Showing : rtracklayer • reset
0
votes
4
replies
9.0k
views
rtracklayer importing gtf files
rtracklayer DESeq GenomicRanges rtracklayer DESeq GenomicRanges
updated 11.8 years ago by ★ 11k • written 11.8 years ago by ★ 13k
9
votes
38
replies
8.4k
views
manipulate bedpe format files
GRanges bedpe structural variants rtracklayer
written 8.9 years ago by ▴ 200
0
votes
3
replies
7.9k
views
rtracklayer gff import
rtracklayer rtracklayer
updated 13.8 years ago by ★ 11k • written 13.8 years ago by ▴ 110
4
votes
5
replies
7.5k
views
Convert an R data.frame to a bed file in R
rtracklayer R bed
updated 2.0 years ago by • 0 • written 2.5 years ago by ▴ 50
2
votes
4
replies
7.0k
views
rtracklayer export GRangesList as gtf and change attributes
grangeslist rtracklayer
updated 2.6 years ago by • 0 • written 9.5 years ago by ▴ 90
28
votes
25
replies
6.4k
views
[FIXED] Error in Gviz (actually, rtracklayer) | IdeogramTrack
Gviz rtracklayer
updated 7.5 years ago by ▴ 10 • written 7.9 years ago by ▴ 100
1
vote
12
replies
6.3k
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
6.1 years ago ruan_wei_dong • 0
9
votes
9
replies
6.0k
views
Importing a BED file with floating point scores?
rtracklayer bed
updated 3.9 years ago by ▴ 140 • written 8.8 years ago by ★ 7.9k
1
vote
1
reply
5.6k
views
Error trying to install GenomicRanges
cummerbund rtracklayer genomicranges s4vectors iranges
updated 9.0 years ago by ★ 6.6k • written 9.0 years ago by • 0
0
votes
0
replies
5.5k
views
Reading GFF files into R and GenomeGraphs
Coverage Annotation Visualization convert GLAD GenomeGraphs rtracklayer IRanges Coverage
15.4 years ago Michael Dondrup ▴ 140
1
vote
5
replies
5.3k
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 4.1 years ago by ★ 11k • written 4.1 years ago by • 0
4
votes
9
replies
5.1k
views
Is it possible to read bigwig files with rtracklayer over https? Comes down to GenomeInfoDb::seqinfo()
rtracklayer genomeinfodb
8.7 years ago Leonardo Collado Torres ★ 1.1k
3
votes
2
replies
4.8k
views
rtracklayer: how to export gff file with gene names included?
rtracklayer gff
updated 7.8 years ago by ★ 11k • written 7.8 years ago by ▴ 260
0
votes
4
replies
4.5k
views
Uploading BED file: rtracklayer
rtracklayer rtracklayer
updated 12.6 years ago by ★ 11k • written 12.6 years ago by ▴ 50
2
votes
8
replies
4.5k
views
"minfi" loading problem because of couldn't "bumphunter" load
bumphunter minfi loading error rtracklayer
updated 7.7 years ago by • 0 • written 7.7 years ago by ▴ 10
3
votes
2
replies
4.5k
views
converting a fasta file to .2bit format
BioStrings rtracklayer
updated 6.3 years ago by 16k • written 6.3 years ago by ▴ 10
5
votes
9
replies
4.4k
views
mm10 phastCons data for use with ATACseqQC
ATACseqQC bsgenome phastcons rtracklayer
updated 7.7 years ago by ★ 1.3k • written 7.7 years ago by ▴ 10
5
votes
5
replies
4.2k
views
Issues with installation status of R package rtracklayer
rtracklayer Bioconductor
updated 2.9 years ago by 4.1k • written 4.0 years ago by ▴ 840
7
votes
16
replies
4.1k
views
How to extract phastcons score for all protein coding genes and lncRNAs using GenomicScores?
genomicscores granges phastCons100way.UCSC.hg38 r rtracklayer
updated 9 weeks ago by • 0 • written 4.8 years ago by ▴ 120
2
votes
8
replies
4.1k
views
Unable to load/install rtracklayer (v1.33.2) on OS X (possibly SSL-related?)
rtracklayer bioc-devel ssl openssl
updated 8.6 years ago by ★ 11k • written 8.6 years ago by ▴ 740
0
votes
3
replies
3.7k
views
UCSC: convert from hg18 to hg19 - rtracklayer?
rtracklayer rtracklayer
updated 13.7 years ago by ★ 11k • written 13.7 years ago by ★ 1.1k
0
votes
8
replies
3.6k
views
views on Rle using GRanges object
RNASeq Coverage GO rtracklayer RNASeq Coverage GO rtracklayer
updated 13.4 years ago by 16k • written 13.4 years ago by ▴ 740
0
votes
3
replies
3.5k
views
Trying to use the liftOver function from the rtracklayer package in R 2.14.0
PROcess rtracklayer bumphunter PROcess rtracklayer bumphunter
updated 13.1 years ago by ★ 11k • written 13.1 years ago by ★ 1.1k
3
votes
15
replies
3.5k
views
(Big)wig file of complete chromosome
bigwig rtracklayer import granges grangeslist
updated 7.5 years ago by ★ 11k • written 7.5 years ago by ★ 1.5k
2
votes
6
replies
3.3k
views
[rtracklayer] Error in .local(con, format, text, ...) : unused argument (asRangedData = FALSE)
software error rtracklayer
updated 9.0 years ago by ★ 11k • written 9.0 years ago by ▴ 130
2
votes
3
replies
3.3k
views
rtracklayer::lifOver one-to-many regions and not match UCSC
rtracklayer liftover bioconductor R
updated 7.4 years ago by ★ 11k • written 7.4 years ago by • 0
6
votes
7
replies
3.3k
views
Error: Failed to set session genome to...
gviz rtracklayer
updated 9.4 years ago by ★ 1.6k • written 9.7 years ago by ▴ 140
0
votes
12
replies
3.2k
views
how to use rtracklayer to retrieve sequence of list of coordinates
rtracklayer rtracklayer
updated 14.9 years ago by ★ 13k • written 14.9 years ago by ▴ 220
0
votes
18
replies
3.1k
views
problem installing ENmix package
ENmix Bioconductor rtracklayer
written 3.9 years ago by • 0
1
vote
2
replies
3.1k
views
How to convert bedgraph to wig
rtracklayer genomicranges
updated 6.1 years ago by ★ 11k • written 6.1 years ago by • 0
0
votes
5
replies
3.1k
views
Rtracklayer not able to set session genome to mm9 using US server. hg19 and european server are working
rtracklayer mm9 ucsc
updated 8.5 years ago by 25k • written 9.7 years ago by • 0
0
votes
2
replies
3.1k
views
rtracklayer /GRange object to BED format?
granges rtracklayer
updated 8.9 years ago by ★ 11k • written 8.9 years ago by ▴ 80
1
vote
4
replies
3.0k
views
Import Chain - Cannot Import Chain File
rtracklayer
updated 4.1 years ago by ▴ 20 • written 6.4 years ago by • 0
1
vote
4
replies
3.0k
views
rtracklayer::import()-ing .bed.gz files from a URL
rtracklayer import bed
updated 8.8 years ago by ★ 11k • written 8.8 years ago by ▴ 740
2
votes
10
replies
2.9k
views
tracklayer - browserSession() Infinite Recursion Error
rtracklayer ucsc
9.6 years ago andrew.j.skelton73 ▴ 370
0
votes
14
replies
2.9k
views
Genome Browser and R
rtracklayer rtracklayer
11.2 years ago khadeeja ismail ▴ 400
8
votes
5
replies
2.9k
views
import wig to coverage
rtracklayer granges import.wig
updated 10.0 years ago by 16k • written 10.0 years ago by ▴ 140
0
votes
6
replies
2.9k
views
Problem with importing bigwig files generated in galaxy into R
import.bw rtracklayer
updated 9.7 years ago by ★ 11k • written 9.7 years ago by ▴ 150
1
vote
1
reply
2.8k
views
Rtracklayer exporting Granges object as bigwig error: Features cannot overlap
rtracklayer genomicranges granges
updated 4.8 years ago by ★ 11k • written 4.8 years ago by ▴ 20
0
votes
1
reply
2.8k
views
Problem with importing bigWig file from GEO with rtracklayer?
rtracklayer rtracklayer
updated 11.4 years ago by ★ 1.5k • written 11.4 years ago by ▴ 260
2
votes
3
replies
2.7k
views
import.bed fails on bed file with no scores
rtracklayer import bed files
8.8 years ago jmr • 0
2
votes
6
replies
2.7k
views
rtracklayer: error in importing bigwig file in r in windows
rtracklayer bigwig file
updated 3.3 years ago by ★ 1.1k • written 4.9 years ago by ▴ 10
3
votes
9
replies
2.6k
views
export.bw produces enormous files (10^5 times bigger than they should be)
rtracklayer bigwig
updated 9.0 years ago by ▴ 30 • written 9.0 years ago by ▴ 30
1
vote
10
replies
2.5k
views
rtracklayer export bedGraph cannot be loaded into UCSC
rtracklayer
updated 6.4 years ago by ★ 11k • written 6.4 years ago by ▴ 260
0
votes
5
replies
2.5k
views
bigBed support in rtracklayer
rtracklayer rtracklayer
updated 8.6 years ago by ▴ 30 • written 12.1 years ago by ★ 4.2k
0
votes
0
replies
2.5k
views
How to plot gene on their chromosome?
Annotation Cancer geneplotter idiogram rtracklayer Annotation Cancer geneplotter idiogram
15.7 years ago Martin Morgan 25k
0
votes
2
replies
2.5k
views
Exporting a GenomicRanges object as GTF/GFF file
genomicranges rtracklayer gtf gff export
7.6 years ago rubi ▴ 110
5
votes
3
replies
2.5k
views
Feature types in TxDb objects
GenomicFeatures rtracklayer
9.9 years ago • updated 9.8 years ago Thomas Girke ★ 1.7k
0
votes
6
replies
2.5k
views
Add columns to granges object that sum score around range
R Grang r granges rtracklayer
updated 7.0 years ago by ★ 11k • written 7.0 years ago by ▴ 20
1
vote
3
replies
2.4k
views
views on Rle using GRanges object
RNASeq Coverage GO Cancer bridge rtracklayer IRanges RNASeq Coverage GO Cancer bridge
updated 10.8 years ago by 16k • written 10.8 years ago by ★ 11k
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Comment: Problems with oarfish + tximport + swish by Michael Love 43k
Great thanks for posting the issue and sticking with it Annaleigh
Comment: Problems with oarfish + tximport + swish by brown.annaleigh • 0
Awesome possum! Update works!! Thank you so much for the help and guidance!
Comment: Postdoctoral Researcher in Spatial Gene Regulatory Networks underlying Stomatal by iqratechnology4 • 0
Iqra Technology is IT Solutions and Services Company. We are salesforce and Microsoft partner company. https://iqratechnology.com/
Comment: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt? by James W. MacDonald 67k
> BTW, shouldn't you be using keep.lib.sizes = F and re-do the calcNormFactors() after filtering of the dglst low-expression ENSGs, as Gord…
Comment: Problems with oarfish + tximport + swish by Michael Love 43k
Let me see if I can add some code to tximeta to cover this case. I've added an argument `skipRanges` in devel branch which should allow: …
Votes
Answer: Error in download.file for TCGAutils::symbolsToRanges
Answer: Error in download.file for TCGAutils::symbolsToRanges
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
Answer: Limma Interaction Effect with Covariates
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