Showing : rtracklayer • reset
9
votes
38
replies
11k
views
manipulate bedpe format files
GRanges bedpe structural variants rtracklayer
written 10.1 years ago by ▴ 200
0
votes
4
replies
10k
views
rtracklayer importing gtf files
rtracklayer DESeq GenomicRanges rtracklayer DESeq GenomicRanges
updated 12.9 years ago by ★ 11k • written 12.9 years ago by ★ 13k
4
votes
5
replies
9.3k
views
Convert an R data.frame to a bed file in R
rtracklayer R bed
updated 3.2 years ago by • 0 • written 3.6 years ago by ▴ 50
0
votes
3
replies
8.8k
views
rtracklayer gff import
rtracklayer rtracklayer
updated 14.9 years ago by ★ 11k • written 14.9 years ago by ▴ 110
2
votes
4
replies
8.0k
views
rtracklayer export GRangesList as gtf and change attributes
grangeslist rtracklayer
updated 3.7 years ago by • 0 • written 10.6 years ago by ▴ 90
28
votes
25
replies
7.5k
views
[FIXED] Error in Gviz (actually, rtracklayer) | IdeogramTrack
Gviz rtracklayer
updated 8.6 years ago by ▴ 10 • written 9.0 years ago by ▴ 100
1
vote
12
replies
7.2k
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
7.3 years ago ruan_wei_dong • 0
1
vote
5
replies
6.9k
views
RStudio vs R: using rtracklayer to import bigwig files from http works in R but not in RStudio.
import.bw rtracklayer http RStudio
updated 5.3 years ago by ★ 11k • written 5.3 years ago by • 0
9
votes
9
replies
6.8k
views
Importing a BED file with floating point scores?
rtracklayer bed
updated 5.1 years ago by ▴ 150 • written 9.9 years ago by ★ 7.9k
1
vote
1
reply
6.2k
views
Error trying to install GenomicRanges
cummerbund rtracklayer genomicranges s4vectors iranges
updated 10.1 years ago by ★ 6.6k • written 10.1 years ago by • 0
0
votes
0
replies
6.0k
views
Reading GFF files into R and GenomeGraphs
Coverage Annotation Visualization convert GLAD GenomeGraphs rtracklayer IRanges Coverage
16.6 years ago Michael Dondrup ▴ 140
4
votes
9
replies
6.0k
views
Is it possible to read bigwig files with rtracklayer over https? Comes down to GenomeInfoDb::seqinfo()
rtracklayer genomeinfodb
9.9 years ago • updated 9.8 years ago Leonardo Collado Torres ★ 1.1k
5
votes
5
replies
5.7k
views
Issues with installation status of R package rtracklayer
rtracklayer Bioconductor
updated 4.1 years ago by 4.3k • written 5.2 years ago by ▴ 840
7
votes
16
replies
5.5k
views
How to extract phastcons score for all protein coding genes and lncRNAs using GenomicScores?
genomicscores granges phastCons100way.UCSC.hg38 r rtracklayer
updated 15 months ago by • 0 • written 6.0 years ago by ▴ 120
3
votes
2
replies
5.5k
views
rtracklayer: how to export gff file with gene names included?
rtracklayer gff
updated 9.0 years ago by ★ 11k • written 9.0 years ago by ▴ 270
5
votes
9
replies
5.5k
views
mm10 phastCons data for use with ATACseqQC
ATACseqQC bsgenome phastcons rtracklayer
updated 8.8 years ago by ★ 1.4k • written 8.8 years ago by ▴ 10
0
votes
4
replies
5.4k
views
Uploading BED file: rtracklayer
rtracklayer rtracklayer
updated 13.8 years ago by ★ 11k • written 13.8 years ago by ▴ 50
3
votes
2
replies
5.1k
views
converting a fasta file to .2bit format
BioStrings rtracklayer
updated 7.4 years ago by 16k • written 7.4 years ago by ▴ 10
2
votes
8
replies
5.1k
views
"minfi" loading problem because of couldn't "bumphunter" load
bumphunter minfi loading error rtracklayer
updated 8.8 years ago by • 0 • written 8.8 years ago by ▴ 10
2
votes
8
replies
4.8k
views
Unable to load/install rtracklayer (v1.33.2) on OS X (possibly SSL-related?)
rtracklayer bioc-devel ssl openssl
updated 9.8 years ago by ★ 11k • written 9.8 years ago by ▴ 760
3
votes
15
replies
4.5k
views
(Big)wig file of complete chromosome
bigwig rtracklayer import granges grangeslist
updated 8.6 years ago by ★ 11k • written 8.6 years ago by ★ 1.5k
2
votes
3
replies
4.5k
views
rtracklayer::lifOver one-to-many regions and not match UCSC
rtracklayer liftover bioconductor R
updated 8.6 years ago by ★ 11k • written 8.6 years ago by • 0
0
votes
18
replies
4.3k
views
problem installing ENmix package
ENmix Bioconductor rtracklayer
written 5.0 years ago by • 0
0
votes
3
replies
4.2k
views
UCSC: convert from hg18 to hg19 - rtracklayer?
rtracklayer rtracklayer
updated 14.8 years ago by ★ 11k • written 14.8 years ago by ★ 1.1k
0
votes
14
replies
4.2k
views
Genome Browser and R
rtracklayer rtracklayer
12.4 years ago khadeeja ismail ▴ 400
0
votes
8
replies
4.0k
views
views on Rle using GRanges object
RNASeq Coverage GO rtracklayer RNASeq Coverage GO rtracklayer
updated 14.6 years ago by 16k • written 14.6 years ago by ▴ 740
0
votes
3
replies
3.9k
views
Trying to use the liftOver function from the rtracklayer package in R 2.14.0
PROcess rtracklayer bumphunter PROcess rtracklayer bumphunter
updated 14.2 years ago by ★ 11k • written 14.3 years ago by ★ 1.1k
0
votes
12
replies
3.9k
views
how to use rtracklayer to retrieve sequence of list of coordinates
rtracklayer rtracklayer
updated 16.0 years ago by ★ 13k • written 16.0 years ago by ▴ 220
2
votes
6
replies
3.8k
views
[rtracklayer] Error in .local(con, format, text, ...) : unused argument (asRangedData = FALSE)
software error rtracklayer
updated 10.2 years ago by ★ 11k • written 10.2 years ago by ▴ 130
1
vote
4
replies
3.8k
views
Import Chain - Cannot Import Chain File
rtracklayer
updated 5.2 years ago by ▴ 20 • written 7.6 years ago by • 0
1
vote
2
replies
3.7k
views
How to convert bedgraph to wig
rtracklayer genomicranges
updated 7.3 years ago by ★ 11k • written 7.3 years ago by • 0
6
votes
7
replies
3.7k
views
Error: Failed to set session genome to...
gviz rtracklayer
updated 10.5 years ago by ★ 1.6k • written 10.8 years ago by ▴ 140
1
vote
4
replies
3.7k
views
rtracklayer::import()-ing .bed.gz files from a URL
rtracklayer import bed
updated 10.0 years ago by ★ 11k • written 10.0 years ago by ▴ 760
2
votes
6
replies
3.6k
views
rtracklayer: error in importing bigwig file in r in windows
rtracklayer bigwig file
updated 4.4 years ago by ★ 1.1k • written 6.0 years ago by ▴ 10
2
votes
10
replies
3.6k
views
tracklayer - browserSession() Infinite Recursion Error
rtracklayer ucsc
10.7 years ago andrew.j.skelton73 ▴ 370
0
votes
2
replies
3.5k
views
rtracklayer /GRange object to BED format?
granges rtracklayer
updated 10.0 years ago by ★ 11k • written 10.0 years ago by ▴ 80
0
votes
5
replies
3.5k
views
Rtracklayer not able to set session genome to mm9 using US server. hg19 and european server are working
rtracklayer mm9 ucsc
updated 9.7 years ago by 25k • written 10.8 years ago by • 0
0
votes
6
replies
3.5k
views
Problem with importing bigwig files generated in galaxy into R
import.bw rtracklayer
updated 10.8 years ago by ★ 11k • written 10.8 years ago by ▴ 150
2
votes
3
replies
3.3k
views
Packages dependent on rtracklayer fail: ERROR: lazy loading failed, unable to load shared object rtracklayer.so
SingleCellMultiModal ensembldb rtracklayer Annotation
updated 3.1 years ago by • 0 • written 3.3 years ago by ▴ 10
1
vote
1
reply
3.3k
views
Rtracklayer exporting Granges object as bigwig error: Features cannot overlap
rtracklayer genomicranges granges
updated 5.9 years ago by ★ 11k • written 5.9 years ago by ▴ 20
8
votes
5
replies
3.3k
views
import wig to coverage
rtracklayer granges import.wig
updated 11.1 years ago by 16k • written 11.1 years ago by ▴ 140
1
vote
10
replies
3.3k
views
rtracklayer export bedGraph cannot be loaded into UCSC
rtracklayer
updated 7.5 years ago by ★ 11k • written 7.5 years ago by ▴ 260
3
votes
9
replies
3.3k
views
export.bw produces enormous files (10^5 times bigger than they should be)
rtracklayer bigwig
updated 10.1 years ago by ▴ 30 • written 10.1 years ago by ▴ 30
0
votes
8
replies
3.2k
views
rtracklayer bigWig import fails with "'ranges' must have the length of the object to construct"
rtracklayer
updated 3.4 years ago by • 0 • written 3.6 years ago by • 0
2
votes
3
replies
3.2k
views
import.bed fails on bed file with no scores
rtracklayer import bed files
9.9 years ago jmr • 0
0
votes
1
reply
3.1k
views
Problem with importing bigWig file from GEO with rtracklayer?
rtracklayer rtracklayer
updated 12.6 years ago by ★ 1.6k • written 12.6 years ago by ▴ 260
5
votes
3
replies
3.0k
views
Feature types in TxDb objects
GenomicFeatures rtracklayer
11.0 years ago • updated 10.9 years ago Thomas Girke ★ 1.7k
2
votes
4
replies
3.0k
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 8.2 years ago by ★ 11k • written 8.2 years ago by ▴ 30
2
votes
3
replies
3.0k
views
liftOver bug, reproducible
liftOver rtracklayer
updated 5.1 years ago by 68k • written 5.1 years ago by ▴ 30
0
votes
2
replies
3.0k
views
R/Rstudio: using rtracklayer to import bigwig files from http works with MacOS but not with Windows
import.bw rtracklayer Windows http
4.3 years ago sla • 0
262 results • Page 1 of 6
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Replies
Comment: GSEA error by Adithi • 0
Thank you so much. That makes perfect sense to me. I will work on this.
Comment: tximeta cannot open annotation gtf? by Michael Love 43k
Yes, so this is the same type of error you would get if you tried to assemble a *SummarizedExperiment* manually with tximport + GTF process…
Answer: tximeta cannot open annotation gtf? by ATpoint ★ 5.0k
> Timeout of 60 seconds was reached You have to increase the default timeout limits for downloads, `options(timeout=3600)`. GENCODE serve…
Answer: GSEA error by James W. MacDonald 68k
At a very high level, the way non-model organisms are annotated is by using blast to find orthologs in other species that are well annotate…
Comment: Unable to find ENTREZ IDs by Adithi • 0
Hi James, Thank you so much for your reply. My main goal is to find ortholog genes from chinese hamster gene symbols to mouse gene symbols…
Votes
Answer: GSEA error
Answer: OrgDb for maize
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
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