Showing : transcriptdb • reset
1
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1.2k
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Bioconductor for predicting transcription factors from a gene list?
transcription transcriptdb
8.3 years ago hkarakurt ▴ 20
1
vote
5
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2.2k
views
'version' is missing error when running makeTxDbPackageFromUCSC
Cancer TranscriptDb IRanges GenomicFeatures Cancer TranscriptDb IRanges GenomicFeatures
updated 9.8 years ago by ▴ 10 • written 12.0 years ago by 16k
6
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2
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6.1k
views
Get sequences for GRCh38 genome based on TxDb object locations
bsgenome genomeinfodb transcriptdb
updated 10.7 years ago by 16k • written 10.7 years ago by ▴ 760
0
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1
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1.2k
views
BugReports: bug with runValue (strand (GRangesList))
transcriptdb
updated 10.8 years ago by 16k • written 10.8 years ago by ▴ 40
0
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3
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2.4k
views
Error running makeTranscriptDbFromGFF in GenomicFeatures
Genetics TranscriptDb GenomicFeatures
updated 11.0 years ago by ★ 11k • written 11.0 years ago by ▴ 270
0
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0
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2.5k
views
Plot exon number per gene and transcript lengths
Genetics TranscriptDb GenomicFeatures
11.0 years ago Jon Bråte ▴ 270
0
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2
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2.7k
views
Genomic Features - makeTranscriptDbFromGFF()
Organism TranscriptDb GenomicFeatures Organism TranscriptDb GenomicFeatures
updated 11.2 years ago by ★ 7.2k • written 11.2 years ago by ★ 13k
0
votes
2
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2.5k
views
UCSC data anomaly in 50638 transcript(s): the cds cumulative length is
Genetics GO Regression Cancer TranscriptDb Genetics GO Regression Cancer TranscriptDb
updated 11.2 years ago by ▴ 570 • written 11.2 years ago by 16k
2
votes
30
replies
5.6k
views
ggbio 1.12.0 autoplot() with txdb example is broken
TranscriptDb TranscriptDb
updated 11.3 years ago by ▴ 490 • written 11.3 years ago by ★ 1.1k
0
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4
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1.7k
views
Extracting strand information from GenomicFeatures transcript db objects
TranscriptDb biomaRt TranscriptDb biomaRt
updated 11.5 years ago by 16k • written 11.5 years ago by ▴ 100
0
votes
1
reply
1.7k
views
Error in combining GRanges objects into GRangesList object
TranscriptDb TranscriptDb
updated 11.5 years ago by ★ 11k • written 11.5 years ago by ▴ 10
0
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1
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2.3k
views
makeTranscriptDbFromUCSC
TranscriptDb TranscriptDb
11.6 years ago Georg Otto ▴ 120
0
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2
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1.5k
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 11.6 years ago by 16k • written 11.6 years ago by ▴ 60
0
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1
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5.5k
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 11.7 years ago by ▴ 280 • written 11.7 years ago by 16k
0
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0
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2.3k
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
11.7 years ago Hervé Pagès 16k
0
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0
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2.4k
views
BioStrings for current R: RE: BSgenomeForge seed file - seqnames field
GO Cancer BSgenome OrganismDb SNPlocs TranscriptDb Biostrings BSgenome rtracklayer MEDIPS
11.7 years ago Hervé Pagès 16k
0
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1
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1.4k
views
tracks() and plotIdeogram() with non desired results in ggbio 1.10.9
TranscriptDb ideogram ggbio TranscriptDb ideogram ggbio
updated 11.7 years ago by ★ 1.1k • written 11.7 years ago by ▴ 490
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2
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1.8k
views
tracks() and plotIdeogram() with non desired results in ggbio 1.10.9
TranscriptDb ideogram TranscriptDb ideogram
updated 11.7 years ago by ▴ 490 • written 11.7 years ago by ★ 1.1k
0
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3
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2.4k
views
autoplot() error on a GRanges object in ggbio 1.10.8
Annotation TranscriptDb Annotation TranscriptDb
updated 11.8 years ago by ▴ 490 • written 11.8 years ago by ★ 1.1k
0
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2
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2.0k
views
autoplot transcriptDb error with some regions
TranscriptDb biovizBase ggbio TranscriptDb biovizBase ggbio
updated 11.8 years ago by ▴ 490 • written 11.8 years ago by ★ 1.6k
0
votes
3
replies
3.8k
views
Working with ensembl 73 & BSGenome
Annotation BSgenome TranscriptDb biomaRt BSgenome Annotation BSgenome TranscriptDb biomaRt
updated 11.8 years ago by 16k • written 11.8 years ago by ★ 13k
0
votes
1
reply
2.0k
views
makeTranscriptDbFromGFF fails on NCBI Bacteria genomes
GO TranscriptDb goseq genomes GO TranscriptDb goseq genomes
updated 11.8 years ago by ★ 7.2k • written 11.8 years ago by ▴ 80
0
votes
4
replies
1.5k
views
autoplot transcriptDb error with some regions
TranscriptDb ggbio TranscriptDb ggbio
updated 11.8 years ago by ▴ 490 • written 11.8 years ago by ★ 1.9k
0
votes
2
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1.5k
views
GenomicFeatures- disjointExons error
TranscriptDb TranscriptDb
updated 11.9 years ago by 16k • written 11.9 years ago by ★ 4.3k
0
votes
2
replies
1.4k
views
'version' is missing error when running makeTxDbPackageFromUCSC
TranscriptDb IRanges TranscriptDb IRanges
updated 12.0 years ago by ★ 8.2k • written 12.0 years ago by ▴ 40
0
votes
3
replies
2.1k
views
makeTranscriptDbFromGFF fails on NCBI Bacteria genomes
TranscriptDb convert GenomicFeatures TranscriptDb convert GenomicFeatures
12.0 years ago Sarah Pohl ▴ 30
0
votes
3
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1.8k
views
TranscriptDb object to RangedData for ChIPpeakAnno
Annotation GO AnnotationData Organism BSgenome TranscriptDb convert BSgenome ChIPpeakAnno
12.1 years ago Alan Smith ▴ 150
0
votes
3
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2.8k
views
DEXSeq Issue
Alignment Annotation GO Homo sapiens TranscriptDb PROcess GenomicFeatures DEXSeq Alignment
updated 12.2 years ago by 43k • written 12.2 years ago by ▴ 150
0
votes
4
replies
2.4k
views
makeTranscriptDbFromGFF for Unstranded Transcripts
TranscriptDb TranscriptDb
updated 12.3 years ago by 16k • written 12.3 years ago by ★ 1.6k
0
votes
10
replies
3.5k
views
MakeTranscriptDbFromGFF
Annotation TranscriptDb Annotation TranscriptDb
updated 12.3 years ago by ★ 7.2k • written 12.3 years ago by ▴ 340
0
votes
3
replies
2.1k
views
retrieving external Gene IDs from TranscriptDB Object
Yeast TranscriptDb Yeast TranscriptDb
updated 12.3 years ago by ▴ 340 • written 12.3 years ago by ▴ 360
0
votes
1
reply
1.7k
views
makeTranscriptDbFromBiomart - chrominfo failure
TranscriptDb GenomicFeatures TranscriptDb GenomicFeatures
updated 12.4 years ago by ★ 7.2k • written 12.4 years ago by ▴ 360
0
votes
1
reply
1.6k
views
Building a TranscriptDb object from a lncRNA gft file
TranscriptDb TranscriptDb
updated 12.5 years ago by ★ 7.2k • written 12.5 years ago by ▴ 320
0
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2
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2.4k
views
Extracting strand information from GenomicFeatures transcript db objects
TranscriptDb biomaRt TranscriptDb biomaRt
updated 12.5 years ago by ★ 6.8k • written 12.5 years ago by ▴ 100
0
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4
replies
2.5k
views
predictCoding() return empty Granges
Annotation Cancer Arabidopsis thaliana BSgenome SNPlocs TranscriptDb BSgenome Annotation
updated 12.9 years ago by 16k • written 12.9 years ago by ▴ 100
0
votes
3
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1.7k
views
predictCoding() return empty Granges
Annotation Cancer Arabidopsis thaliana BSgenome SNPlocs TranscriptDb BSgenome Annotation
updated 12.9 years ago by 16k • written 12.9 years ago by ▴ 100
0
votes
1
reply
889
views
creating transcriptDB from gff3 files
TranscriptDb GenomicFeatures TranscriptDb GenomicFeatures
updated 13.1 years ago by ★ 6.8k • written 13.1 years ago by ▴ 210
0
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0
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1.5k
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
13.2 years ago Malcolm Cook ★ 1.6k
0
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1
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1.6k
views
FW: Overlay Gene Expression on SNP (copy number) data
SNP Coverage Network Cancer TranscriptDb IRanges RCytoscape ggbio Gviz SNP Coverage
updated 13.3 years ago by ★ 4.2k • written 13.3 years ago by ▴ 370
0
votes
1
reply
1.3k
views
VariantAnnotation locateVariants - meaning of precedesID and followsID
BSgenome TranscriptDb BSgenome GenomicFeatures BSgenome TranscriptDb BSgenome
updated 13.4 years ago by ★ 6.8k • written 13.4 years ago by ▴ 80
1
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2
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1.7k
views
load a TranscriptDb object in another R session?
TranscriptDb TranscriptDb
updated 13.4 years ago by ★ 1.6k • written 13.4 years ago by ▴ 230
0
votes
18
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2.5k
views
Create transcriptDb using gff3 files? - library GenomicFeatures and rtracklayer
TranscriptDb TranscriptDb
updated 13.4 years ago by ★ 13k • written 13.4 years ago by ▴ 230
0
votes
3
replies
2.2k
views
RE : maping SNPs
SNP Annotation Cancer SNPlocs TranscriptDb GenomicFeatures GenomicRanges SNP Annotation
updated 13.5 years ago by 16k • written 13.5 years ago by ▴ 450
0
votes
0
replies
935
views
Genomicfeatures chromosome names matching
Cancer TranscriptDb convert Cancer TranscriptDb convert
13.5 years ago Hervé Pagès 16k
0
votes
0
replies
1.5k
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
13.5 years ago Malcolm Cook ★ 1.6k
0
votes
1
reply
908
views
subsetting transcriptDb
TranscriptDb GenomicFeatures TranscriptDb GenomicFeatures
updated 13.6 years ago by ★ 7.2k • written 13.6 years ago by ▴ 360
0
votes
4
replies
1.8k
views
GenomicFeatures makeTranscriptDbFromBiomart failure
TranscriptDb biomaRt TranscriptDb biomaRt
updated 13.8 years ago by ★ 11k • written 13.8 years ago by ▴ 270
0
votes
1
reply
2.1k
views
TranscriptDB object
TranscriptDb TranscriptDb
updated 14.1 years ago by 16k • written 14.1 years ago by ★ 1.5k
0
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0
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1.2k
views
inconsistency between GRangesList and transcriptDB object.
TranscriptDb GenomicFeatures TranscriptDb GenomicFeatures
14.3 years ago zhenjiang xu ▴ 10
0
votes
2
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1.2k
views
GenomicFeatures: Unable to save TranscriptDb object
TranscriptDb TranscriptDb
updated 14.4 years ago by 16k • written 14.4 years ago by ▴ 20
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Comment: Updated Support Site Editor by vs • 0
Thanks for posting this comment, I had the same issue and was able to solve it with the ASCII clue. I am a non-native speaker of English, a…
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi by ATpoint ★ 4.9k
No, cells from the same donor are correlated due to the donor effect. There is literature on this you should read to get started. https:/…
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi by Raya • 0
Wouldn't each sample in the single cell rna seq act as a biological replicate? each condition (eg: mab3_20C) has ~70 single cell samples.
Comment: Getting way too many DEGs with LRT for time-series RNA-seq! by James W. MacDonald 68k
>Sequential post-exposure measurements of the same set of genes is not the same thing as having multiple treated groups! They are not the…
Comment: Getting way too many DEGs with LRT for time-series RNA-seq! by Denise • 0
Sequential post-exposure measurements of the same set of genes is not the same thing as having multiple treated groups! And I suppose ther…
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Comment: Updated Support Site Editor
Updated Support Site Editor
Comment: Updated Support Site Editor
Comment: DESeq2 used with zinbwave weights - Differences on contrasts calculations
Comment: DESeq2 used with zinbwave weights - Differences on contrasts calculations
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