Showing : rtracklayer • reset
9
votes
38
replies
8.9k
views
manipulate bedpe format files
GRanges bedpe structural variants rtracklayer
written 9.1 years ago by ▴ 200
28
votes
25
replies
6.6k
views
[FIXED] Error in Gviz (actually, rtracklayer) | IdeogramTrack
Gviz rtracklayer
updated 7.7 years ago by ▴ 10 • written 8.1 years ago by ▴ 100
0
votes
18
replies
3.3k
views
problem installing ENmix package
ENmix Bioconductor rtracklayer
written 4.0 years ago by • 0
7
votes
16
replies
4.3k
views
How to extract phastcons score for all protein coding genes and lncRNAs using GenomicScores?
genomicscores granges phastCons100way.UCSC.hg38 r rtracklayer
updated 4 months ago by • 0 • written 5.0 years ago by ▴ 120
3
votes
15
replies
3.7k
views
(Big)wig file of complete chromosome
bigwig rtracklayer import granges grangeslist
updated 7.6 years ago by ★ 11k • written 7.6 years ago by ★ 1.5k
0
votes
14
replies
3.0k
views
Genome Browser and R
rtracklayer rtracklayer
11.4 years ago khadeeja ismail ▴ 400
0
votes
12
replies
3.3k
views
how to use rtracklayer to retrieve sequence of list of coordinates
rtracklayer rtracklayer
updated 15.1 years ago by ★ 13k • written 15.1 years ago by ▴ 220
1
vote
12
replies
6.5k
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
6.3 years ago ruan_wei_dong • 0
1
vote
10
replies
2.7k
views
rtracklayer export bedGraph cannot be loaded into UCSC
rtracklayer
updated 6.5 years ago by ★ 11k • written 6.5 years ago by ▴ 260
1
vote
10
replies
2.4k
views
UCSC web service API
txdb.hsapiens.ucsc.hg19.knowngene rtracklayer
updated 8.7 years ago by 25k • written 8.7 years ago by ▴ 290
2
votes
10
replies
3.0k
views
tracklayer - browserSession() Infinite Recursion Error
rtracklayer ucsc
9.8 years ago andrew.j.skelton73 ▴ 370
4
votes
9
replies
5.2k
views
Is it possible to read bigwig files with rtracklayer over https? Comes down to GenomeInfoDb::seqinfo()
rtracklayer genomeinfodb
8.9 years ago Leonardo Collado Torres ★ 1.1k
9
votes
9
replies
6.1k
views
Importing a BED file with floating point scores?
rtracklayer bed
updated 4.1 years ago by ▴ 150 • written 8.9 years ago by ★ 7.9k
5
votes
9
replies
4.6k
views
mm10 phastCons data for use with ATACseqQC
ATACseqQC bsgenome phastcons rtracklayer
updated 7.8 years ago by ★ 1.3k • written 7.8 years ago by ▴ 10
3
votes
9
replies
2.7k
views
export.bw produces enormous files (10^5 times bigger than they should be)
rtracklayer bigwig
updated 9.1 years ago by ▴ 30 • written 9.1 years ago by ▴ 30
2
votes
8
replies
4.2k
views
Unable to load/install rtracklayer (v1.33.2) on OS X (possibly SSL-related?)
rtracklayer bioc-devel ssl openssl
updated 8.8 years ago by ★ 11k • written 8.8 years ago by ▴ 750
0
votes
8
replies
2.6k
views
rtracklayer bigWig import fails with "'ranges' must have the length of the object to construct"
rtracklayer
updated 2.4 years ago by • 0 • written 2.7 years ago by • 0
2
votes
8
replies
4.6k
views
"minfi" loading problem because of couldn't "bumphunter" load
bumphunter minfi loading error rtracklayer
updated 7.8 years ago by • 0 • written 7.9 years ago by ▴ 10
0
votes
8
replies
3.6k
views
views on Rle using GRanges object
RNASeq Coverage GO rtracklayer RNASeq Coverage GO rtracklayer
updated 13.6 years ago by 16k • written 13.6 years ago by ▴ 740
2
votes
7
replies
1.0k
views
distanceToNearest
rtracklayer ranges distanceToNearest
14 months ago robjohn70000 • 0
2
votes
7
replies
1.4k
views
How to set track attributes in rtracklayer
rtracklayer browserView browserSession
updated 6.0 years ago by ★ 11k • written 6.0 years ago by ▴ 100
0
votes
7
replies
1.8k
views
export Views of Rle in rtracklayer
Coverage rtracklayer Coverage rtracklayer
updated 13.3 years ago by ★ 11k • written 13.3 years ago by ▴ 190
0
votes
7
replies
1.9k
views
read gz compressed wig files?
Cancer rtracklayer Cancer rtracklayer
updated 14.0 years ago by ★ 13k • written 14.0 years ago by ▴ 50
0
votes
7
replies
1.5k
views
rtracklayer cannot export empty BED file
rtracklayer bed genomicranges
updated 6.3 years ago by ★ 11k • written 6.3 years ago by ▴ 100
6
votes
7
replies
3.4k
views
Error: Failed to set session genome to...
gviz rtracklayer
updated 9.5 years ago by ★ 1.6k • written 9.8 years ago by ▴ 140
0
votes
6
replies
2.3k
views
Advice on reading big BED/BAM and ChIP-seq quality control
GO rtracklayer Rsamtools GO rtracklayer Rsamtools
updated 11.8 years ago by ▴ 350 • written 11.8 years ago by ▴ 240
1
vote
6
replies
1.8k
views
"rtracklayer" compilation error
rtracklayer
updated 8.7 years ago by ★ 6.6k • written 8.7 years ago by ▴ 120
0
votes
6
replies
2.3k
views
rtracklayer issue: Tracks don't show up
rtracklayer bug session
updated 9.9 years ago by ★ 11k • written 9.9 years ago by • 0
0
votes
6
replies
2.2k
views
IdeogramTrack and bigWig file errors in Gviz
ChIPSeq GO rtracklayer CAMERA chipseq Gviz ChIPSeq GO rtracklayer CAMERA chipseq Gviz
updated 11.9 years ago by ▴ 750 • written 11.9 years ago by ★ 13k
0
votes
6
replies
1.8k
views
load failed for 'Rlibstree'
hgu133plus2 rtracklayer hgu133plus2 rtracklayer
updated 14.9 years ago by ★ 7.4k • written 14.9 years ago by ★ 1.1k
0
votes
6
replies
1.3k
views
rtracklayer laying a track
rtracklayer rtracklayer
updated 13.2 years ago by ★ 11k • written 13.2 years ago by ★ 13k
2
votes
6
replies
2.9k
views
rtracklayer: error in importing bigwig file in r in windows
rtracklayer bigwig file
updated 3.5 years ago by ★ 1.1k • written 5.0 years ago by ▴ 10
3
votes
6
replies
2.3k
views
Issue with UCSC and rtracklayer: 'names' attribute [210] must be the same length as the vector [209]
rtracklayer ucsc ensgene
updated 6.9 years ago by ▴ 10 • written 6.9 years ago by • 0
0
votes
6
replies
2.5k
views
Add columns to granges object that sum score around range
R Grang r granges rtracklayer
updated 7.2 years ago by ★ 11k • written 7.2 years ago by ▴ 20
0
votes
6
replies
1.9k
views
GenomicFeatures: makeTranscriptDbFromUCSC on "refGene" supported?
rtracklayer GenomicFeatures rtracklayer GenomicFeatures
updated 14.7 years ago by 6.7k • written 14.7 years ago by ▴ 50
0
votes
6
replies
1.8k
views
rtracklayer: Problems running vignette
rtracklayer rtracklayer
updated 15.8 years ago by ▴ 620 • written 15.8 years ago by ▴ 150
2
votes
6
replies
3.4k
views
[rtracklayer] Error in .local(con, format, text, ...) : unused argument (asRangedData = FALSE)
software error rtracklayer
updated 9.2 years ago by ★ 11k • written 9.2 years ago by ▴ 130
0
votes
6
replies
3.0k
views
Problem with importing bigwig files generated in galaxy into R
import.bw rtracklayer
updated 9.8 years ago by ★ 11k • written 9.8 years ago by ▴ 150
0
votes
5
replies
2.0k
views
BED15 format for rtracklayer
Microarray Visualization rtracklayer Microarray Visualization rtracklayer
updated 15.6 years ago by ▴ 620 • written 15.6 years ago by ▴ 500
0
votes
5
replies
3.2k
views
Rtracklayer not able to set session genome to mm9 using US server. hg19 and european server are working
rtracklayer mm9 ucsc
updated 8.7 years ago by 25k • written 9.9 years ago by • 0
0
votes
5
replies
690
views
Help using rtracklayer for gene ID extraction
rtracklayer
written 3 months ago by • 0
0
votes
5
replies
1.5k
views
rtracklayer error?
Cancer rtracklayer Cancer rtracklayer
11.6 years ago Janet Young ▴ 740
5
votes
5
replies
4.5k
views
Issues with installation status of R package rtracklayer
rtracklayer Bioconductor
updated 3.1 years ago by 4.1k • written 4.2 years ago by ▴ 840
0
votes
5
replies
2.6k
views
bigBed support in rtracklayer
rtracklayer rtracklayer
updated 8.8 years ago by ▴ 30 • written 12.3 years ago by ★ 4.2k
0
votes
5
replies
1.5k
views
rtracklayer export fails
rtracklayer rtracklayer
updated 14.1 years ago by 6.7k • written 14.1 years ago by ▴ 550
8
votes
5
replies
3.0k
views
import wig to coverage
rtracklayer granges import.wig
updated 10.1 years ago by 16k • written 10.1 years ago by ▴ 140
0
votes
5
replies
1.8k
views
Finding my un-counted reads
Sequencing rtracklayer ShortRead GenomicRanges Sequencing rtracklayer ShortRead
updated 11.6 years ago by ★ 6.8k • written 11.6 years ago by ▴ 300
0
votes
5
replies
1.9k
views
How to plot microRNA chromosome location
miRNA ideogram GenomeGraphs rtracklayer microRNA miRNA ideogram GenomeGraphs rtracklayer
updated 16.4 years ago by ▴ 40 • written 16.4 years ago by ▴ 620
1
vote
5
replies
5.7k
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 4.3 years ago by ★ 11k • written 4.3 years ago by • 0
4
votes
5
replies
8.0k
views
Convert an R data.frame to a bed file in R
rtracklayer R bed
updated 2.2 years ago by • 0 • written 2.6 years ago by ▴ 50
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Exact OMCIS reproduction down to the values without code and software version is borderline impossible. Either use the values as provided o…
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You've got it backwards. It should be ``` adult_res_df$symbol <- mapIds(org.Rn.eg.db, keys = rownames(adult_res_df), column = "ENSEMBL"…
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Alternatively, you could have added a column with the common gene names. Assuming your dataframe `df` was created using `DESeq()`, somethin…
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It appears that 'negative regulation of glycogen biosynthesis' has an 'is a' relationship with 'glycogen biosynthetic process' https://www.…
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Thank you, this was super useful!
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