Showing : rtracklayer • reset
28
votes
25
replies
5.8k
views
[FIXED] Error in Gviz (actually, rtracklayer) | IdeogramTrack
Gviz rtracklayer
updated 6.8 years ago by ▴ 10 • written 7.2 years ago by ▴ 100
9
votes
9
replies
5.4k
views
Importing a BED file with floating point scores?
rtracklayer bed
updated 3.2 years ago by ▴ 120 • written 8.1 years ago by ★ 7.9k
9
votes
38
replies
6.7k
views
manipulate bedpe format files
GRanges bedpe structural variants rtracklayer
written 8.2 years ago by ▴ 190
8
votes
5
replies
2.6k
views
import wig to coverage
rtracklayer granges import.wig
updated 9.2 years ago by 16k • written 9.2 years ago by ▴ 140
7
votes
13
replies
2.5k
views
How to extract phastcons score for all protein coding genes and lncRNAs using GenomicScores?
genomicscores granges phastCons100way.UCSC.hg38 r rtracklayer
updated 4.1 years ago by ★ 3.3k • written 4.1 years ago by ▴ 110
6
votes
7
replies
2.9k
views
Error: Failed to set session genome to...
gviz rtracklayer
updated 8.6 years ago by ★ 1.6k • written 8.9 years ago by ▴ 140
5
votes
3
replies
2.2k
views
Feature types in TxDb objects
GenomicFeatures rtracklayer
9.2 years ago • updated 9.1 years ago Thomas Girke ★ 1.7k
5
votes
9
replies
3.8k
views
mm10 phastCons data for use with ATACseqQC
ATACseqQC bsgenome phastcons rtracklayer
updated 6.9 years ago by ★ 1.3k • written 6.9 years ago by ▴ 10
5
votes
5
replies
3.2k
views
Issues with installation status of R package rtracklayer
rtracklayer Bioconductor
updated 2.2 years ago by 3.8k • written 3.3 years ago by ▴ 830
4
votes
2
replies
990
views
rtracklayer: how to view coordinates that failed liftover?
rtracklayer
updated 7.3 years ago by ★ 11k • written 7.3 years ago by ▴ 30
4
votes
9
replies
4.4k
views
Is it possible to read bigwig files with rtracklayer over https? Comes down to GenomeInfoDb::seqinfo()
rtracklayer genomeinfodb
8.0 years ago Leonardo Collado Torres ★ 1.0k
4
votes
2
replies
864
views
How to extract transcripts from Txdb with length >100
genomicfeatures rtracklayer
updated 7.6 years ago by 25k • written 7.6 years ago by ▴ 50
4
votes
5
replies
5.4k
views
Convert an R data.frame to a bed file in R
rtracklayer R bed
updated 15 months ago by • 0 • written 21 months ago by ▴ 50
4
votes
1
reply
1.1k
views
What's the recommended way to overwrite the seqinfo of a GRanges?
GRanges seqinfo import.bw BigWigFile rtracklayer
updated 5.1 years ago by ★ 11k • written 5.1 years ago by ▴ 170
3
votes
15
replies
3.0k
views
(Big)wig file of complete chromosome
bigwig rtracklayer import granges grangeslist
updated 6.7 years ago by ★ 11k • written 6.7 years ago by ★ 1.5k
3
votes
4
replies
1.1k
views
Convert a bed file to bigBed with rtracklayer
bed bigBed rtracklayer ucsc
17 months ago L ▴ 50
3
votes
2
replies
1.1k
views
Import gff from character?
rtracklayer gff gtf import import.gff3
updated 6.8 years ago by 25k • written 6.8 years ago by ▴ 20
3
votes
2
replies
4.2k
views
rtracklayer: how to export gff file with gene names included?
rtracklayer gff
updated 7.1 years ago by ★ 11k • written 7.1 years ago by ▴ 250
3
votes
4
replies
1.9k
views
rtracklayer import.gff3 function no longer working in R 3.4
rtracklayer import.gff3 gff
updated 7.0 years ago by 25k • written 7.0 years ago by ▴ 180
3
votes
2
replies
957
views
does import.bw with the selection argument take into account strand?
rtracklayer import.bw
updated 7.6 years ago by ★ 11k • written 7.6 years ago by ▴ 170
3
votes
3
replies
1.3k
views
Bug in rtracklayer::import of amino acid fasta sequences
rtracklayer fasta import Biostrings
updated 5.2 years ago by ★ 11k • written 5.2 years ago by ▴ 120
3
votes
2
replies
4.0k
views
converting a fasta file to .2bit format
BioStrings rtracklayer
updated 5.5 years ago by 16k • written 5.5 years ago by ▴ 10
3
votes
6
replies
1.8k
views
Issue with UCSC and rtracklayer: 'names' attribute [210] must be the same length as the vector [209]
rtracklayer ucsc ensgene
updated 6.0 years ago by ▴ 10 • written 6.0 years ago by • 0
3
votes
9
replies
2.2k
views
export.bw produces enormous files (10^5 times bigger than they should be)
rtracklayer bigwig
updated 8.2 years ago by ▴ 30 • written 8.2 years ago by ▴ 30
3
votes
2
replies
934
views
Long elapsed time using `import.gff3` with a toy example
rtracklayer import.gff3
updated 7.4 years ago by 25k • written 7.4 years ago by ▴ 20
2
votes
7
replies
479
views
distanceToNearest
rtracklayer ranges distanceToNearest
3 months ago robjohn70000 • 0
2
votes
3
replies
2.8k
views
rtracklayer::lifOver one-to-many regions and not match UCSC
rtracklayer liftover bioconductor R
updated 6.7 years ago by ★ 11k • written 6.7 years ago by • 0
2
votes
4
replies
1.4k
views
rtracklayer::import.bed does not close connections.
rtracklayer
updated 7.0 years ago by ★ 11k • written 7.0 years ago by ▴ 180
2
votes
2
replies
1.4k
views
Error in normSplitFactor(f, x)
GenomicRanges rtracklayer goseq
updated 6.6 years ago by ★ 11k • written 6.6 years ago by ▴ 10
2
votes
4
replies
2.1k
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 6.4 years ago by ★ 11k • written 6.4 years ago by ▴ 30
2
votes
2
replies
1.2k
views
How to access metadata of GAlignments objects
rtracklayer Rsamtools GAlignments GRanges metadata
updated 3.9 years ago by 16k • written 3.9 years ago by ▴ 10
2
votes
8
replies
4.0k
views
"minfi" loading problem because of couldn't "bumphunter" load
bumphunter minfi loading error rtracklayer
updated 6.9 years ago by • 0 • written 7.0 years ago by ▴ 10
2
votes
1
reply
837
views
Why export of empty GRanges to GFF fails?
rtracklayer
updated 7.1 years ago by ★ 11k • written 7.2 years ago by ▴ 10
2
votes
3
replies
1.6k
views
liftOver bug, reproducible
liftOver rtracklayer
updated 3.2 years ago by 65k • written 3.2 years ago by ▴ 30
2
votes
3
replies
1.7k
views
Importing a bed file
rtracklayer
2.9 years ago Skylar • 0
2
votes
3
replies
1.4k
views
rtracklayer - export.bw bug
bigwig rtracklayer export.bw
updated 7.5 years ago by ★ 11k • written 7.5 years ago by ▴ 20
2
votes
0
replies
958
views
How to liftOver Paired BED (bedpe) data
rtracklayer
3.4 years ago Mikhail Dozmorov ▴ 30
2
votes
3
replies
2.4k
views
import.bed fails on bed file with no scores
rtracklayer import bed files
8.1 years ago • updated 8.0 years ago jmr • 0
2
votes
1
reply
1.1k
views
Strange first_time object in rtracklayer import
rtracklayer bigwig import
updated 7.5 years ago by ★ 11k • written 7.5 years ago by ▴ 10
2
votes
3
replies
1.5k
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 4.8 years ago by ★ 13k • written 4.8 years ago by ▴ 30
2
votes
6
replies
1.9k
views
rtracklayer: error in importing bigwig file in r in windows
rtracklayer bigwig file
updated 2.6 years ago by ★ 1.0k • written 4.1 years ago by ▴ 10
2
votes
1
reply
1.5k
views
rtracklayer BigBed format
ngs rtracklayer bigbed
updated 5.3 years ago by ★ 11k • written 5.3 years ago by ▴ 100
2
votes
8
replies
3.5k
views
Unable to load/install rtracklayer (v1.33.2) on OS X (possibly SSL-related?)
rtracklayer bioc-devel ssl openssl
updated 7.9 years ago by ★ 11k • written 7.9 years ago by ▴ 740
2
votes
1
reply
1.1k
views
Obsolete use of AC_INIT macro
rtracklayer
updated 8.0 years ago by ★ 11k • written 8.0 years ago by ▴ 180
2
votes
6
replies
3.0k
views
[rtracklayer] Error in .local(con, format, text, ...) : unused argument (asRangedData = FALSE)
software error rtracklayer
updated 8.3 years ago by ★ 11k • written 8.3 years ago by ▴ 120
2
votes
1
reply
1.3k
views
problem with export() in rtracklayer
rtracklayer export
updated 8.7 years ago by ★ 11k • written 8.7 years ago by ★ 28k
2
votes
10
replies
2.6k
views
tracklayer - browserSession() Infinite Recursion Error
rtracklayer ucsc
8.9 years ago andrew.j.skelton73 ▴ 370
2
votes
7
replies
1.2k
views
How to set track attributes in rtracklayer
rtracklayer browserView browserSession
updated 5.2 years ago by ★ 11k • written 5.2 years ago by ▴ 100
2
votes
4
replies
5.9k
views
rtracklayer export GRangesList as gtf and change attributes
grangeslist rtracklayer
updated 22 months ago by • 0 • written 8.8 years ago by ▴ 90
2
votes
4
replies
1.1k
views
default behaviour of import.bw
import.bw rtracklayer
2.5 years ago Yixin • 0
50 results • Page 1 of 1
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Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR) by Michael Love 41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Comment: Trying to use enrichGO by fernanda.backsouza ▴ 10
With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Answer: Opposite sign of LFC in count plots of DEGs (DESeq2) by swbarnes2 ★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error by James W. MacDonald 65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Votes
C: when to apply quantile normalization with voom in limma/voom framework with RNA-
A: How to know if I should use voomWithQualityWeights() or not?
A: Weird results (ribosomal proteins / Y-linked genes) in limma/voom
Answer: Log-cpm values from limma
Answer: Log-cpm values from limma
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