Showing : GenomicFeatures • reset
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biomart webservice error during makeTxDbFromBiomart in r package GenomicFeatures
biomart txdb makeTxDbFromBiomart GenomicFeatures
updated 6.1 years ago by 68k • written 6.1 years ago by • 0
8
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12
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7.3k
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Intergenic coordinates with Genomic Feaures
genomicranges genomicfeatures iranges
updated 3.6 years ago by • 0 • written 10.9 years ago by ▴ 20
2
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3
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1.9k
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GenomicFeatures promotersByOverlap: Identify promoters by overlap?
GenomicFeatures GenomicRanges
updated 6.1 years ago by 68k • written 6.1 years ago by ▴ 30
0
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3
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1.4k
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Resize exons in transcript to total width
genomicranges genomicfeatures
updated 6.2 years ago by ★ 11k • written 6.2 years ago by ▴ 90
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8
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2.8k
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exonsBy does not order exons by ascending rank, is it a bug or outdated documentation?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 6.3 years ago by 16k • written 6.3 years ago by ▴ 90
2
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SOLVED. finding distance to nearest neighbour (non-self) within a list in GenomicRanges
GenomicRanges GenomicFeatures grange distanceToNearest R
6.3 years ago rmash ▴ 20
4
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3
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4.1k
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TxDb error: external pointer is not valid
software error GenomicFeatures
6.4 years ago O. William McClung • 0
0
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2
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1.5k
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Error while creating txDb from gtf file
genomicfeatures
6.5 years ago bioinagesh • 0
5
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5
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2.9k
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threeUTRsByTranscript per GENE
GenomicFeatures Transcript gene threeUTRsByTranscript
updated 5.0 years ago by ★ 1.6k • written 6.5 years ago by ▴ 10
0
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1
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1.6k
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create a full TXDB object from GFF3 data for a non-system organism / denovo assembly
GenomicFeatures rtracklayer
updated 6.8 years ago by 16k • written 6.8 years ago by ▴ 10
0
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0
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2.1k
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error with makeTxDbFromGFF
genomicfeatures gff custom genome makeTxDbFromGFF makeTxDbFromGRanges
6.9 years ago xvazquezc • 0
0
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0
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972
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Features function from genomicFeatures package worked in 2014 but currently doesn't work (upload of a deleted post)
genomicfeatures
updated 6.9 years ago by 25k • written 6.9 years ago by • 0
6
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5
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7.4k
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Using GenomicFeatures to extract the upstream and downstream region of a transcript
genomicfeatures
updated 3.8 years ago by 16k • written 7.0 years ago by • 0
5
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6
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4.5k
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error in makeTxDbFromUCSC
genomicfeatures R bioconductor maketxdbfromucsc
updated 7.1 years ago by 16k • written 7.1 years ago by • 0
0
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5
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1.5k
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GenomicFeatures supportedUCSCFeatureDbTracks never returns and has to be terminated with C-c
genomicfeatures bug
updated 7.2 years ago by 68k • written 7.2 years ago by ★ 1.6k
1
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2
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2.0k
views
makeTxDbFromUCSC: error in Make the TxDb object
GenomicFeatures makeTxDbFromUCSC R
7.3 years ago DMA1 ▴ 10
0
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2
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1.4k
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Preparation of summarizedExperiment for dexSeq
dexseq genomicalignments genomicfeatures genomicranges
7.4 years ago A ▴ 60
0
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1
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1.2k
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NCBI hg38 transcript annotation package GenomicFeatures
GenomicFeatures
updated 7.4 years ago by 68k • written 7.4 years ago by • 0
0
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0
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1.9k
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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
7.4 years ago Wojeff • 0
1
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8
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3.8k
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Trying to map nucleotide position from a transcript to genomic location
genomicfeatures mapfromtranscripts mirna
updated 7.4 years ago by ★ 6.8k • written 7.5 years ago by ▴ 20
0
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1
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2.2k
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getPromoterSeq error "Error in value[[3L]](cond) : record 1 (1:-XXXX-XXX) was truncated"
getPromoterSeq GRanges GenomicFeatures
7.5 years ago jerrywu1987 • 0
1
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1
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3.6k
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Extracting gene structures from a GFF3 file for use with annotateWithGeneParts()
genomicfeatures genomation genomicranges methylation annotation
updated 7.6 years ago by ▴ 20 • written 7.6 years ago by • 0
0
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1
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1.7k
views
getting mouse gene ids from makeTxDbFromUCSC()
GenomicFeatures makeTxDbFromUCSC
updated 7.6 years ago by 4.3k • written 7.6 years ago by • 0
0
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5
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1.8k
views
Custom BSgenome with makeTxDbFromGFF
bsgenome genomicfeatures
7.6 years ago michael.weber.1 • 0
0
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1
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1.9k
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makeTxDbFromGFF error "stop codons that cannot be mapped to an exon"
genomicfeatures txdb maketxdbfromgff
updated 7.6 years ago by ▴ 50 • written 7.6 years ago by ▴ 10
1
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1
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1.1k
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makeTxdbFromUCSC fails to download
maketxdbpackagefromucsc rtracklayer genomicfeatures
updated 7.6 years ago by 68k • written 7.6 years ago by • 0
0
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1
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3.4k
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TxDb.Hsapiens.UCSC.hg19.knownGen installation fail - non-zero exit status
software error package installation genomicfeatures
updated 7.6 years ago by 25k • written 7.6 years ago by • 0
3
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1
reply
4.0k
views
How does GenomicFeature calculate 3'UTR?
genomicfeatures annotation utr
updated 7.7 years ago by 16k • written 7.7 years ago by • 0
1
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3
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2.3k
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GenomicFeatures::makeTxDbFromEnsembl fails to create a TxDb object
genomicfeatures
updated 7.7 years ago by 68k • written 7.7 years ago by ▴ 30
0
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1
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2.1k
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TPM and FPKM for lncRNA
GenomicFeatures TPM FPKM lncRNA
7.7 years ago Ina Hoeschele ▴ 620
0
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2
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1.5k
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Cannot get TxDb object using makeTxDbFromUCSC in any table:
software error genomicfeatures
updated 7.8 years ago by 68k • written 7.8 years ago by • 0
1
vote
1
reply
1.5k
views
installation of "GenomicFeatures"
GenomicFeatures
updated 7.8 years ago by 68k • written 7.8 years ago by • 0
1
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14
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4.5k
views
DEXSeq - dexseq_count.py issue
dexseq dexseq_count genomicfeatures
updated 7.8 years ago by • 0 • written 8.0 years ago by • 0
0
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1
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1.1k
views
Setting up PLAYRDesign gives error on makeTxDbFromUCSC, error in tableNames
genomicfeatures R
7.9 years ago songshan.guo • 0
5
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5
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3.0k
views
makeTxDbFromUCSC("hg19", "refGene") gives "not supported" error
genomicfeatures
updated 7.9 years ago by 68k • written 7.9 years ago by ▴ 20
0
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1
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1.4k
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GenomicFeatures: could not find symbol "recursive" in environment of the generic function
genomicfeatures rnaseq txdb
7.9 years ago lucasmacielbiotec • 0
2
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2
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1.9k
views
Get canonical exon locations for gene
genomicfeatures r bioconductor
updated 8.0 years ago by 68k • written 8.0 years ago by • 0
1
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5
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2.7k
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Extract genomic features from a TxDb-like object
TxDB genomicfeatures promoter getpromoterseq
updated 8.0 years ago by 16k • written 8.0 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
8.0 years ago chrisclarkson100 ▴ 50
0
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2
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1.3k
views
Error with makeTxDbFromBiomart in GenomicFeatures package
genomicfeatures
updated 8.1 years ago by 16k • written 8.1 years ago by • 0
1
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4
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2.3k
views
Genomic Features UCSC refseq genes "Download the knownGene table ... Error: Bad Request"
genomicfeatures
updated 8.1 years ago by ★ 11k • written 8.1 years ago by ▴ 30
1
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3
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1.9k
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how to get intron with ensembldb. package?
granges ensembldb GenomicFeatures
8.1 years ago alessandro.pastore ▴ 20
3
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1
reply
1.1k
views
Error in makeTxDbFromBiomart for fungi_mart
genomicfeatures biomart
8.1 years ago JohnTownsend ▴ 20
3
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6
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2.7k
views
cummeRbund installation fails
bioconductor cummerbund software error GenomicFeatures
updated 8.2 years ago by 25k • written 8.2 years ago by ▴ 30
0
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2
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1.3k
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How to specify transcript_ids in makeTxDbFromUCSC function in GenomicFeatures package?
genomicfeatures maketxdbfromucsc
8.2 years ago rbacher ▴ 20
2
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4
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3.0k
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 8.2 years ago by ★ 11k • written 8.2 years ago by ▴ 30
0
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0
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998
views
Missing Information with transcriptlengthsfunction
bioconductor genomicfeatures rtracklayer transriptlengths
8.2 years ago michael.soutschek • 0
0
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5
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2.0k
views
makeTxdbFromUCSC in genomicfeatures package is broken
genomicfeatures
updated 8.2 years ago by ★ 11k • written 8.2 years ago by • 0
2
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2
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2.7k
views
Intron length per transcript using GenomicFeatures
intron GenomicFeatures
updated 8.2 years ago by ★ 11k • written 8.3 years ago by ▴ 10
0
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2
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1.2k
views
GRangesList: wiered error
genomicranges genomicfeatures
8.3 years ago Fabian Grammes ▴ 20
293 results • Page 2 of 6
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Answer: Issue loading and downloading Bioconductor 3.22 packages after update by James W. MacDonald 68k
As Robert and ATpoint have mentioned, you need to allow more time to download a large file like this. ``` > options(timeout = 5e5) > l…
Answer: Issue loading and downloading Bioconductor 3.22 packages after update by Robert Castelo ★ 3.4k
Hi, the package you refer to is not called `SNPlocs.HSapiens.dbSNP155.GRCh38`, but `SNPlocs.Hsapiens.dbSNP155.GRCh38`, note the lowercase l…
Comment: Issue loading and downloading Bioconductor 3.22 packages after update by ATpoint ★ 5.0k
"Breaks" needs a more detailed explanation, together with code and error messages. Can you confirm it's not just the R download timeout aft…
Comment: Reproducibility of code in various Bioconductor versions by strawberry3 • 0
Thank you for advice! I have updated Bioconductor to the newest one, but now some of my commands don't work anymore, and I cannot download …
Answer: Reproducibility of code in various Bioconductor versions by Gordon Smyth 53k
I'm not familiar with the packages you mention, but the whole reason why Bioconductor has versions is that code and annotation change. Code…
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Answer: Question on processing compound protein groups in limpa
Answer: Correct usage of limpa for protein input
Answer: Correct usage of limpa for protein input
Answer: Correct usage of limpa for protein input
A: Interpretaion of dendrogram height in WGCNA?
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