Showing : rtracklayer • reset
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1.6k
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create a full TXDB object from GFF3 data for a non-system organism / denovo assembly
GenomicFeatures rtracklayer
updated 6.7 years ago by 16k • written 6.7 years ago by ▴ 10
4
votes
1
reply
1.8k
views
What's the recommended way to overwrite the seqinfo of a GRanges?
GRanges seqinfo import.bw BigWigFile rtracklayer
updated 6.9 years ago by ★ 11k • written 6.9 years ago by ▴ 180
2
votes
7
replies
1.7k
views
How to set track attributes in rtracklayer
rtracklayer browserView browserSession
updated 6.9 years ago by ★ 11k • written 6.9 years ago by ▴ 100
0
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4
replies
1.6k
views
Change sign from Granges scores to visualize negative strand data
granges rtracklayer
updated 6.9 years ago by 68k • written 6.9 years ago by • 0
0
votes
1
reply
1.6k
views
How to filter gff based on certain gene list in rtracklayer?
rtracklayer gff filter
updated 7.0 years ago by ★ 11k • written 7.0 years ago by • 0
3
votes
3
replies
2.0k
views
Bug in rtracklayer::import of amino acid fasta sequences
rtracklayer fasta import Biostrings
updated 7.0 years ago by ★ 11k • written 7.0 years ago by ▴ 120
2
votes
1
reply
2.0k
views
rtracklayer BigBed format
ngs rtracklayer bigbed
updated 7.0 years ago by ★ 11k • written 7.0 years ago by ▴ 100
1
vote
12
replies
7.1k
views
Install rtracklayer with the Error undefined symbol: OPENSSL_init_ssl (system Centos7.3 R3.5.1 openssl-1.1.1)
software error rtracklayer bioconductor openssl
7.1 years ago ruan_wei_dong • 0
0
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1
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1.7k
views
rtracklayer::Problem with export.bw of GRanges object created by unlisted after liftover from mm9 to mm10 of wig file
rtracklayer export.bw liftover
updated 7.2 years ago by ★ 11k • written 7.2 years ago by ▴ 20
1
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2
replies
3.7k
views
How to convert bedgraph to wig
rtracklayer genomicranges
updated 7.2 years ago by ★ 11k • written 7.2 years ago by • 0
0
votes
7
replies
2.0k
views
rtracklayer cannot export empty BED file
rtracklayer bed genomicranges
updated 7.2 years ago by ★ 11k • written 7.2 years ago by ▴ 100
0
votes
3
replies
2.1k
views
browseGenome with Shiny
rtracklayer browsegenome shiny
updated 7.3 years ago by ★ 11k • written 7.3 years ago by • 0
3
votes
2
replies
5.0k
views
converting a fasta file to .2bit format
BioStrings rtracklayer
updated 7.3 years ago by 16k • written 7.3 years ago by ▴ 10
1
vote
10
replies
3.2k
views
rtracklayer export bedGraph cannot be loaded into UCSC
rtracklayer
updated 7.4 years ago by ★ 11k • written 7.4 years ago by ▴ 260
1
vote
4
replies
3.7k
views
Import Chain - Cannot Import Chain File
rtracklayer
updated 5.1 years ago by ▴ 20 • written 7.4 years ago by • 0
0
votes
1
reply
1.0k
views
motifs order on importing the motifs from bigWig file
R rtracklayer data import
updated 7.5 years ago by ★ 11k • written 7.5 years ago by • 0
1
vote
1
reply
1.1k
views
makeTxdbFromUCSC fails to download
maketxdbpackagefromucsc rtracklayer genomicfeatures
updated 7.5 years ago by 68k • written 7.5 years ago by • 0
0
votes
2
replies
1.4k
views
Can't install rtracklayer - make: *** [ucsc/os.o] Error 1
rtracklayer
7.6 years ago creasyt • 0
3
votes
6
replies
2.7k
views
Issue with UCSC and rtracklayer: 'names' attribute [210] must be the same length as the vector [209]
rtracklayer ucsc ensgene
updated 7.7 years ago by ▴ 10 • written 7.7 years ago by • 0
0
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1
reply
1.7k
views
rtracklayer::liftOver parameters (minMatch)
rtracklayer liftOver parameters minMatch
updated 7.8 years ago by ★ 11k • written 7.8 years ago by ▴ 10
0
votes
2
replies
1.2k
views
rtracklayer colorByStrand - is it possible to add quotes?
rtracklayer
7.8 years ago Janet Young ▴ 740
0
votes
1
reply
1.2k
views
import bed file with track line fails
rtracklayer
updated 7.8 years ago by ★ 11k • written 7.8 years ago by • 0
1
vote
2
replies
1.3k
views
rtracklayer demo bug
rtracklayer
7.8 years ago felix.ernst • 0
0
votes
4
replies
2.4k
views
Gviz IdeogramTrack fails with Error: failed to load HTTP resource
gviz gviz-package rtracklayer http
8.0 years ago enricoferrero ▴ 680
1
vote
1
reply
1.5k
views
seqnames versus chrom
BiocGen rtracklayer genomeinfodb
updated 8.0 years ago by ★ 11k • written 8.0 years ago by • 0
0
votes
6
replies
2.8k
views
Add columns to granges object that sum score around range
R Grang r granges rtracklayer
updated 8.1 years ago by ★ 11k • written 8.1 years ago by ▴ 20
2
votes
4
replies
2.9k
views
possible Rtracklayer issue: TxDb errors in GenomicFeatures package-- cannot load TxDb with standard params from UCSC (issue began last night)
genomicfeatures txdb maketxdbfromucsc maketxdbfrombiomart rtracklayer
updated 8.1 years ago by ★ 11k • written 8.1 years ago by ▴ 30
0
votes
0
replies
988
views
Missing Information with transcriptlengthsfunction
bioconductor genomicfeatures rtracklayer transriptlengths
8.1 years ago michael.soutschek • 0
0
votes
2
replies
1.7k
views
How to get UCSC url when use rtracklayer, contain the track in the url ,it may be very useful
rtracklayer UCSC ucsctrack
updated 8.1 years ago by 68k • written 8.1 years ago by • 0
0
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1
reply
1.6k
views
Error: subscript out of bounds when using ucscGenomes() and supportedGenomes() functions in goseq and rtracklayer packages respctively
goseq rtracklayer
8.3 years ago mgdrnl • 0
1
vote
2
replies
1.2k
views
The track cannot show in UCSC
rtracklayer
8.3 years ago zhangqshxxzz • 0
1
vote
2
replies
1.6k
views
Can rtracklayer import tab-delimited BED files with unquoted spaces in fields?
rtracklayer bed software error
updated 8.4 years ago by ★ 11k • written 8.4 years ago by ★ 7.9k
2
votes
2
replies
1.9k
views
Error in normSplitFactor(f, x)
GenomicRanges rtracklayer goseq
updated 8.4 years ago by ★ 11k • written 8.4 years ago by ▴ 10
2
votes
3
replies
4.1k
views
rtracklayer::lifOver one-to-many regions and not match UCSC
rtracklayer liftover bioconductor R
updated 8.4 years ago by ★ 11k • written 8.4 years ago by • 0
0
votes
2
replies
2.3k
views
liftOver function in rtracklayer package is not working
liftover rtracklayer
updated 8.5 years ago by ★ 11k • written 8.5 years ago by • 0
3
votes
15
replies
4.3k
views
(Big)wig file of complete chromosome
bigwig rtracklayer import granges grangeslist
updated 8.5 years ago by ★ 11k • written 8.5 years ago by ★ 1.5k
28
votes
25
replies
7.4k
views
[FIXED] Error in Gviz (actually, rtracklayer) | IdeogramTrack
Gviz rtracklayer
updated 8.5 years ago by ▴ 10 • written 8.9 years ago by ▴ 100
3
votes
2
replies
1.7k
views
Import gff from character?
rtracklayer gff gtf import import.gff3
updated 8.5 years ago by 25k • written 8.5 years ago by ▴ 20
0
votes
1
reply
1.6k
views
why merged paired end reads still have strand infomation?
dnaseq rtracklayer paired-end reads
8.6 years ago zwfanwz678 • 0
0
votes
0
replies
1.6k
views
How to generate CpG island Unmasked.bed file format for finding CpG island shores and shelves?
bioconductor annotation rtracklayer genomes homo.sapiens
8.6 years ago sivabala76 • 0
0
votes
2
replies
2.8k
views
Exporting a GenomicRanges object as GTF/GFF file
genomicranges rtracklayer gtf gff export
8.6 years ago rubi ▴ 110
2
votes
8
replies
5.1k
views
"minfi" loading problem because of couldn't "bumphunter" load
bumphunter minfi loading error rtracklayer
updated 8.7 years ago by • 0 • written 8.7 years ago by ▴ 10
5
votes
9
replies
5.3k
views
mm10 phastCons data for use with ATACseqQC
ATACseqQC bsgenome phastcons rtracklayer
updated 8.7 years ago by ★ 1.3k • written 8.7 years ago by ▴ 10
2
votes
4
replies
1.9k
views
rtracklayer::import.bed does not close connections.
rtracklayer
updated 8.7 years ago by ★ 11k • written 8.7 years ago by ▴ 180
3
votes
4
replies
2.6k
views
rtracklayer import.gff3 function no longer working in R 3.4
rtracklayer import.gff3 gff
updated 8.7 years ago by 25k • written 8.7 years ago by ▴ 180
3
votes
2
replies
5.4k
views
rtracklayer: how to export gff file with gene names included?
rtracklayer gff
updated 8.9 years ago by ★ 11k • written 8.9 years ago by ▴ 270
0
votes
3
replies
2.5k
views
Accessing the BigWig files from the web
rtracklayer
8.9 years ago Mustafa ABUELQUMSAN • 0
2
votes
1
reply
1.2k
views
Why export of empty GRanges to GFF fails?
rtracklayer
updated 8.9 years ago by ★ 11k • written 8.9 years ago by ▴ 10
0
votes
3
replies
2.7k
views
browseGenome rtracklayer, save / export UCSC genome browser image e.g. as pdf
rtracklayer browseGenome save file image UCSC
updated 8.9 years ago by ▴ 10 • written 10.8 years ago by ▴ 60
0
votes
2
replies
1.4k
views
rtracklayer redistributes UCSC source without the original license?
rtracklayer
updated 8.9 years ago by ▴ 10 • written 10.1 years ago by • 0
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Answer: Are individual-mouse-based statistics possible in CellChat? by ATpoint ★ 5.0k
Not a Bioconductor package, I commented on the crosspost at https://www.biostars.org/p/9617271/
Comment: DESeq2 - how to shrink LFC for pairwise comparisons having multiple groups by ATpoint ★ 5.0k
apeglm is more cumbersome than ashr as with apeglm the coefficients need to be explicitely available in the resultsNames.So, you need to re…
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Martin Morgan 25k
I see rstudioapi in the `sessionInfo()`. RStudio does not support forked ('multicore') processes. Does the BiocParallel example work when y…
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
Given that this is an issue with BiocParallel on your machine and we have a minimal reproducible example, you may want to repost the issue.…
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Benjamin • 0
Still happening using pre-existing size factors estimating dispersions gene-wise dispersion estimates: 15 workers mean-dis…
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