomicvars iranges
updated 6.6 years ago by 16k • written 6.6 years ago by ▴ 20
0
votes
6
replies
1.3k
views
distances for IRanges
IRanges IRanges
updated 13.9 years ago by ★ 11k • written 13.9 years ago by ★ 6.5k
0
votes
6
replies
1.2k
views
Subscripting GenomicRanges objects with [[ or $
IRanges IRanges
updated 13.7 years ago by ▴ 160 • written 13.7 years ago by ▴ 250
0
votes
6
replies
1.6k
views
Merging RandData object with names on the IRanges part
IRanges IRanges
14.7 years ago Ulrike Goebel ▴ 110
0
votes
6
replies
1.6k
views
query and subject hits in findOverlaps through different space names
IRanges IRanges
updated 14.0 years ago by ★ 11k • written 14.0 years ago by ★ 3.2k
4
votes
6
replies
1.1k
views
CAGEr - Error with aggregateTagClusters() - invalid class IRanges object: width(x) cannot contain negative integers
CAGEr IRanges aggregateTagClusters
3.9 years ago mirkocelii ▴ 40
0
votes
6
replies
1.3k
views
iranges
IRanges IRanges
updated 9.7 years ago by ★ 6.8k • written 9.7 years ago by ▴ 680
0
votes
6
replies
6.2k
views
GRanges: problem with multiple seqnames and seqlengths
GRanges seqnames seqlengths IRanges
9.6 years ago topher.hamm • 0
0
votes
5
replies
1.5k
views
GenomicRanges: nearest() for GRanges not returning overlaps
IRanges IRanges
updated 11.8 years ago by ★ 11k • written 11.8 years ago by ▴ 300
0
votes
5
replies
1.2k
views
IRanges causes bug in complete.cases
Regression IRanges Regression IRanges
updated 14.4 years ago by ★ 11k • written 14.4 years ago by ★ 6.5k
0
votes
5
replies
1.5k
views
HiTC importC not working
HiTC IRanges windows debian
updated 6.1 years ago by ▴ 260 • written 6.1 years ago by • 0
17
votes
5
replies
4.1k
views
Combining RangedData objects is broken (IRanges 2.8.1 with R version 3.3.3 RC)
IRanges
updated 7.1 years ago by 25k • written 7.1 years ago by ▴ 20
0
votes
5
replies
1.3k
views
A code kata: evening-out *Ranges ends.
Infrastructure Cancer IRanges Infrastructure Cancer IRanges
13.7 years ago Steve Lianoglou ★ 13k
0
votes
5
replies
1.4k
views
Splitting a fasta file based on specific Amino acid for plotting
iranges biostrings fasta protein readaastringset
updated 7.5 years ago by ★ 11k • written 7.5 years ago by ★ 1.5k
2
votes
5
replies
4.9k
views
unlist doesn't work for IRanges
iranges
updated 5.9 years ago by 65k • written 5.9 years ago by ▴ 450
0
votes
5
replies
1.2k
views
IRanges : Strange behavior subsetting an IntervalTree with an indexing variable from within a function
Cancer IRanges Cancer IRanges
14.6 years ago Steve Lianoglou ★ 13k
1
vote
5
replies
1.9k
views
'version' is missing error when running makeTxDbPackageFromUCSC
Cancer TranscriptDb IRanges GenomicFeatures Cancer TranscriptDb IRanges GenomicFeatures
updated 8.5 years ago by ▴ 10 • written 10.6 years ago by 16k
2
votes
5
replies
1.4k
views
making a RleViewsList object gets slow with many chromosomes
views iranges rle
9.2 years ago Janet Young ▴ 740
0
votes
5
replies
2.1k
views
Problem installing XVector package
software error gcrma Xvector iranges
7.7 years ago gary_smith • 0
3
votes
5
replies
3.1k
views
Element-wise setdiff when psetdiff fails for GenomicRanges
genomicranges iranges genomics
updated 9.3 years ago by ▴ 60 • written 9.3 years ago by ▴ 150
3
votes
5
replies
1.0k
views
IRanges start bigger than end
iranges
8.2 years ago vedran.franke • 0
50 results • Page 1 of 1
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Comment: How to retrieve detailed regression results from deseq2 by Weiqian ▴ 10
Hi Michael, thanks for the answer! I'll have a look : )
Comment: DESeq filtering specific to contrasts by Michael Love 41k
It will likely not filter it out, but really the per-dataset details would affect the results.
Comment: DESeq filtering specific to contrasts by Carlin95 • 0
Thanks for clarifying. Could I ask maybe one more thing for my sanity? Let's say you had a multi-factor experiment with contrasts including…
Comment: FilterByExpr low counts with small sample size by Jonathan ▴ 10
Thank you for your answer; However, I have some follow-up questions. Following up in In your [1-2-3 article][1], you say that > "... the…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa by Seyram M. • 0
Thank you very much for your reply! I will do so. Kind regards, Seyram
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Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
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Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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