Showing : transcriptdb • reset
1
vote
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784
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Bioconductor for predicting transcription factors from a gene list?
transcription transcriptdb
6.0 years ago hkarakurt ▴ 20
1
vote
5
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1.6k
views
'version' is missing error when running makeTxDbPackageFromUCSC
Cancer TranscriptDb IRanges GenomicFeatures Cancer TranscriptDb IRanges GenomicFeatures
updated 7.6 years ago by ▴ 10 • written 9.7 years ago by 16k
6
votes
2
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4.7k
views
Get sequences for GRCh38 genome based on TxDb object locations
bsgenome genomeinfodb transcriptdb
updated 8.4 years ago by 16k • written 8.4 years ago by ▴ 760
0
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1
reply
834
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BugReports: bug with runValue (strand (GRangesList))
transcriptdb
updated 8.5 years ago by 16k • written 8.6 years ago by ▴ 40
0
votes
3
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1.8k
views
Error running makeTranscriptDbFromGFF in GenomicFeatures
Genetics TranscriptDb GenomicFeatures
updated 8.7 years ago by 11k • written 8.7 years ago by ▴ 240
0
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0
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1.8k
views
Plot exon number per gene and transcript lengths
Genetics TranscriptDb GenomicFeatures
8.7 years ago Jon Bråte ▴ 240
0
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2
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2.1k
views
Genomic Features - makeTranscriptDbFromGFF()
Organism TranscriptDb GenomicFeatures Organism TranscriptDb GenomicFeatures
updated 9.0 years ago by ★ 7.2k • written 9.0 years ago by ★ 12k
0
votes
2
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1.6k
views
UCSC data anomaly in 50638 transcript(s): the cds cumulative length is
Genetics GO Regression Cancer TranscriptDb Genetics GO Regression Cancer TranscriptDb
updated 9.0 years ago by ▴ 570 • written 9.0 years ago by 16k
2
votes
30
replies
3.0k
views
ggbio 1.12.0 autoplot() with txdb example is broken
TranscriptDb TranscriptDb
updated 9.1 years ago by ▴ 490 • written 9.1 years ago by ★ 1.0k
0
votes
4
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1.3k
views
Extracting strand information from GenomicFeatures transcript db objects
TranscriptDb biomaRt TranscriptDb biomaRt
updated 9.2 years ago by 16k • written 9.2 years ago by ▴ 100
0
votes
1
reply
1.3k
views
Error in combining GRanges objects into GRangesList object
TranscriptDb TranscriptDb
updated 9.3 years ago by 11k • written 9.3 years ago by ▴ 10
0
votes
1
reply
1.9k
views
makeTranscriptDbFromUCSC
TranscriptDb TranscriptDb
9.4 years ago Georg Otto ▴ 120
0
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2
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1.0k
views
Where can I download/install old packages like 'org.Rn.eg.db' based on rn4?
Annotation GO BSgenome TranscriptDb BSgenome GenomicFeatures Annotation GO BSgenome
updated 9.4 years ago by 16k • written 9.4 years ago by ▴ 60
0
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1
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1.2k
views
Question about MEDIPS extend parameter : RE: Success: RE: Seed file error: RE: BioStrings for current R: RE: BSgenomeForge seed file - seqnames field
Annotation GO Cancer BSgenome OrganismDb SNPlocs TranscriptDb Biostrings BSgenome MEDIPS
updated 9.5 years ago by ▴ 230 • written 9.5 years ago by 16k
0
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0
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1.7k
views
Seed file error: RE: BioStrings for current R: RE: BSgenomeForge seed file - seqnames field
Annotation GO Cancer BSgenome OrganismDb SNPlocs TranscriptDb Biostrings BSgenome GO
9.5 years ago Hervé Pagès 16k
0
votes
0
replies
1.8k
views
BioStrings for current R: RE: BSgenomeForge seed file - seqnames field
GO Cancer BSgenome OrganismDb SNPlocs TranscriptDb Biostrings BSgenome rtracklayer MEDIPS
9.5 years ago Hervé Pagès 16k
0
votes
1
reply
996
views
tracks() and plotIdeogram() with non desired results in ggbio 1.10.9
TranscriptDb ideogram ggbio TranscriptDb ideogram ggbio
updated 9.5 years ago by ★ 1.0k • written 9.5 years ago by ▴ 490
0
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2
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1.1k
views
tracks() and plotIdeogram() with non desired results in ggbio 1.10.9
TranscriptDb ideogram TranscriptDb ideogram
updated 9.5 years ago by ▴ 490 • written 9.5 years ago by ★ 1.0k
0
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3
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1.5k
views
autoplot() error on a GRanges object in ggbio 1.10.8
Annotation TranscriptDb Annotation TranscriptDb
updated 9.5 years ago by ▴ 490 • written 9.5 years ago by ★ 1.0k
0
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2
replies
1.5k
views
autoplot transcriptDb error with some regions
TranscriptDb biovizBase ggbio TranscriptDb biovizBase ggbio
updated 9.6 years ago by ▴ 490 • written 9.6 years ago by ★ 1.6k
0
votes
3
replies
3.2k
views
Working with ensembl 73 & BSGenome
Annotation BSgenome TranscriptDb biomaRt BSgenome Annotation BSgenome TranscriptDb biomaRt
updated 9.6 years ago by 16k • written 9.6 years ago by ★ 12k
0
votes
1
reply
1.4k
views
makeTranscriptDbFromGFF fails on NCBI Bacteria genomes
GO TranscriptDb goseq genomes GO TranscriptDb goseq genomes
updated 9.6 years ago by ★ 7.2k • written 9.6 years ago by ▴ 80
0
votes
4
replies
945
views
autoplot transcriptDb error with some regions
TranscriptDb ggbio TranscriptDb ggbio
updated 9.6 years ago by ▴ 490 • written 9.6 years ago by ★ 1.8k
0
votes
2
replies
974
views
GenomicFeatures- disjointExons error
TranscriptDb TranscriptDb
updated 9.6 years ago by 16k • written 9.6 years ago by ★ 4.3k
0
votes
2
replies
999
views
'version' is missing error when running makeTxDbPackageFromUCSC
TranscriptDb IRanges TranscriptDb IRanges
updated 9.8 years ago by ★ 8.2k • written 9.8 years ago by ▴ 40
0
votes
3
replies
1.5k
views
makeTranscriptDbFromGFF fails on NCBI Bacteria genomes
TranscriptDb convert GenomicFeatures TranscriptDb convert GenomicFeatures
9.8 years ago Sarah Pohl ▴ 30
0
votes
3
replies
1.2k
views
TranscriptDb object to RangedData for ChIPpeakAnno
Annotation GO AnnotationData Organism BSgenome TranscriptDb convert BSgenome ChIPpeakAnno
9.9 years ago Alan Smith ▴ 150
0
votes
3
replies
2.1k
views
DEXSeq Issue
Alignment Annotation GO Homo sapiens TranscriptDb PROcess GenomicFeatures DEXSeq Alignment
updated 10.0 years ago by 40k • written 10.0 years ago by ▴ 150
0
votes
4
replies
1.6k
views
makeTranscriptDbFromGFF for Unstranded Transcripts
TranscriptDb TranscriptDb
updated 10.1 years ago by 16k • written 10.1 years ago by ★ 1.5k
0
votes
10
replies
2.3k
views
MakeTranscriptDbFromGFF
Annotation TranscriptDb Annotation TranscriptDb
updated 10.1 years ago by ★ 7.2k • written 10.1 years ago by ▴ 340
0
votes
3
replies
1.4k
views
retrieving external Gene IDs from TranscriptDB Object
Yeast TranscriptDb Yeast TranscriptDb
updated 10.1 years ago by ▴ 340 • written 10.1 years ago by ▴ 360
0
votes
1
reply
1.2k
views
makeTranscriptDbFromBiomart - chrominfo failure
TranscriptDb GenomicFeatures TranscriptDb GenomicFeatures
updated 10.2 years ago by ★ 7.2k • written 10.2 years ago by ▴ 360
0
votes
1
reply
1.1k
views
Building a TranscriptDb object from a lncRNA gft file
TranscriptDb TranscriptDb
updated 10.3 years ago by ★ 7.2k • written 10.3 years ago by ▴ 320
0
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2
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1.6k
views
Extracting strand information from GenomicFeatures transcript db objects
TranscriptDb biomaRt TranscriptDb biomaRt
updated 10.3 years ago by ★ 6.7k • written 10.3 years ago by ▴ 100
0
votes
4
replies
1.6k
views
predictCoding() return empty Granges
Annotation Cancer Arabidopsis thaliana BSgenome SNPlocs TranscriptDb BSgenome Annotation
updated 10.7 years ago by 16k • written 10.7 years ago by ▴ 100
0
votes
3
replies
1.2k
views
predictCoding() return empty Granges
Annotation Cancer Arabidopsis thaliana BSgenome SNPlocs TranscriptDb BSgenome Annotation
updated 10.7 years ago by 16k • written 10.7 years ago by ▴ 100
0
votes
1
reply
558
views
creating transcriptDB from gff3 files
TranscriptDb GenomicFeatures TranscriptDb GenomicFeatures
updated 10.8 years ago by ★ 6.7k • written 10.8 years ago by ▴ 210
0
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0
replies
1.0k
views
[Engineers for ensemblgenomes.org #251937] BioMart data anomaly: for some transcripts, the cds cumulative length inferred from the exon and UTR info …
Drosophila melanogaster TranscriptDb biomaRt GenomicFeatures genomes Drosophila melanogaster
11.0 years ago Malcolm Cook ★ 1.6k
0
votes
1
reply
1.2k
views
FW: Overlay Gene Expression on SNP (copy number) data
SNP Coverage Network Cancer TranscriptDb IRanges RCytoscape ggbio Gviz SNP Coverage
updated 11.1 years ago by ★ 4.2k • written 11.1 years ago by ▴ 370
0
votes
1
reply
901
views
VariantAnnotation locateVariants - meaning of precedesID and followsID
BSgenome TranscriptDb BSgenome GenomicFeatures BSgenome TranscriptDb BSgenome
updated 11.1 years ago by ★ 6.7k • written 11.1 years ago by ▴ 80
1
vote
2
replies
1.1k
views
load a TranscriptDb object in another R session?
TranscriptDb TranscriptDb
updated 11.2 years ago by ★ 1.6k • written 11.2 years ago by ▴ 230
0
votes
18
replies
1.2k
views
Create transcriptDb using gff3 files? - library GenomicFeatures and rtracklayer
TranscriptDb TranscriptDb
updated 11.2 years ago by 13k • written 11.2 years ago by ▴ 230
0
votes
3
replies
1.4k
views
RE : maping SNPs
SNP Annotation Cancer SNPlocs TranscriptDb GenomicFeatures GenomicRanges SNP Annotation
updated 11.3 years ago by 16k • written 11.3 years ago by ▴ 450
0
votes
0
replies
622
views
Genomicfeatures chromosome names matching
Cancer TranscriptDb convert Cancer TranscriptDb convert
11.3 years ago Hervé Pagès 16k
0
votes
0
replies
1.1k
views
BioMart data anomaly: for some transcripts, the cds cumulative length inferred from the exon and UTR info doesn't match the "cds_length" attribute fr…
TranscriptDb biomaRt GenomicFeatures TranscriptDb biomaRt GenomicFeatures
11.3 years ago Malcolm Cook ★ 1.6k
0
votes
1
reply
551
views
subsetting transcriptDb
TranscriptDb GenomicFeatures TranscriptDb GenomicFeatures
updated 11.3 years ago by ★ 7.2k • written 11.3 years ago by ▴ 360
0
votes
4
replies
1.3k
views
GenomicFeatures makeTranscriptDbFromBiomart failure
TranscriptDb biomaRt TranscriptDb biomaRt
updated 11.6 years ago by 11k • written 11.6 years ago by ▴ 270
0
votes
1
reply
1.6k
views
TranscriptDB object
TranscriptDb TranscriptDb
updated 11.8 years ago by 16k • written 11.8 years ago by ★ 1.5k
0
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0
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843
views
inconsistency between GRangesList and transcriptDB object.
TranscriptDb GenomicFeatures TranscriptDb GenomicFeatures
12.1 years ago zhenjiang xu ▴ 10
0
votes
2
replies
820
views
GenomicFeatures: Unable to save TranscriptDb object
TranscriptDb TranscriptDb
updated 12.2 years ago by 16k • written 12.2 years ago by ▴ 20
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Comment: BiocGenerics binary is outdated for macOS ARM by jennifer.wokaty ▴ 60
Thanks, Mike, for posting about this and thanks to Lori for noticing the lock. I removed it and RProtoBufLib passes R CMD check. Unfortunat…
Comment: BiocGenerics binary is outdated for macOS ARM by Michael Steinbaugh ▴ 90
Ah thanks for the update. Yeah I see that the flowClust release is the culprit: https://www.bioconductor.org/packages/release/bioc/html/flo…
Comment: Submitting BSgenome package for a new assembly by Manish • 0
Thanks for the info. This is very helpful. -Manish
Comment: Merge 2 accounts, or delete 1 account. by shepherl 3.5k
are you talking specifically on the support site or elsewhere also?
Comment: BiocGenerics binary is outdated for macOS ARM by shepherl 3.5k
That is because it is failing from dependencies not being available. https://bioconductor.org/checkResults/3.17/bioc-mac-arm64-LATEST/BiocG…
Votes
flowCore: using read.FCS with which.lines is not time efficient?
Comment: BiocGenerics binary is outdated for macOS ARM
Comment: Submitting BSgenome package for a new assembly
How to create "trait data" file for WGCNA
Comment: Visualization of negative log CPM values
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