Showing : rtracklayer • reset
0
votes
18
replies
1.7k
views
problem installing ENmix package
ENmix Bioconductor rtracklayer
updated 25 days ago by • 0 • written 2.6 years ago by • 0
0
votes
0
replies
330
views
Problem with loading rtracklayer
rtracklayer
updated 7 months ago by 3.5k • written 7 months ago by • 0
0
votes
0
replies
304
views
rtracklayer ignores ranges argument
rtracklayer
7 months ago Kyle • 0
0
votes
0
replies
285
views
Error importing UCSC phastCons annotation in BigWig format
GenomicRanges rtracklayer
8 months ago Delta._.43 ▴ 20
2
votes
3
replies
1.1k
views
Packages dependent on rtracklayer fail: ERROR: lazy loading failed, unable to load shared object rtracklayer.so
SingleCellMultiModal ensembldb rtracklayer Annotation
updated 8 months ago by • 0 • written 10 months ago by ▴ 10
3
votes
4
replies
755
views
Convert a bed file to bigBed with rtracklayer
bed bigBed rtracklayer ucsc
10 months ago L ▴ 50
1
vote
3
replies
533
views
rtacklayer::import.bed silently adds 1 to the start coordinates
rtracklayer
updated 12 months ago by ★ 3.4k • written 12 months ago by ▴ 30
2
votes
2
replies
521
views
[BigWigFile] import as RLE vs default and length comparaison
BSgenome.Hsapiens.UCSC.hg19 rtracklayer AnnotationHub
13 months ago • updated 12 months ago Lenny186 • 0
0
votes
1
reply
352
views
rtracklayer import only subset of ranges
rtracklayer
updated 13 months ago by 3.5k • written 13 months ago by ▴ 90
4
votes
5
replies
3.5k
views
Convert an R data.frame to a bed file in R
rtracklayer R bed
updated 8 months ago by • 0 • written 14 months ago by ▴ 50
0
votes
8
replies
1.2k
views
rtracklayer bigWig import fails with "'ranges' must have the length of the object to construct"
rtracklayer
updated 11 months ago by • 0 • written 14 months ago by • 0
0
votes
1
reply
557
views
Can´t install GenomicRanges and rtracklayer
rtracklayer GenomicRanges Installation
updated 15 months ago by 63k • written 15 months ago by • 0
1
vote
2
replies
1.0k
views
Extracting Score/Coverage From GRange Object
IRanges rtracklayer GenomicRanges
17 months ago vanbelj ▴ 20
0
votes
1
reply
510
views
Rtracklayer
rtracklayer RNASeq gff
updated 18 months ago by 63k • written 18 months ago by • 0
1
vote
4
replies
790
views
seqinfo got changed after `library(rtracklayer)`
rtracklayer GenomeInfoDb
21 months ago Ge Tan ▴ 20
0
votes
2
replies
1.5k
views
R/Rstudio: using rtracklayer to import bigwig files from http works with MacOS but not with Windows
import.bw rtracklayer Windows http
22 months ago sla • 0
0
votes
4
replies
1.1k
views
rtracklayer can't access hg38 on UCSC?
rtracklayer Visualization
updated 22 months ago by 16k • written 22 months ago by • 0
0
votes
0
replies
395
views
Bug in rtracklayer
rtracklayer
22 months ago You • 0
2
votes
4
replies
842
views
default behaviour of import.bw
import.bw rtracklayer
23 months ago • updated 22 months ago Yixin • 0
0
votes
2
replies
767
views
Failed to get promoters using promoters() in R 4.0.3.
promoter GenomicRanges rtracklayer GRanges
2.1 years ago • updated 2.0 years ago Arslan • 0
0
votes
0
replies
450
views
rtracklayer v 1.53.1 refuses to load xz-compressed files.
rtracklayer
2.1 years ago Charles • 0
2
votes
3
replies
1.2k
views
Importing a bed file
rtracklayer
2.3 years ago Skylar • 0
0
votes
1
reply
916
views
Bug in rtracklayer liftOver function
rtracklayer
updated 2.4 years ago by 63k • written 2.4 years ago by • 0
2
votes
3
replies
1.3k
views
liftOver bug, reproducible
liftOver rtracklayer
updated 2.6 years ago by 63k • written 2.6 years ago by ▴ 30
5
votes
5
replies
2.6k
views
Issues with installation status of R package rtracklayer
rtracklayer Bioconductor
updated 19 months ago by 3.5k • written 2.7 years ago by ▴ 810
1
vote
5
replies
3.0k
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 2.8 years ago by 11k • written 2.8 years ago by • 0
2
votes
0
replies
731
views
How to liftOver Paired BED (bedpe) data
rtracklayer
2.8 years ago Mikhail Dozmorov ▴ 30
9
votes
9
replies
4.7k
views
Importing a BED file with floating point scores?
rtracklayer bed
updated 2.6 years ago by ▴ 90 • written 7.5 years ago by 7.8k
0
votes
0
replies
506
views
Can you compute summary stats of coverage directly when importing using rtracklayer?
Coverage rtracklayer
2.9 years ago David • 0
2
votes
2
replies
933
views
How to access metadata of GAlignments objects
rtracklayer Rsamtools GAlignments GRanges metadata
updated 3.4 years ago by 16k • written 3.4 years ago by ▴ 10
1
vote
1
reply
1.7k
views
Rtracklayer exporting Granges object as bigwig error: Features cannot overlap
rtracklayer genomicranges granges
updated 3.5 years ago by 11k • written 3.5 years ago by ▴ 20
7
votes
13
replies
2.0k
views
How to extract phastcons score for all protein coding genes and lncRNAs using GenomicScores?
genomicscores granges phastCons100way.UCSC.hg38 r rtracklayer
updated 3.5 years ago by ★ 3.0k • written 3.5 years ago by ▴ 110
2
votes
6
replies
1.5k
views
rtracklayer: error in importing bigwig file in r in windows
rtracklayer bigwig file
updated 24 months ago by ★ 1.0k • written 3.6 years ago by ▴ 10
0
votes
1
reply
597
views
getting snp and restriction Enzyme site from ucsc genome browswer
rtracklayer
updated 3.6 years ago by 11k • written 3.6 years ago by • 0
1
vote
1
reply
485
views
Rtracklayer fails to export TxDb as GFF3 without CDS
rtracklayer
updated 3.6 years ago by 11k • written 3.6 years ago by • 0
0
votes
0
replies
852
views
Rsamtools / rtracklayer creating csi index for BAM files
rsamtools rtracklayer
3.8 years ago ATpoint ★ 3.4k
1
vote
2
replies
656
views
rtracklayer::export empty score
rtracklayer
updated 3.8 years ago by 11k • written 3.9 years ago by • 0
0
votes
4
replies
1.3k
views
IRanges: solving row 5: range cannot be determined from the supplied arguments (too many NAs)
IRanges rtracklayer
updated 3.9 years ago by 63k • written 3.9 years ago by ▴ 10
0
votes
0
replies
565
views
DMDeepm6A: solve_user_SEW0", start, end, width, PACKAGE = "IRanges
rtracklayer IRanges DMDeepm6A
3.9 years ago jovel_juan ▴ 10
2
votes
3
replies
1.2k
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 4.2 years ago by 13k • written 4.2 years ago by ▴ 30
0
votes
1
reply
691
views
rtracklayer import bigwig error
rtracklayer
updated 8 months ago by ▴ 20 • written 4.2 years ago by ▴ 100
0
votes
1
reply
912
views
create a full TXDB object from GFF3 data for a non-system organism / denovo assembly
GenomicFeatures rtracklayer
updated 4.4 years ago by 16k • written 4.4 years ago by ▴ 10
4
votes
1
reply
880
views
What's the recommended way to overwrite the seqinfo of a GRanges?
GRanges seqinfo import.bw BigWigFile rtracklayer
updated 4.5 years ago by 11k • written 4.5 years ago by ▴ 170
2
votes
7
replies
916
views
How to set track attributes in rtracklayer
rtracklayer browserView browserSession
updated 4.6 years ago by 11k • written 4.6 years ago by ▴ 80
0
votes
4
replies
898
views
Change sign from Granges scores to visualize negative strand data
granges rtracklayer
updated 4.6 years ago by 63k • written 4.6 years ago by • 0
0
votes
1
reply
869
views
How to filter gff based on certain gene list in rtracklayer?
rtracklayer gff filter
updated 4.6 years ago by 11k • written 4.6 years ago by • 0
3
votes
3
replies
1.1k
views
Bug in rtracklayer::import of amino acid fasta sequences
rtracklayer fasta import Biostrings
updated 4.7 years ago by 11k • written 4.7 years ago by ▴ 120
2
votes
1
reply
1.3k
views
rtracklayer BigBed format
ngs rtracklayer bigbed
updated 4.7 years ago by 11k • written 4.7 years ago by ▴ 80
1
vote
12
replies
4.9k
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
4.8 years ago ruan_wei_dong • 0
0
votes
1
reply
1.0k
views
rtracklayer::Problem with export.bw of GRanges object created by unlisted after liftover from mm9 to mm10 of wig file
rtracklayer export.bw liftover
updated 4.8 years ago by 11k • written 4.8 years ago by ▴ 20
50 results • Page 1 of 1
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Replies
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Michael Love 40k
Oh, I see. If you can't use counts + offset then I prefer lengthScaledTPM to DESeq2, i.e. `txi$counts` to `DESeqDataSetFromMatrix()`. So …
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Christian • 0
I´m sorry causing confusion here, but the gene matrices I refer to are actually obtained via https://nf-co.re/rnaseq. The problem with the…
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Michael Love 40k
For the reasons outlined in the Soneson paper, I'd prefer this pipeline: https://nf-co.re/rnaseq You cannot use these scaled TPM approach…
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Christian • 0
I get your point as we already starting with TPM. This was more to clarify that I understand the principle correctly. However, further I´m…
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Michael Love 40k
I do not follow why calculate TPM from something derived from TPM.
Votes
batch effect : comBat or blocking in limma ?
Batch correction and repeated measures
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
Comment: Phenotype effect - building a contrast matrix - grouping vs interaction
Answer: Batch correction and repeated measures
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