Showing : rtracklayer • reset
0
votes
4
replies
9.4k
views
rtracklayer importing gtf files
rtracklayer DESeq GenomicRanges rtracklayer DESeq GenomicRanges
updated 12.1 years ago by ★ 11k • written 12.1 years ago by ★ 13k
9
votes
38
replies
9.2k
views
manipulate bedpe format files
GRanges bedpe structural variants rtracklayer
written 9.2 years ago by ▴ 200
4
votes
5
replies
8.3k
views
Convert an R data.frame to a bed file in R
rtracklayer R bed
updated 2.3 years ago by • 0 • written 2.7 years ago by ▴ 50
0
votes
3
replies
8.2k
views
rtracklayer gff import
rtracklayer rtracklayer
updated 14.0 years ago by ★ 11k • written 14.0 years ago by ▴ 110
2
votes
4
replies
7.3k
views
rtracklayer export GRangesList as gtf and change attributes
grangeslist rtracklayer
updated 2.8 years ago by • 0 • written 9.8 years ago by ▴ 90
28
votes
25
replies
6.7k
views
[FIXED] Error in Gviz (actually, rtracklayer) | IdeogramTrack
Gviz rtracklayer
updated 7.8 years ago by ▴ 10 • written 8.2 years ago by ▴ 100
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
6.4 years ago ruan_wei_dong • 0
9
votes
9
replies
6.2k
views
Importing a BED file with floating point scores?
rtracklayer bed
updated 4.2 years ago by ▴ 150 • written 9.0 years ago by ★ 7.9k
1
vote
5
replies
5.9k
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 4.4 years ago by ★ 11k • written 4.4 years ago by • 0
1
vote
1
reply
5.8k
views
Error trying to install GenomicRanges
cummerbund rtracklayer genomicranges s4vectors iranges
updated 9.3 years ago by ★ 6.6k • written 9.3 years ago by • 0
0
votes
0
replies
5.6k
views
Reading GFF files into R and GenomeGraphs
Coverage Annotation Visualization convert GLAD GenomeGraphs rtracklayer IRanges Coverage
15.7 years ago Michael Dondrup ▴ 140
4
votes
9
replies
5.3k
views
Is it possible to read bigwig files with rtracklayer over https? Comes down to GenomeInfoDb::seqinfo()
rtracklayer genomeinfodb
9.0 years ago Leonardo Collado Torres ★ 1.1k
3
votes
2
replies
5.0k
views
rtracklayer: how to export gff file with gene names included?
rtracklayer gff
updated 8.1 years ago by ★ 11k • written 8.1 years ago by ▴ 260
3
votes
2
replies
4.7k
views
converting a fasta file to .2bit format
BioStrings rtracklayer
updated 6.5 years ago by 16k • written 6.5 years ago by ▴ 10
0
votes
4
replies
4.7k
views
Uploading BED file: rtracklayer
rtracklayer rtracklayer
updated 12.9 years ago by ★ 11k • written 12.9 years ago by ▴ 50
2
votes
8
replies
4.7k
views
"minfi" loading problem because of couldn't "bumphunter" load
bumphunter minfi loading error rtracklayer
updated 7.9 years ago by • 0 • written 8.0 years ago by ▴ 10
5
votes
9
replies
4.7k
views
mm10 phastCons data for use with ATACseqQC
ATACseqQC bsgenome phastcons rtracklayer
updated 7.9 years ago by ★ 1.3k • written 7.9 years ago by ▴ 10
5
votes
5
replies
4.6k
views
Issues with installation status of R package rtracklayer
rtracklayer Bioconductor
updated 3.2 years ago by 4.1k • written 4.3 years ago by ▴ 840
7
votes
16
replies
4.4k
views
How to extract phastcons score for all protein coding genes and lncRNAs using GenomicScores?
genomicscores granges phastCons100way.UCSC.hg38 r rtracklayer
updated 5 months ago by • 0 • written 5.1 years ago by ▴ 120
2
votes
8
replies
4.3k
views
Unable to load/install rtracklayer (v1.33.2) on OS X (possibly SSL-related?)
rtracklayer bioc-devel ssl openssl
updated 8.9 years ago by ★ 11k • written 8.9 years ago by ▴ 750
0
votes
3
replies
3.9k
views
UCSC: convert from hg18 to hg19 - rtracklayer?
rtracklayer rtracklayer
updated 14.0 years ago by ★ 11k • written 14.0 years ago by ★ 1.1k
3
votes
15
replies
3.7k
views
(Big)wig file of complete chromosome
bigwig rtracklayer import granges grangeslist
updated 7.7 years ago by ★ 11k • written 7.7 years ago by ★ 1.5k
0
votes
8
replies
3.7k
views
views on Rle using GRanges object
RNASeq Coverage GO rtracklayer RNASeq Coverage GO rtracklayer
updated 13.7 years ago by 16k • written 13.7 years ago by ▴ 740
0
votes
3
replies
3.6k
views
Trying to use the liftOver function from the rtracklayer package in R 2.14.0
PROcess rtracklayer bumphunter PROcess rtracklayer bumphunter
updated 13.4 years ago by ★ 11k • written 13.4 years ago by ★ 1.1k
2
votes
3
replies
3.5k
views
rtracklayer::lifOver one-to-many regions and not match UCSC
rtracklayer liftover bioconductor R
updated 7.7 years ago by ★ 11k • written 7.7 years ago by • 0
2
votes
6
replies
3.4k
views
[rtracklayer] Error in .local(con, format, text, ...) : unused argument (asRangedData = FALSE)
software error rtracklayer
updated 9.3 years ago by ★ 11k • written 9.3 years ago by ▴ 130
6
votes
7
replies
3.4k
views
Error: Failed to set session genome to...
gviz rtracklayer
updated 9.6 years ago by ★ 1.6k • written 9.9 years ago by ▴ 140
0
votes
18
replies
3.4k
views
problem installing ENmix package
ENmix Bioconductor rtracklayer
written 4.1 years ago by • 0
0
votes
12
replies
3.4k
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
2
replies
3.3k
views
How to convert bedgraph to wig
rtracklayer genomicranges
updated 6.4 years ago by ★ 11k • written 6.4 years ago by • 0
1
vote
4
replies
3.2k
views
Import Chain - Cannot Import Chain File
rtracklayer
updated 4.3 years ago by ▴ 20 • written 6.7 years ago by • 0
0
votes
2
replies
3.2k
views
rtracklayer /GRange object to BED format?
granges rtracklayer
updated 9.2 years ago by ★ 11k • written 9.2 years ago by ▴ 80
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 8.8 years ago by 25k • written 10.0 years ago by • 0
1
vote
4
replies
3.2k
views
rtracklayer::import()-ing .bed.gz files from a URL
rtracklayer import bed
updated 9.1 years ago by ★ 11k • written 9.1 years ago by ▴ 750
0
votes
14
replies
3.2k
views
Genome Browser and R
rtracklayer rtracklayer
11.5 years ago khadeeja ismail ▴ 400
2
votes
10
replies
3.1k
views
tracklayer - browserSession() Infinite Recursion Error
rtracklayer ucsc
9.9 years ago andrew.j.skelton73 ▴ 370
0
votes
6
replies
3.0k
views
Problem with importing bigwig files generated in galaxy into R
import.bw rtracklayer
updated 9.9 years ago by ★ 11k • written 9.9 years ago by ▴ 150
8
votes
5
replies
3.0k
views
import wig to coverage
rtracklayer granges import.wig
updated 10.2 years ago by 16k • written 10.2 years ago by ▴ 140
1
vote
1
reply
3.0k
views
Rtracklayer exporting Granges object as bigwig error: Features cannot overlap
rtracklayer genomicranges granges
updated 5.0 years ago by ★ 11k • written 5.0 years ago by ▴ 20
2
votes
6
replies
3.0k
views
rtracklayer: error in importing bigwig file in r in windows
rtracklayer bigwig file
updated 3.6 years ago by ★ 1.1k • written 5.1 years ago by ▴ 10
2
votes
3
replies
2.9k
views
import.bed fails on bed file with no scores
rtracklayer import bed files
9.0 years ago jmr • 0
0
votes
1
reply
2.8k
views
Problem with importing bigWig file from GEO with rtracklayer?
rtracklayer rtracklayer
updated 11.7 years ago by ★ 1.6k • written 11.7 years ago by ▴ 260
3
votes
9
replies
2.8k
views
export.bw produces enormous files (10^5 times bigger than they should be)
rtracklayer bigwig
updated 9.2 years ago by ▴ 30 • written 9.2 years ago by ▴ 30
1
vote
10
replies
2.7k
views
rtracklayer export bedGraph cannot be loaded into UCSC
rtracklayer
updated 6.6 years ago by ★ 11k • written 6.6 years ago by ▴ 260
0
votes
8
replies
2.6k
views
rtracklayer bigWig import fails with "'ranges' must have the length of the object to construct"
rtracklayer
updated 2.5 years ago by • 0 • written 2.7 years ago by • 0
2
votes
3
replies
2.6k
views
Packages dependent on rtracklayer fail: ERROR: lazy loading failed, unable to load shared object rtracklayer.so
SingleCellMultiModal ensembldb rtracklayer Annotation
updated 2.2 years ago by • 0 • written 2.4 years ago by ▴ 10
0
votes
5
replies
2.6k
views
bigBed support in rtracklayer
rtracklayer rtracklayer
updated 8.9 years ago by ▴ 30 • written 12.4 years ago by ★ 4.2k
0
votes
2
replies
2.6k
views
Exporting a GenomicRanges object as GTF/GFF file
genomicranges rtracklayer gtf gff export
7.8 years ago rubi ▴ 110
5
votes
3
replies
2.6k
views
Feature types in TxDb objects
GenomicFeatures rtracklayer
10.2 years ago • updated 10.0 years ago Thomas Girke ★ 1.7k
0
votes
0
replies
2.6k
views
How to plot gene on their chromosome?
Annotation Cancer geneplotter idiogram rtracklayer Annotation Cancer geneplotter idiogram
15.9 years ago Martin Morgan 25k
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Comment: DeSeq Strategies for run to run Replication by Michael Love 43k
You shouldn't need to run `DESeq` on the test data, or manually compute normalization factors. ``` dds_test <- ... # create object dds_te…
Answer: Feature Counts - potential bug with outfile.jcounts by Wei Shi ★ 3.6k
We have made significant changes to how featureCounts annotates junctions detected in read mapping results. These updates are included in t…
Comment: How to perform batch correction on scRNA-seq with confounding plate effects? by 瑞宏 • 0
I would like to share my own understanding: in single-cell RNA sequencing (scRNA-seq), batch correction is solely intended to identify the …
Comment: DiffBind can't find a DAR by Mengjun • 0
Additionally, i checked my bigwig in igv, it shows that the ctrl_1 is more like ko_1, and ctrl_2's track is more like ko_2's track. Did an…
Comment: European Bioconductor Conference 2023 planning by ht • 0
Great news about the European Bioconductor Conference 2023 planning! As someone who enjoys statistical computing and bioinformatics, I'm ex…
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Answer: Feature Counts - potential bug with outfile.jcounts
Bioconductor 3.21 is Released!
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