Showing : transcriptdb • reset
1
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917
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Bioconductor for predicting transcription factors from a gene list?
transcription transcriptdb
7.0 years ago hkarakurt ▴ 20
1
vote
5
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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 10.6 years ago by 16k
6
votes
2
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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
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1
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1.0k
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BugReports: bug with runValue (strand (GRangesList))
transcriptdb
updated 9.5 years ago by 16k • written 9.5 years ago by ▴ 40
0
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3
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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
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0
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2.2k
views
Plot exon number per gene and transcript lengths
Genetics TranscriptDb GenomicFeatures
9.6 years ago Jon Bråte ▴ 250
0
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2
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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
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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 10.1 years ago by 16k • written 10.1 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
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1
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2.1k
views
makeTranscriptDbFromUCSC
TranscriptDb TranscriptDb
10.3 years ago Georg Otto ▴ 120
0
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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
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0
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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
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1
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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
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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
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3
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1.9k
views
autoplot() error on a GRanges object in ggbio 1.10.8
Annotation TranscriptDb Annotation TranscriptDb
updated 10.4 years ago by ▴ 490 • written 10.4 years ago by ★ 1.0k
0
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2
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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
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4
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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
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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
1.2k
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
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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
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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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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
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4
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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
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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
690
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
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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
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1
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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
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1
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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
1
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2
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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
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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
741
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
676
views
subsetting transcriptDb
TranscriptDb GenomicFeatures TranscriptDb GenomicFeatures
updated 12.2 years ago by ★ 7.2k • written 12.2 years ago by ▴ 360
0
votes
4
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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 12.7 years ago by 16k • written 12.8 years ago by ★ 1.5k
0
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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
950
views
GenomicFeatures: Unable to save TranscriptDb object
TranscriptDb TranscriptDb
updated 13.1 years ago by 16k • written 13.1 years ago by ▴ 20
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Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR) by Michael Love 41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Comment: Trying to use enrichGO by fernanda.backsouza ▴ 10
With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Answer: Opposite sign of LFC in count plots of DEGs (DESeq2) by swbarnes2 ★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error by James W. MacDonald 65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Votes
Answer: How to retrieve gene ontology GO class from gene list?
Answer: How to retrieve gene ontology GO class from gene list?
C: when to apply quantile normalization with voom in limma/voom framework with RNA-
A: How to know if I should use voomWithQualityWeights() or not?
A: Weird results (ribosomal proteins / Y-linked genes) in limma/voom
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