Showing : rtracklayer • reset
28
votes
25
replies
7.3k
views
[FIXED] Error in Gviz (actually, rtracklayer) | IdeogramTrack
Gviz rtracklayer
updated 8.4 years ago by ▴ 10 • written 8.8 years ago by ▴ 100
9
votes
9
replies
6.6k
views
Importing a BED file with floating point scores?
rtracklayer bed
updated 4.8 years ago by ▴ 150 • written 9.7 years ago by ★ 7.9k
9
votes
38
replies
10k
views
manipulate bedpe format files
GRanges bedpe structural variants rtracklayer
written 9.8 years ago by ▴ 200
8
votes
5
replies
3.2k
views
import wig to coverage
rtracklayer granges import.wig
updated 10.9 years ago by 16k • written 10.9 years ago by ▴ 140
7
votes
16
replies
5.1k
views
How to extract phastcons score for all protein coding genes and lncRNAs using GenomicScores?
genomicscores granges phastCons100way.UCSC.hg38 r rtracklayer
updated 13 months ago by • 0 • written 5.7 years ago by ▴ 120
6
votes
7
replies
3.6k
views
Error: Failed to set session genome to...
gviz rtracklayer
updated 10.3 years ago by ★ 1.6k • written 10.6 years ago by ▴ 140
5
votes
3
replies
2.8k
views
Feature types in TxDb objects
GenomicFeatures rtracklayer
10.8 years ago • updated 10.7 years ago Thomas Girke ★ 1.7k
5
votes
9
replies
5.2k
views
mm10 phastCons data for use with ATACseqQC
ATACseqQC bsgenome phastcons rtracklayer
updated 8.6 years ago by ★ 1.3k • written 8.6 years ago by ▴ 10
5
votes
5
replies
5.2k
views
Issues with installation status of R package rtracklayer
rtracklayer Bioconductor
updated 3.8 years ago by 4.2k • written 4.9 years ago by ▴ 840
4
votes
2
replies
1.5k
views
rtracklayer: how to view coordinates that failed liftover?
rtracklayer
updated 8.9 years ago by ★ 11k • written 8.9 years ago by ▴ 30
4
votes
9
replies
5.7k
views
Is it possible to read bigwig files with rtracklayer over https? Comes down to GenomeInfoDb::seqinfo()
rtracklayer genomeinfodb
9.6 years ago Leonardo Collado Torres ★ 1.1k
4
votes
2
replies
1.3k
views
How to extract transcripts from Txdb with length >100
genomicfeatures rtracklayer
updated 9.2 years ago by 25k • written 9.2 years ago by ▴ 50
4
votes
5
replies
9.0k
views
Convert an R data.frame to a bed file in R
rtracklayer R bed
updated 2.9 years ago by • 0 • written 3.4 years ago by ▴ 50
4
votes
1
reply
1.7k
views
What's the recommended way to overwrite the seqinfo of a GRanges?
GRanges seqinfo import.bw BigWigFile rtracklayer
updated 6.8 years ago by ★ 11k • written 6.8 years ago by ▴ 180
3
votes
15
replies
4.2k
views
(Big)wig file of complete chromosome
bigwig rtracklayer import granges grangeslist
updated 8.4 years ago by ★ 11k • written 8.4 years ago by ★ 1.5k
3
votes
4
replies
2.1k
views
Convert a bed file to bigBed with rtracklayer
bed bigBed rtracklayer ucsc
3.1 years ago L ▴ 50
3
votes
2
replies
1.6k
views
Import gff from character?
rtracklayer gff gtf import import.gff3
updated 8.4 years ago by 25k • written 8.4 years ago by ▴ 20
3
votes
2
replies
5.3k
views
rtracklayer: how to export gff file with gene names included?
rtracklayer gff
updated 8.7 years ago by ★ 11k • written 8.7 years ago by ▴ 270
3
votes
4
replies
2.5k
views
rtracklayer import.gff3 function no longer working in R 3.4
rtracklayer import.gff3 gff
updated 8.6 years ago by 25k • written 8.6 years ago by ▴ 180
3
votes
2
replies
1.3k
views
does import.bw with the selection argument take into account strand?
rtracklayer import.bw
updated 9.2 years ago by ★ 11k • written 9.2 years ago by ▴ 180
3
votes
3
replies
1.9k
views
Bug in rtracklayer::import of amino acid fasta sequences
rtracklayer fasta import Biostrings
updated 6.9 years ago by ★ 11k • written 6.9 years ago by ▴ 120
3
votes
2
replies
5.0k
views
converting a fasta file to .2bit format
BioStrings rtracklayer
updated 7.2 years ago by 16k • written 7.2 years ago by ▴ 10
3
votes
6
replies
2.6k
views
Issue with UCSC and rtracklayer: 'names' attribute [210] must be the same length as the vector [209]
rtracklayer ucsc ensgene
updated 7.6 years ago by ▴ 10 • written 7.6 years ago by • 0
3
votes
9
replies
3.1k
views
export.bw produces enormous files (10^5 times bigger than they should be)
rtracklayer bigwig
updated 9.9 years ago by ▴ 30 • written 9.9 years ago by ▴ 30
3
votes
2
replies
1.3k
views
Long elapsed time using `import.gff3` with a toy example
rtracklayer import.gff3
updated 9.0 years ago by 25k • written 9.1 years ago by ▴ 20
2
votes
7
replies
1.4k
views
distanceToNearest
rtracklayer ranges distanceToNearest
23 months ago robjohn70000 • 0
2
votes
3
replies
3.9k
views
rtracklayer::lifOver one-to-many regions and not match UCSC
rtracklayer liftover bioconductor R
updated 8.3 years ago by ★ 11k • written 8.3 years ago by • 0
2
votes
4
replies
1.9k
views
rtracklayer::import.bed does not close connections.
rtracklayer
updated 8.6 years ago by ★ 11k • written 8.6 years ago by ▴ 180
2
votes
2
replies
1.9k
views
Error in normSplitFactor(f, x)
GenomicRanges rtracklayer goseq
updated 8.3 years ago by ★ 11k • written 8.3 years ago by ▴ 10
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 8.0 years ago by ★ 11k • written 8.0 years ago by ▴ 30
2
votes
2
replies
1.9k
views
How to access metadata of GAlignments objects
rtracklayer Rsamtools GAlignments GRanges metadata
updated 5.6 years ago by 16k • written 5.6 years ago by ▴ 10
2
votes
8
replies
5.0k
views
"minfi" loading problem because of couldn't "bumphunter" load
bumphunter minfi loading error rtracklayer
updated 8.6 years ago by • 0 • written 8.6 years ago by ▴ 10
2
votes
1
reply
1.1k
views
Why export of empty GRanges to GFF fails?
rtracklayer
updated 8.8 years ago by ★ 11k • written 8.8 years ago by ▴ 10
2
votes
3
replies
2.5k
views
liftOver bug, reproducible
liftOver rtracklayer
updated 4.8 years ago by 68k • written 4.9 years ago by ▴ 30
2
votes
3
replies
2.6k
views
Importing a bed file
rtracklayer
4.5 years ago Skylar • 0
2
votes
3
replies
1.9k
views
rtracklayer - export.bw bug
bigwig rtracklayer export.bw
updated 9.1 years ago by ★ 11k • written 9.1 years ago by ▴ 20
2
votes
0
replies
1.5k
views
How to liftOver Paired BED (bedpe) data
rtracklayer
5.0 years ago Mikhail Dozmorov ▴ 30
2
votes
3
replies
3.1k
views
import.bed fails on bed file with no scores
rtracklayer import bed files
9.7 years ago jmr • 0
2
votes
1
reply
1.6k
views
Strange first_time object in rtracklayer import
rtracklayer bigwig import
updated 9.1 years ago by ★ 11k • written 9.1 years ago by ▴ 10
2
votes
3
replies
2.2k
views
"Packages required but not available." rtracklayer in OSX is not available to CRAN, resulting in errors for downstream dependencies.
GenomicRanges rtracklayer VariantAnnotation S4Vectors SummarizedExperiment
updated 6.4 years ago by ★ 13k • written 6.4 years ago by ▴ 30
2
votes
6
replies
3.4k
views
rtracklayer: error in importing bigwig file in r in windows
rtracklayer bigwig file
updated 4.2 years ago by ★ 1.1k • written 5.8 years ago by ▴ 10
2
votes
1
reply
2.0k
views
rtracklayer BigBed format
ngs rtracklayer bigbed
updated 6.9 years ago by ★ 11k • written 6.9 years ago by ▴ 100
2
votes
8
replies
4.6k
views
Unable to load/install rtracklayer (v1.33.2) on OS X (possibly SSL-related?)
rtracklayer bioc-devel ssl openssl
updated 9.5 years ago by ★ 11k • written 9.5 years ago by ▴ 760
2
votes
1
reply
1.4k
views
Obsolete use of AC_INIT macro
rtracklayer
updated 9.6 years ago by ★ 11k • written 9.6 years ago by ▴ 180
2
votes
6
replies
3.6k
views
[rtracklayer] Error in .local(con, format, text, ...) : unused argument (asRangedData = FALSE)
software error rtracklayer
updated 9.9 years ago by ★ 11k • written 9.9 years ago by ▴ 130
2
votes
1
reply
1.7k
views
problem with export() in rtracklayer
rtracklayer export
updated 10.3 years ago by ★ 11k • written 10.3 years ago by ★ 29k
2
votes
10
replies
3.4k
views
tracklayer - browserSession() Infinite Recursion Error
rtracklayer ucsc
10.5 years ago andrew.j.skelton73 ▴ 370
2
votes
7
replies
1.7k
views
How to set track attributes in rtracklayer
rtracklayer browserView browserSession
updated 6.8 years ago by ★ 11k • written 6.8 years ago by ▴ 100
2
votes
4
replies
7.7k
views
rtracklayer export GRangesList as gtf and change attributes
grangeslist rtracklayer
updated 3.5 years ago by • 0 • written 10.4 years ago by ▴ 90
2
votes
4
replies
1.7k
views
default behaviour of import.bw
import.bw rtracklayer
4.1 years ago Yixin • 0
262 results • Page 1 of 6
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Comment: p.adjust BH Question by TikTsoksocissalpc • 0
Thanks for sharing your question about RMA limma analysis While working on your experiment, it s always helpful to have some background mu…
Answer: NUPOP usage by shepherl 4.2k
You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
Comment: How can I correctly use phyloseq with Docker? by fnfgame • 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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