Showing : transcriptdb • reset
1
vote
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924
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Bioconductor for predicting transcription factors from a gene list?
transcription transcriptdb
7.0 years ago hkarakurt ▴ 20
1
vote
5
replies
1.9k
views
'version' is missing error when running makeTxDbPackageFromUCSC
Cancer TranscriptDb IRanges GenomicFeatures Cancer TranscriptDb IRanges GenomicFeatures
updated 8.5 years ago by ▴ 10 • written 10.7 years ago by 16k
6
votes
2
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5.3k
views
Get sequences for GRCh38 genome based on TxDb object locations
bsgenome genomeinfodb transcriptdb
updated 9.4 years ago by 16k • written 9.4 years ago by ▴ 760
0
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1
reply
1.0k
views
BugReports: bug with runValue (strand (GRangesList))
transcriptdb
updated 9.5 years ago by 16k • written 9.5 years ago by ▴ 40
0
votes
3
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2.0k
views
Error running makeTranscriptDbFromGFF in GenomicFeatures
Genetics TranscriptDb GenomicFeatures
updated 9.7 years ago by ★ 11k • written 9.7 years ago by ▴ 250
0
votes
0
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2.2k
views
Plot exon number per gene and transcript lengths
Genetics TranscriptDb GenomicFeatures
9.7 years ago Jon Bråte ▴ 250
0
votes
2
replies
2.4k
views
Genomic Features - makeTranscriptDbFromGFF()
Organism TranscriptDb GenomicFeatures Organism TranscriptDb GenomicFeatures
updated 9.9 years ago by ★ 7.2k • written 9.9 years ago by ★ 13k
0
votes
2
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2.0k
views
UCSC data anomaly in 50638 transcript(s): the cds cumulative length is
Genetics GO Regression Cancer TranscriptDb Genetics GO Regression Cancer TranscriptDb
updated 9.9 years ago by ▴ 570 • written 9.9 years ago by 16k
2
votes
30
replies
4.3k
views
ggbio 1.12.0 autoplot() with txdb example is broken
TranscriptDb TranscriptDb
updated 10.0 years ago by ▴ 490 • written 10.0 years ago by ★ 1.0k
0
votes
4
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1.4k
views
Extracting strand information from GenomicFeatures transcript db objects
TranscriptDb biomaRt TranscriptDb biomaRt
updated 10.2 years ago by 16k • written 10.2 years ago by ▴ 100
0
votes
1
reply
1.5k
views
Error in combining GRanges objects into GRangesList object
TranscriptDb TranscriptDb
updated 10.2 years ago by ★ 11k • written 10.2 years ago by ▴ 10
0
votes
1
reply
2.1k
views
makeTranscriptDbFromUCSC
TranscriptDb TranscriptDb
10.3 years ago Georg Otto ▴ 120
0
votes
2
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1.2k
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 10.3 years ago by 16k • written 10.3 years ago by ▴ 60
0
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1
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1.4k
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 10.4 years ago by ▴ 240 • written 10.4 years ago by 16k
0
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0
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1.9k
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
10.4 years ago Hervé Pagès 16k
0
votes
0
replies
2.1k
views
BioStrings for current R: RE: BSgenomeForge seed file - seqnames field
GO Cancer BSgenome OrganismDb SNPlocs TranscriptDb Biostrings BSgenome rtracklayer MEDIPS
10.4 years ago Hervé Pagès 16k
0
votes
1
reply
1.2k
views
tracks() and plotIdeogram() with non desired results in ggbio 1.10.9
TranscriptDb ideogram ggbio TranscriptDb ideogram ggbio
updated 10.4 years ago by ★ 1.0k • written 10.4 years ago by ▴ 490
0
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2
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1.4k
views
tracks() and plotIdeogram() with non desired results in ggbio 1.10.9
TranscriptDb ideogram TranscriptDb ideogram
updated 10.4 years ago by ▴ 490 • written 10.4 years ago by ★ 1.0k
0
votes
3
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1.9k
views
autoplot() error on a GRanges object in ggbio 1.10.8
Annotation TranscriptDb Annotation TranscriptDb
updated 10.5 years ago by ▴ 490 • written 10.5 years ago by ★ 1.0k
0
votes
2
replies
1.7k
views
autoplot transcriptDb error with some regions
TranscriptDb biovizBase ggbio TranscriptDb biovizBase ggbio
updated 10.5 years ago by ▴ 490 • written 10.5 years ago by ★ 1.6k
0
votes
3
replies
3.4k
views
Working with ensembl 73 & BSGenome
Annotation BSgenome TranscriptDb biomaRt BSgenome Annotation BSgenome TranscriptDb biomaRt
updated 10.5 years ago by 16k • written 10.5 years ago by ★ 13k
0
votes
1
reply
1.6k
views
makeTranscriptDbFromGFF fails on NCBI Bacteria genomes
GO TranscriptDb goseq genomes GO TranscriptDb goseq genomes
updated 10.5 years ago by ★ 7.2k • written 10.5 years ago by ▴ 80
0
votes
4
replies
1.2k
views
autoplot transcriptDb error with some regions
TranscriptDb ggbio TranscriptDb ggbio
updated 10.5 years ago by ▴ 490 • written 10.5 years ago by ★ 1.9k
0
votes
2
replies
1.2k
views
GenomicFeatures- disjointExons error
TranscriptDb TranscriptDb
updated 10.6 years ago by 16k • written 10.6 years ago by ★ 4.3k
0
votes
2
replies
1.2k
views
'version' is missing error when running makeTxDbPackageFromUCSC
TranscriptDb IRanges TranscriptDb IRanges
updated 10.7 years ago by ★ 8.2k • written 10.7 years ago by ▴ 40
0
votes
3
replies
1.7k
views
makeTranscriptDbFromGFF fails on NCBI Bacteria genomes
TranscriptDb convert GenomicFeatures TranscriptDb convert GenomicFeatures
10.7 years ago Sarah Pohl ▴ 30
0
votes
3
replies
1.5k
views
TranscriptDb object to RangedData for ChIPpeakAnno
Annotation GO AnnotationData Organism BSgenome TranscriptDb convert BSgenome ChIPpeakAnno
10.8 years ago Alan Smith ▴ 150
0
votes
3
replies
2.4k
views
DEXSeq Issue
Alignment Annotation GO Homo sapiens TranscriptDb PROcess GenomicFeatures DEXSeq Alignment
updated 10.9 years ago by 41k • written 10.9 years ago by ▴ 150
0
votes
4
replies
1.9k
views
makeTranscriptDbFromGFF for Unstranded Transcripts
TranscriptDb TranscriptDb
updated 11.0 years ago by 16k • written 11.0 years ago by ★ 1.5k
0
votes
10
replies
2.8k
views
MakeTranscriptDbFromGFF
Annotation TranscriptDb Annotation TranscriptDb
updated 11.0 years ago by ★ 7.2k • written 11.0 years ago by ▴ 340
0
votes
3
replies
1.7k
views
retrieving external Gene IDs from TranscriptDB Object
Yeast TranscriptDb Yeast TranscriptDb
updated 11.0 years ago by ▴ 340 • written 11.0 years ago by ▴ 360
0
votes
1
reply
1.4k
views
makeTranscriptDbFromBiomart - chrominfo failure
TranscriptDb GenomicFeatures TranscriptDb GenomicFeatures
updated 11.1 years ago by ★ 7.2k • written 11.1 years ago by ▴ 360
0
votes
1
reply
1.3k
views
Building a TranscriptDb object from a lncRNA gft file
TranscriptDb TranscriptDb
updated 11.2 years ago by ★ 7.2k • written 11.2 years ago by ▴ 320
0
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2
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2.0k
views
Extracting strand information from GenomicFeatures transcript db objects
TranscriptDb biomaRt TranscriptDb biomaRt
updated 11.2 years ago by ★ 6.8k • written 11.2 years ago by ▴ 100
0
votes
4
replies
2.0k
views
predictCoding() return empty Granges
Annotation Cancer Arabidopsis thaliana BSgenome SNPlocs TranscriptDb BSgenome Annotation
updated 11.6 years ago by 16k • written 11.6 years ago by ▴ 100
0
votes
3
replies
1.4k
views
predictCoding() return empty Granges
Annotation Cancer Arabidopsis thaliana BSgenome SNPlocs TranscriptDb BSgenome Annotation
updated 11.6 years ago by 16k • written 11.6 years ago by ▴ 100
0
votes
1
reply
691
views
creating transcriptDB from gff3 files
TranscriptDb GenomicFeatures TranscriptDb GenomicFeatures
updated 11.8 years ago by ★ 6.8k • written 11.8 years ago by ▴ 210
0
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0
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1.3k
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
11.9 years ago Malcolm Cook ★ 1.6k
0
votes
1
reply
1.3k
views
FW: Overlay Gene Expression on SNP (copy number) data
SNP Coverage Network Cancer TranscriptDb IRanges RCytoscape ggbio Gviz SNP Coverage
updated 12.0 years ago by ★ 4.2k • written 12.0 years ago by ▴ 370
0
votes
1
reply
1.1k
views
VariantAnnotation locateVariants - meaning of precedesID and followsID
BSgenome TranscriptDb BSgenome GenomicFeatures BSgenome TranscriptDb BSgenome
updated 12.1 years ago by ★ 6.8k • written 12.1 years ago by ▴ 80
1
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2
replies
1.3k
views
load a TranscriptDb object in another R session?
TranscriptDb TranscriptDb
updated 12.1 years ago by ★ 1.6k • written 12.1 years ago by ▴ 230
0
votes
18
replies
1.7k
views
Create transcriptDb using gff3 files? - library GenomicFeatures and rtracklayer
TranscriptDb TranscriptDb
updated 12.1 years ago by ★ 13k • written 12.1 years ago by ▴ 230
0
votes
3
replies
1.8k
views
RE : maping SNPs
SNP Annotation Cancer SNPlocs TranscriptDb GenomicFeatures GenomicRanges SNP Annotation
updated 12.2 years ago by 16k • written 12.2 years ago by ▴ 450
0
votes
0
replies
746
views
Genomicfeatures chromosome names matching
Cancer TranscriptDb convert Cancer TranscriptDb convert
12.2 years ago Hervé Pagès 16k
0
votes
0
replies
1.3k
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
12.2 years ago Malcolm Cook ★ 1.6k
0
votes
1
reply
684
views
subsetting transcriptDb
TranscriptDb GenomicFeatures TranscriptDb GenomicFeatures
updated 12.3 years ago by ★ 7.2k • written 12.3 years ago by ▴ 360
0
votes
4
replies
1.5k
views
GenomicFeatures makeTranscriptDbFromBiomart failure
TranscriptDb biomaRt TranscriptDb biomaRt
updated 12.5 years ago by ★ 11k • written 12.5 years ago by ▴ 270
0
votes
1
reply
1.8k
views
TranscriptDB object
TranscriptDb TranscriptDb
updated 12.8 years ago by 16k • written 12.8 years ago by ★ 1.5k
0
votes
0
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1.0k
views
inconsistency between GRangesList and transcriptDB object.
TranscriptDb GenomicFeatures TranscriptDb GenomicFeatures
13.0 years ago zhenjiang xu ▴ 10
0
votes
2
replies
952
views
GenomicFeatures: Unable to save TranscriptDb object
TranscriptDb TranscriptDb
updated 13.1 years ago by 16k • written 13.1 years ago by ▴ 20
50 results • Page 1 of 1
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Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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