Showing : maketxdbfromgff • reset
0
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7
replies
1.9k
views
Get wrong tx_type when using GenomicFeatures::makeTxDbFromGTF
genomicfeatures maketxdbfromgff tx_type gtf
updated 8.4 years ago by 16k • written 8.4 years ago by • 0
0
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7
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2.3k
views
makeTxDbFromGFF yields an empty TxDb
annotation maketxdbfromgff genomicfeatures
8.5 years ago José Luis Lavín ▴ 10
8
votes
7
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3.5k
views
Generating a proper TxDb instance from NCBI GFF Annotations File
ncbi refseq maketxdbfromgff fetchExtendedChromInfoFromUCSC genomeinfodb
updated 8.3 years ago by 16k • written 8.3 years ago by ▴ 10
0
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5
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1.7k
views
makeTxDbFromGFF returns empty object
genomicfeatures txdb maketxdbfromgff
8.0 years ago TimothéeFlutre ▴ 80
3
votes
4
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2.6k
views
Saving and retrieving TxDB object
makeTxDBFromGFF EISA
updated 3.7 years ago by 65k • written 3.7 years ago by • 0
0
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4
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2.0k
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MakeTxDbFromGFF creates empty object
maketxdbfromgff
updated 8.5 years ago by 16k • written 8.5 years ago by • 0
0
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3
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3.7k
views
makeTxDbFromGFF Error: subscript contains NAs
genomicfeatures granges maketxdbfromgff
updated 6.7 years ago by 16k • written 6.8 years ago by • 0
2
votes
2
replies
852
views
Problem with MakeTxDbFromGFF
makeTxDbFromGff
14 months ago stacy.genovese • 0
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2
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2.0k
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makeTxDbFromGFF not capturing/displaying 'gene' records from GFF3 file.
genomicfeatures makeTxDbFromGFF
updated 9.0 years ago by 16k • written 9.0 years ago by • 0
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2
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2.2k
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makeTxDbpackage after makeTxDbfromGFF --> Error in spc[[2]] : subscript out of bounds
gtf TxDb maketxdbfromgff
updated 8.9 years ago by 16k • written 8.9 years ago by • 0
1
vote
2
replies
1.4k
views
mRNA start used instead of gene start in makeTxDbFromGFF
maketxdbfromgff genomicfeatures
updated 8.0 years ago by 16k • written 8.0 years ago by ▴ 80
4
votes
2
replies
1.3k
views
distinguish DataSource from Provider and ProviderVersion in makeTxDbPackage
genomicfeatures txdb maketxdbfromgff metadata
updated 8.0 years ago by ★ 6.8k • written 8.0 years ago by ▴ 80
3
votes
2
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2.2k
views
makeTxDbFromGFF drops genes which have multiple chromosome locations. (with iGenome GTF)
genomicfeatures gtf maketxdbfromgff iGenome
updated 7.5 years ago by 25k • written 7.5 years ago by ▴ 20
1
vote
2
replies
1.1k
views
Error while using GenomicFeatures package
genomicfeatures maketxdbfromgff
updated 7.2 years ago by 16k • written 7.2 years ago by ▴ 10
0
votes
2
replies
2.3k
views
makeTxDbFromGFF errors too many NAs and make.splicings
maketxdbfromgff limma
updated 5.6 years ago by 16k • written 5.6 years ago by ▴ 20
0
votes
1
reply
1.2k
views
Error in .merge_transcript_parts(transcripts)
maketxdbfromgff
5.5 years ago csijcs • 0
0
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1
reply
1.4k
views
makeTxDbFromGFF error "stop codons that cannot be mapped to an exon"
genomicfeatures txdb maketxdbfromgff
updated 5.8 years ago by ▴ 50 • written 5.8 years ago by • 0
0
votes
1
reply
3.9k
views
create a txdb using makeTxDbFromGFF
bioconductor txdb maketxdbfromgff
6.4 years ago Nader.Aryamanesh • 0
0
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0
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898
views
Error using the makeTxDbFromGFF
maketxdbfromgff
6.2 years ago bright602 • 0
0
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0
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1.5k
views
error with makeTxDbFromGFF
genomicfeatures gff custom genome makeTxDbFromGFF makeTxDbFromGRanges
5.1 years ago xvazquezc • 0
0
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0
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950
views
Annotation missing when using makeTxDbFromGFF
makeTxDbFromGFF
8.2 years ago Udi Landau ▴ 30
0
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0
replies
1.2k
views
Get wrong tx_type when using GenomicFeatures::makeTxDbFromGTF
genomicfeatures maketxdbfromgff tx_type gtf
8.4 years ago Karolin Wiedemann • 0
22 results • Page 1 of 1
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Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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