Showing : Genomicfeatures • reset
2
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3
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GenomicFeatures promotersByOverlap: Identify promoters by overlap?
GenomicFeatures GenomicRanges
updated 5.8 years ago by 68k • written 5.8 years ago by ▴ 30
0
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3
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1.3k
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Resize exons in transcript to total width
genomicranges genomicfeatures
updated 5.9 years ago by ★ 11k • written 5.9 years ago by ▴ 90
0
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8
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2.6k
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exonsBy does not order exons by ascending rank, is it a bug or outdated documentation?
GenomicFeatures GenomicAlignment GenomicAlignments exonBy coverageByTranscript
updated 6.0 years ago by 16k • written 6.0 years ago by ▴ 90
2
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0
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1.1k
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SOLVED. finding distance to nearest neighbour (non-self) within a list in GenomicRanges
GenomicRanges GenomicFeatures grange distanceToNearest R
6.0 years ago rmash ▴ 20
4
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3
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4.0k
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TxDb error: external pointer is not valid
software error GenomicFeatures
6.1 years ago O. William McClung • 0
0
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2
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1.4k
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Error while creating txDb from gtf file
genomicfeatures
6.2 years ago bioinagesh • 0
5
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5
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2.8k
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threeUTRsByTranscript per GENE
GenomicFeatures Transcript gene threeUTRsByTranscript
updated 4.7 years ago by ★ 1.6k • written 6.2 years ago by ▴ 10
0
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1
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1.5k
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create a full TXDB object from GFF3 data for a non-system organism / denovo assembly
GenomicFeatures rtracklayer
updated 6.5 years ago by 16k • written 6.5 years ago by ▴ 10
0
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0
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2.0k
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error with makeTxDbFromGFF
genomicfeatures gff custom genome makeTxDbFromGFF makeTxDbFromGRanges
6.6 years ago xvazquezc • 0
0
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0
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906
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Features function from genomicFeatures package worked in 2014 but currently doesn't work (upload of a deleted post)
genomicfeatures
updated 6.6 years ago by 25k • written 6.6 years ago by • 0
6
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5
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6.9k
views
Using GenomicFeatures to extract the upstream and downstream region of a transcript
genomicfeatures
updated 3.5 years ago by 16k • written 6.7 years ago by • 0
5
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6
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4.4k
views
error in makeTxDbFromUCSC
genomicfeatures R bioconductor maketxdbfromucsc
updated 6.8 years ago by 16k • written 6.8 years ago by • 0
0
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5
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1.4k
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GenomicFeatures supportedUCSCFeatureDbTracks never returns and has to be terminated with C-c
genomicfeatures bug
updated 7.0 years ago by 68k • written 7.0 years ago by ★ 1.6k
1
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2
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2.0k
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makeTxDbFromUCSC: error in Make the TxDb object
GenomicFeatures makeTxDbFromUCSC R
7.0 years ago DMA1 ▴ 10
0
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2
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1.4k
views
Preparation of summarizedExperiment for dexSeq
dexseq genomicalignments genomicfeatures genomicranges
7.1 years ago A ▴ 60
0
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1
reply
1.1k
views
NCBI hg38 transcript annotation package GenomicFeatures
GenomicFeatures
updated 7.1 years ago by 68k • written 7.1 years ago by • 0
0
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0
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1.8k
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GenomicFeatures: How to extract a gene's upstream region of TSS up to the end position of the flanking (nearby) gene.
genomicranges genomicfeatures promoter upstream_flank
7.1 years ago Wojeff • 0
1
vote
8
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3.4k
views
Trying to map nucleotide position from a transcript to genomic location
genomicfeatures mapfromtranscripts mirna
updated 7.1 years ago by ★ 6.8k • written 7.2 years ago by ▴ 20
0
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1
reply
2.1k
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getPromoterSeq error "Error in value[[3L]](cond) : record 1 (1:-XXXX-XXX) was truncated"
getPromoterSeq GRanges GenomicFeatures
7.2 years ago jerrywu1987 • 0
1
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1
reply
3.1k
views
Extracting gene structures from a GFF3 file for use with annotateWithGeneParts()
genomicfeatures genomation genomicranges methylation annotation
updated 7.3 years ago by ▴ 20 • written 7.3 years ago by • 0
0
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1
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1.6k
views
getting mouse gene ids from makeTxDbFromUCSC()
GenomicFeatures makeTxDbFromUCSC
updated 7.3 years ago by 4.2k • written 7.3 years ago by • 0
0
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5
replies
1.7k
views
Custom BSgenome with makeTxDbFromGFF
bsgenome genomicfeatures
7.3 years ago michael.weber.1 • 0
0
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1
reply
1.8k
views
makeTxDbFromGFF error "stop codons that cannot be mapped to an exon"
genomicfeatures txdb maketxdbfromgff
updated 7.3 years ago by ▴ 50 • written 7.3 years ago by • 0
1
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1
reply
1.0k
views
makeTxdbFromUCSC fails to download
maketxdbpackagefromucsc rtracklayer genomicfeatures
updated 7.3 years ago by 68k • written 7.3 years ago by • 0
0
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1
reply
3.3k
views
TxDb.Hsapiens.UCSC.hg19.knownGen installation fail - non-zero exit status
software error package installation genomicfeatures
updated 7.3 years ago by 25k • written 7.3 years ago by • 0
3
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1
reply
3.6k
views
How does GenomicFeature calculate 3'UTR?
genomicfeatures annotation utr
updated 7.4 years ago by 16k • written 7.4 years ago by • 0
1
vote
3
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2.2k
views
GenomicFeatures::makeTxDbFromEnsembl fails to create a TxDb object
genomicfeatures
updated 7.4 years ago by 68k • written 7.4 years ago by ▴ 30
0
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1
reply
2.0k
views
TPM and FPKM for lncRNA
GenomicFeatures TPM FPKM lncRNA
7.4 years ago Ina Hoeschele ▴ 620
0
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2
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1.4k
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Cannot get TxDb object using makeTxDbFromUCSC in any table:
software error genomicfeatures
updated 7.5 years ago by 68k • written 7.5 years ago by • 0
1
vote
1
reply
1.4k
views
installation of "GenomicFeatures"
GenomicFeatures
updated 7.5 years ago by 68k • written 7.5 years ago by • 0
1
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14
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4.4k
views
DEXSeq - dexseq_count.py issue
dexseq dexseq_count genomicfeatures
updated 7.5 years ago by • 0 • written 7.7 years ago by • 0
0
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1
reply
1.0k
views
Setting up PLAYRDesign gives error on makeTxDbFromUCSC, error in tableNames
genomicfeatures R
7.6 years ago songshan.guo • 0
5
votes
5
replies
2.8k
views
makeTxDbFromUCSC("hg19", "refGene") gives "not supported" error
genomicfeatures
updated 7.6 years ago by 68k • written 7.6 years ago by ▴ 20
0
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1
reply
1.3k
views
GenomicFeatures: could not find symbol "recursive" in environment of the generic function
genomicfeatures rnaseq txdb
7.6 years ago lucasmacielbiotec • 0
2
votes
2
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1.8k
views
Get canonical exon locations for gene
genomicfeatures r bioconductor
updated 7.7 years ago by 68k • written 7.7 years ago by • 0
1
vote
5
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2.5k
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Extract genomic features from a TxDb-like object
TxDB genomicfeatures promoter getpromoterseq
updated 7.7 years ago by 16k • written 7.7 years ago by ▴ 50
0
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2
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2.0k
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circular genome visualisation: genomic.labels: Error in if (cr != chr) { : missing value where TRUE/FALSE needed
genomicfeatures rcircos
7.7 years ago chrisclarkson100 ▴ 50
0
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2
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1.2k
views
Error with makeTxDbFromBiomart in GenomicFeatures package
genomicfeatures
updated 7.8 years ago by 16k • written 7.8 years ago by • 0
1
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4
replies
2.1k
views
Genomic Features UCSC refseq genes "Download the knownGene table ... Error: Bad Request"
genomicfeatures
updated 7.8 years ago by ★ 11k • written 7.8 years ago by ▴ 30
1
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3
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1.8k
views
how to get intron with ensembldb. package?
granges ensembldb GenomicFeatures
7.8 years ago alessandro.pastore ▴ 20
3
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1
reply
1.0k
views
Error in makeTxDbFromBiomart for fungi_mart
genomicfeatures biomart
7.8 years ago JohnTownsend ▴ 20
3
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6
replies
2.6k
views
cummeRbund installation fails
bioconductor cummerbund software error GenomicFeatures
updated 7.9 years ago by 25k • written 7.9 years ago by ▴ 30
0
votes
2
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1.3k
views
How to specify transcript_ids in makeTxDbFromUCSC function in GenomicFeatures package?
genomicfeatures maketxdbfromucsc
7.9 years ago rbacher ▴ 20
2
votes
4
replies
2.8k
views
possible Rtracklayer issue: TxDb errors in GenomicFeatures package-- cannot load TxDb with standard params from UCSC (issue began last night)
genomicfeatures txdb maketxdbfromucsc maketxdbfrombiomart rtracklayer
updated 7.9 years ago by ★ 11k • written 7.9 years ago by ▴ 30
0
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0
replies
954
views
Missing Information with transcriptlengthsfunction
bioconductor genomicfeatures rtracklayer transriptlengths
7.9 years ago michael.soutschek • 0
0
votes
5
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1.8k
views
makeTxdbFromUCSC in genomicfeatures package is broken
genomicfeatures
updated 7.9 years ago by ★ 11k • written 7.9 years ago by • 0
2
votes
2
replies
2.5k
views
Intron length per transcript using GenomicFeatures
intron GenomicFeatures
updated 8.0 years ago by ★ 11k • written 8.0 years ago by ▴ 10
0
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2
replies
1.2k
views
GRangesList: wiered error
genomicranges genomicfeatures
8.0 years ago Fabian Grammes ▴ 20
2
votes
4
replies
2.2k
views
How to build a RNA-seq table of counts for repeatmasker annotations
GenomicFeatures repeatmasker GenomicAlignments
updated 8.0 years ago by ★ 11k • written 8.0 years ago by ★ 3.4k
2
votes
4
replies
2.3k
views
Cannot extract TxFeatures for a defined GRanges object
TxDB genomicranges genomicfeatures
updated 8.0 years ago by 16k • written 8.0 years ago by ▴ 40
291 results • Page 2 of 6
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Comment: VariantAnnotation does escape = within header string quotes by Daniel Cameron ▴ 40
I'm just stripping the entire line as a workaround using `meta(header(vcf))$DRAGENCommandLine = NULL`. Not ideal but at least subsequent pa…
Comment: Setting up a DESeq2 Design with Paired Data by Alexander • 0
Hi Kevin, Firstly, thank you so much for not only a very prompt response, but one that is incredibly insightful and helps me learn DESeq2 …
Comment: featureCounts -L: high unassigned:mapq fraction by eja.gssssssse.r.m • 0
If you re looking to enjoy a fun mobile experience, the 3 patti vegas game offers a seamless way to play classic card games on your phone. …
Answer: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif by Kevin Blighe ★ 4.0k
Hello Matthew, Thanks for the detailed description-this sounds like a classic challenge in sncRNA analysis, where piRNAs (and other tsRN…
Answer: VariantAnnotation does escape = within header string quotes by Kevin Blighe ★ 4.0k
Hi, Thanks for the minimal reproduction - this is very clear and confirms a bug in `VariantAnnotation::writeVcf()`. The issue is that th…
Votes
Answer: DESeq2 design for haplotype MPRA
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Suppress warning in RHDF5 write
Answer: Suppress warning in RHDF5 write
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