Showing : transcriptdb • reset
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
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
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
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
0
votes
4
replies
1.4k
views
Extracting strand information from GenomicFeatures transcript db objects
TranscriptDb biomaRt TranscriptDb biomaRt
updated 10.1 years ago by 16k • written 10.1 years ago by ▴ 100
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
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
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
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
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
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
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
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
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
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
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
1.9k
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
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
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
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
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
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
2
replies
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
0
votes
2
replies
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
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
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
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
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
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
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
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
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
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
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
951
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
2
replies
1.5k
views
RE : RE : maping SNPs
SNP SNPlocs TranscriptDb IRanges GenomicFeatures SNP SNPlocs TranscriptDb IRanges
updated 13.3 years ago by ★ 6.8k • written 13.3 years ago by ▴ 450
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
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
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
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
955
views
TranscriptDb and genomicranges questions
Cancer TranscriptDb Category IRanges GenomicRanges Cancer TranscriptDb Category IRanges
13.7 years ago Hervé Pagès 16k
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
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
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
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
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
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
1.4k
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
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
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Answer: Dominance Index for Shotgun Metagenomics Data by Leo Lahti ▴ 40
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
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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 …
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For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
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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…
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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…
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Answer: Dominance Index for Shotgun Metagenomics Data
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)
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