Showing : makeTxDbFromGFF • reset
8
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7
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4.2k
views
Generating a proper TxDb instance from NCBI GFF Annotations File
ncbi refseq maketxdbfromgff fetchExtendedChromInfoFromUCSC genomeinfodb
updated 9.3 years ago by 16k • written 9.3 years ago by ▴ 10
4
votes
2
replies
1.6k
views
distinguish DataSource from Provider and ProviderVersion in makeTxDbPackage
genomicfeatures txdb maketxdbfromgff metadata
updated 9.0 years ago by ★ 6.8k • written 9.0 years ago by ▴ 80
3
votes
4
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3.7k
views
Saving and retrieving TxDB object
makeTxDBFromGFF EISA
updated 4.7 years ago by 68k • written 4.7 years ago by • 0
3
votes
2
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2.6k
views
makeTxDbFromGFF drops genes which have multiple chromosome locations. (with iGenome GTF)
genomicfeatures gtf maketxdbfromgff iGenome
updated 8.5 years ago by 25k • written 8.5 years ago by ▴ 20
2
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2
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1.5k
views
Problem with MakeTxDbFromGFF
makeTxDbFromGff
2.2 years ago stacy.genovese • 0
1
vote
2
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1.3k
views
Error while using GenomicFeatures package
genomicfeatures maketxdbfromgff
updated 8.2 years ago by 16k • written 8.2 years ago by ▴ 10
1
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2
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1.6k
views
mRNA start used instead of gene start in makeTxDbFromGFF
maketxdbfromgff genomicfeatures
updated 9.0 years ago by 16k • written 9.0 years ago by ▴ 80
0
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0
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1.1k
views
Annotation missing when using makeTxDbFromGFF
makeTxDbFromGFF
9.2 years ago Udi Landau ▴ 30
0
votes
5
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2.0k
views
makeTxDbFromGFF returns empty object
genomicfeatures txdb maketxdbfromgff
9.0 years ago TimothéeFlutre ▴ 80
0
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7
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2.8k
views
makeTxDbFromGFF yields an empty TxDb
annotation maketxdbfromgff genomicfeatures
9.5 years ago José Luis Lavín ▴ 10
0
votes
2
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2.6k
views
makeTxDbpackage after makeTxDbfromGFF --> Error in spc[[2]] : subscript out of bounds
gtf TxDb maketxdbfromgff
updated 9.8 years ago by 16k • written 9.9 years ago by • 0
0
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3
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4.3k
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makeTxDbFromGFF Error: subscript contains NAs
genomicfeatures granges maketxdbfromgff
updated 7.7 years ago by 16k • written 7.8 years ago by • 0
0
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1
reply
4.4k
views
create a txdb using makeTxDbFromGFF
bioconductor txdb maketxdbfromgff
7.4 years ago Nader.Aryamanesh • 0
0
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0
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1.1k
views
Error using the makeTxDbFromGFF
maketxdbfromgff
7.2 years ago bright602 • 0
0
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1
reply
1.7k
views
makeTxDbFromGFF error "stop codons that cannot be mapped to an exon"
genomicfeatures txdb maketxdbfromgff
updated 6.8 years ago by ▴ 50 • written 6.8 years ago by • 0
0
votes
2
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2.7k
views
makeTxDbFromGFF errors too many NAs and make.splicings
maketxdbfromgff limma
updated 6.5 years ago by 16k • written 6.6 years ago by ▴ 20
0
votes
1
reply
1.5k
views
Error in .merge_transcript_parts(transcripts)
maketxdbfromgff
6.4 years ago csijcs • 0
0
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0
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1.8k
views
error with makeTxDbFromGFF
genomicfeatures gff custom genome makeTxDbFromGFF makeTxDbFromGRanges
6.0 years ago xvazquezc • 0
0
votes
2
replies
2.3k
views
makeTxDbFromGFF not capturing/displaying 'gene' records from GFF3 file.
genomicfeatures makeTxDbFromGFF
updated 10.0 years ago by 16k • written 10.0 years ago by • 0
0
votes
0
replies
1.4k
views
Get wrong tx_type when using GenomicFeatures::makeTxDbFromGTF
genomicfeatures maketxdbfromgff tx_type gtf
9.4 years ago Karolin Wiedemann • 0
0
votes
4
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2.3k
views
MakeTxDbFromGFF creates empty object
maketxdbfromgff
updated 9.4 years ago by 16k • written 9.4 years ago by • 0
0
votes
7
replies
2.2k
views
Get wrong tx_type when using GenomicFeatures::makeTxDbFromGTF
genomicfeatures maketxdbfromgff tx_type gtf
updated 9.4 years ago by 16k • written 9.4 years ago by • 0
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Comment: GSEA preranked analysis downstream of DEseq2 by Ajay • 0
`logFC * -log10(pval)` seems to be the pi-score proposed in this [paper][1] [1]: https://pmc.ncbi.nlm.nih.gov/articles/PMC3957066/
Comment: error in ChAMP loading file by janwilseo • 0
Any update on this post? I also had an issue with this. [erosion control](https://charlestonhydroseeding.com/)
Answer: CluserProfiler message "No gene can be mapped" by James W. MacDonald 68k
Two things. First, the order of your term2gene is backwards (should be term and then gene, like the name), and by default `enricher` adjust…
Comment: Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis by donnycrimson • 0
One potential workaround might be to adjust for these factors using a combination of design matrices perhaps including batch as a covariate…
Comment: DESeq2 Design controlling for gender by donnycrimson • 0
On a lighter note, while you are tackling such complex data, you might enjoy a quick break playing the [Slope Game](https://slopegame.lol)…
Votes
DiffBind; Error: No sites have activity greater than filter value
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
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