Showing : transcriptdb • reset
6
votes
2
replies
5.2k
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
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
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
1
vote
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
1
vote
0
replies
919
views
Bioconductor for predicting transcription factors from a gene list?
transcription transcriptdb
7.0 years ago hkarakurt ▴ 20
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
0
replies
1.0k
views
TranscriptDb and genomicranges questions
TranscriptDb IRanges GenomicRanges TranscriptDb IRanges GenomicRanges
13.8 years ago Patrick Aboyoun ★ 1.6k
0
votes
2
replies
1.1k
views
building a refseq-based transcriptDb: warnings of interest?
TranscriptDb TranscriptDb
updated 13.8 years ago by 16k • written 13.8 years ago by 6.7k
0
votes
0
replies
834
views
error in makeTranscriptDbFromUCSC of library(GenomicFeatures)
TranscriptDb TranscriptDb
13.7 years ago Yuan Jian ▴ 250
0
votes
1
reply
955
views
TranscriptDb and genomicranges questions
Cancer TranscriptDb Category IRanges GenomicRanges Cancer TranscriptDb Category IRanges
13.7 years ago Hervé Pagès 16k
0
votes
0
replies
840
views
how to create a TranscriptDb object from bed file
TranscriptDb convert edgeR TranscriptDb convert edgeR
13.6 years ago Ann Loraine ▴ 110
0
votes
4
replies
1.6k
views
getting gene ranges from a TranscriptDb (GenomicFeatures package)
GO TranscriptDb GO TranscriptDb
updated 13.6 years ago by 21k • written 13.6 years ago by ▴ 210
0
votes
2
replies
909
views
IRanges, GenomicRanges, GenomicFeatures?
Coverage Annotation TranscriptDb convert GenomicFeatures Coverage Annotation TranscriptDb
updated 13.5 years ago by ★ 13k • written 13.5 years ago by ▴ 60
0
votes
3
replies
883
views
Question about TranscriptDb and makeTranscriptDb method
TranscriptDb TranscriptDb
updated 13.4 years ago by 16k • written 13.4 years ago by ▴ 60
0
votes
3
replies
1.1k
views
Is there a place to download GenomicFeatures' sqlite from ensembl.
TranscriptDb TranscriptDb
updated 13.4 years ago by ★ 11k • written 13.4 years ago by ▴ 970
0
votes
2
replies
809
views
Is there a place to download GenomicFeatures'
TranscriptDb TranscriptDb
updated 13.4 years ago by ★ 13k • written 13.4 years ago by ▴ 20
0
votes
3
replies
1.1k
views
RE : RE : RE : maping SNPs
GO TranscriptDb GO TranscriptDb
updated 13.3 years ago by 16k • written 13.3 years ago by ▴ 450
0
votes
1
reply
832
views
In the TranscriptDb object, where do the Entrez Gene IDs come from ?
TranscriptDb TranscriptDb
updated 13.2 years ago by ★ 7.2k • written 13.3 years ago by ▴ 10
0
votes
2
replies
1.6k
views
extending GenomicFeatures to makeTranscriptDbFrom other sources (i.e. GFF3)
TranscriptDb biomaRt TranscriptDb biomaRt
updated 13.2 years ago by ★ 7.2k • written 13.2 years ago by ★ 1.6k
0
votes
2
replies
950
views
GenomicFeatures: Unable to save TranscriptDb object
TranscriptDb TranscriptDb
updated 13.1 years ago by 16k • written 13.1 years ago by ▴ 20
0
votes
0
replies
1.0k
views
inconsistency between GRangesList and transcriptDB object.
TranscriptDb GenomicFeatures TranscriptDb GenomicFeatures
13.0 years ago zhenjiang xu ▴ 10
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
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
679
views
subsetting transcriptDb
TranscriptDb GenomicFeatures TranscriptDb GenomicFeatures
updated 12.2 years ago by ★ 7.2k • written 12.2 years ago by ▴ 360
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
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
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
1
reply
1.1k
views
VariantAnnotation locateVariants - meaning of precedesID and followsID
BSgenome TranscriptDb BSgenome GenomicFeatures BSgenome TranscriptDb BSgenome
updated 12.0 years ago by ★ 6.8k • written 12.0 years ago by ▴ 80
0
votes
0
replies
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
691
views
creating transcriptDB from gff3 files
TranscriptDb GenomicFeatures TranscriptDb GenomicFeatures
updated 11.7 years ago by ★ 6.8k • written 11.7 years ago by ▴ 210
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
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
2
replies
1.9k
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
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
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
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
1
reply
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
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
0
replies
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
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
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
2.0k
views
Error running makeTranscriptDbFromGFF in GenomicFeatures
Genetics TranscriptDb GenomicFeatures
updated 9.6 years ago by ★ 11k • written 9.6 years ago by ▴ 250
0
votes
2
replies
1.2k
views
GenomicFeatures- disjointExons error
TranscriptDb TranscriptDb
updated 10.5 years ago by 16k • written 10.5 years ago by ★ 4.3k
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
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
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
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
1.9k
views
autoplot() error on a GRanges object in ggbio 1.10.8
Annotation TranscriptDb Annotation TranscriptDb
updated 10.4 years ago by ▴ 490 • written 10.4 years ago by ★ 1.0k
0
votes
2
replies
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
50 results • Page 1 of 1
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Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks by ATpoint ★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Votes
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
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