Showing : TxDb • reset
0
votes
5
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2.4k
views
makeTxDbFromGFF returns empty object
genomicfeatures txdb maketxdbfromgff
9.9 years ago TimothéeFlutre ▴ 80
0
votes
2
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1.6k
views
how to get transcript annotation (unique)
txdb
9.9 years ago KB ▴ 50
9
votes
4
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4.3k
views
PDCD1 missing from TxDb.Hsapiens.UCSC.hg38.knownGene?
txdb txdb.hsapiens.ucsc.hg19.knowngene txdb.hsapiens.ucsc.hg38.knowngene org.hs.eg.db annotation
9.9 years ago enricoferrero ▴ 680
0
votes
0
replies
1.4k
views
extractUpstreamSeqs with custom genome, no gene_id shown
genomicranges txdb genomicfeatures featureextraction
updated 9.9 years ago by 25k • written 9.9 years ago by ▴ 30
4
votes
4
replies
2.7k
views
Why does Homo.sapiens import TxDb.Hsapiens.UCSC.hg19.knownGene instead of TxDb.Hsapiens.UCSC.hg38.knownGene?
homo.sapiens txdb annotation
updated 9.9 years ago by ★ 6.8k • written 9.9 years ago by ▴ 680
0
votes
1
reply
1.7k
views
How to find index position of desired feature_by in TxDb granges?
granges txdb genomicfeatures
updated 10.0 years ago by 25k • written 10.0 years ago by ▴ 50
2
votes
2
replies
1.9k
views
How to rename seqlevels style (I, II, III, ...,XVI, Mito to 1,2,3,...16, 17.) in txdb granges?
renameSeqlevels mapSeqlevels grangeslist granges txdb
10.0 years ago vinod.acear ▴ 50
1
vote
6
replies
2.7k
views
problem creating txdb object and bsgenome for solanum pennellii
bsgenome txdb promoter
updated 10.1 years ago by 25k • written 10.1 years ago by ▴ 20
0
votes
3
replies
2.0k
views
extracting promoter region error for A.thaliana
promoter region txdb
updated 10.1 years ago by 25k • written 10.1 years ago by ▴ 20
4
votes
7
replies
3.6k
views
How to get Genomic feature in txdb format from biomart for sacCer2 (EF4) assembly?
makeTxDbFromBiomart genomicfeatures txdb biomart
updated 10.4 years ago by 68k • written 10.4 years ago by ▴ 50
0
votes
4
replies
1.9k
views
threeUTRsByTranscript appears to not work after invoking setter seqlevelsStyle
txdb threeutrsbytranscript seqlevelsstyle seqlevels
10.4 years ago Robert K. Bradley ▴ 40
0
votes
3
replies
1.9k
views
possible conflict between renameSeqLevels (TxDb) and isActiveSeq (TxDb)
bug txdb genomicfeatures
10.5 years ago Robert K. Bradley ▴ 40
0
votes
2
replies
1.4k
views
renamed seqlevels (TxDb) don't persist through a save-load cycle
GenomicFeatures TxDb
10.5 years ago Robert K. Bradley ▴ 40
2
votes
6
replies
3.4k
views
Working with Arabidopsis Databases
bsgenome biomart getPromoterSeq txdb
10.6 years ago oliwindram ▴ 10
0
votes
2
replies
2.8k
views
makeTxDbpackage after makeTxDbfromGFF --> Error in spc[[2]] : subscript out of bounds
gtf TxDb maketxdbfromgff
updated 10.7 years ago by 16k • written 10.7 years ago by • 0
8
votes
16
replies
4.1k
views
Setting package name in makeTxDbPackage
genomicfeatures txdb
updated 10.8 years ago by ★ 7.2k • written 10.8 years ago by ▴ 760
2
votes
2
replies
1.8k
views
Setting genome information on a TxDb object
genomicfeatures txdb
updated 10.8 years ago by 16k • written 10.8 years ago by ▴ 760
3
votes
3
replies
4.6k
views
Installation of TxDb.Hsapiens.UCSC.hg19.knownGene fails.
biocinstaller installation TxDb
updated 11.1 years ago by ★ 7.2k • written 11.1 years ago by 1.6k
68 results • Page 2 of 2
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Answer: GSEA error by James W. MacDonald 68k
At a very high level, the way non-model organisms are annotated is by using blast to find orthologs in other species that are well annotate…
Comment: Unable to find ENTREZ IDs by Adithi • 0
Hi James, Thank you so much for your reply. My main goal is to find ortholog genes from chinese hamster gene symbols to mouse gene symbols…
Comment: Unable to find ENTREZ IDs by Adithi • 0
Hi James, Thank you so much for your reply. My main goal is to find ortholog genes from chinese hamster gene symbols to mouse gene symbols…
Answer: Unable to find ENTREZ IDs by James W. MacDonald 68k
Those are the 'symbols', and are a concatenation of LOC and the NCBI Gene ID (what used to be called an Entrez Gene ID). As an example:http…
Answer: Inconsistencies between accessor functions for TxDb databases with selected seql by a2a2hd42aa • 0
Technical inconsistencies in database accessors can disrupt your workflow, but finding a reliable source to download online mobile games sh…
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Answer: GSEA error
Answer: OrgDb for maize
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
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