Showing : txdb • reset
1
vote
7
replies
133
views
How to get annotations for all genes that overlap a region with annotatePeak
txdb R annotatation
19 days ago • updated 17 days ago pegah.taklifi ▴ 30
0
votes
5
replies
270
views
Genomic Features error in TxDbfromGFF
GenomicFeatures TxDb
4 months ago sieminsk • 0
0
votes
6
replies
225
views
Splitting TxDb by Strand
GenomicFeatures TxDb
5 months ago rproendo • 0
0
votes
2
replies
159
views
Revisiting gene name inclusion in TxDB
Bioconductor GenomicFeatures TxDB
8 months ago k.vitting.seerup ▴ 100
0
votes
1
reply
435
views
Add gene symbol when making TxDb
txdb genomicfeatures
updated 11 months ago by 57k • written 11 months ago by ▴ 90
0
votes
5
replies
227
views
Error using DRIMSeq with Salmon count data
DRIMSeq tximport txdb Salmon
updated 11 months ago by 33k • written 11 months ago by • 0
3
votes
6
replies
285
views
TxDb, GenomicFeatures load from GTF file (Mmul_8)
TxDb GenomicFeatures
updated 12 months ago by 25k • written 12 months ago by ▴ 120
3
votes
6
replies
223
views
Extremely big genes in annotation TxDb packages
annotation txdb AnnotationData Genetics
updated 13 months ago by 57k • written 13 months ago by ▴ 10
0
votes
2
replies
124
views
Problem in dowloading "TxDb.Hsapiens.UCSC.hg38.knownGene"
annotation software TxDb
updated 14 months ago by 57k • written 14 months ago by • 0
0
votes
0
replies
207
views
ChIPseeker error when I wnat to get tagMatrix
Chipseeker TxDb getpromoters software error
14 months ago hfyuan2016 • 0
0
votes
2
replies
172
views
How to create GRanges for TES
GenomicFeatures TxDb CLIP-Seq
updated 14 months ago by 11k • written 14 months ago by ▴ 10
1
vote
2
replies
210
views
Any possibility to "cache" TxDb object?
GenomicFeatures TxDb
updated 17 months ago by 13k • written 17 months ago by ▴ 40
0
votes
2
replies
141
views
biomart webservice error during makeTxDbFromBiomart in r package GenomicFeatures
biomart txdb makeTxDbFromBiomart GenomicFeatures
updated 18 months ago by 57k • written 18 months ago by • 0
0
votes
5
replies
191
views
Changing Gene ID annotation style - working with Salmon output [NM...] and resulting count files are numeric-only IDs
tximport Gene IDs txdb RefSeq Salmon
updated 18 months ago by 33k • written 18 months ago by • 0
6
votes
5
replies
188
views
PTEN missing from TxDb.Hsapiens.UCSC.hg38.knownGene?
TxDb annotation TxDb.Hsapiens.UCSC.hg38.knownGene
updated 18 months ago by 2.8k • written 18 months ago by ▴ 130
6
votes
4
replies
633
views
the coordinates of exons of RefSeq or ENSEMBL genes
txdb genome exons
updated 24 months ago by 25k • written 24 months ago by ▴ 620
2
votes
5
replies
665
views
Warning in makeTxDbFromGFF
txdb
updated 3 months ago by 15k • written 2.1 years ago by ▴ 10
2
votes
1
reply
305
views
Do TxDb objects contain info about non-transcriptionally active regions?
TxDb GRanges BSGenome variant annotation
updated 2.4 years ago by 57k • written 2.4 years ago by ▴ 40
3
votes
2
replies
601
views
How to use EnsDb in annotatePeak from package "ChIPseeker"
GRanges ChIPseeker annotatePeak TxDb EnsDb
updated 2.4 years ago by ★ 1.9k • written 2.5 years ago by ▴ 60
2
votes
4
replies
486
views
Problem with extracting information about exons from TxDb.Hsapiens.UCSC.hg19.knownGene: incorrect number of exons and overlapping exons
txdb txdb.hsapiens.ucsc.hg19.knowngene granges exons ucsc
updated 2.6 years ago by 57k • written 2.6 years ago by ▴ 10
0
votes
3
replies
660
views
Error in makeTxDbFromBiomart
software error txdb maketxdbfrombiomart
2.8 years ago katie_emelianova • 0
0
votes
1
reply
551
views
makeTxDbFromGFF error "stop codons that cannot be mapped to an exon"
genomicfeatures txdb maketxdbfromgff
updated 3.0 years ago by ▴ 50 • written 3.1 years ago by • 0
0
votes
1
reply
433
views
TxDb basic question
txdb TxDb.Mmulatta.UCSC.rheMac8.refGene
updated 3.1 years ago by ▴ 50 • written 3.1 years ago by ▴ 120
0
votes
4
replies
679
views
Merging each element of a list of Genomic range
txdb granges cds orf R
updated 3.1 years ago by 57k • written 3.1 years ago by • 0
0
votes
1
reply
605
views
GenomicFeatures: could not find symbol "recursive" in environment of the generic function
genomicfeatures rnaseq txdb
3.4 years ago lucasmacielbiotec • 0
1
vote
5
replies
775
views
Extract genomic features from a TxDb-like object
TxDB genomicfeatures promoter getpromoterseq
updated 3.4 years ago by 15k • written 3.4 years ago by ▴ 20
0
votes
1
reply
2.1k
views
create a txdb using makeTxDbFromGFF
bioconductor txdb maketxdbfromgff
3.6 years ago Nader.Aryamanesh • 0
2
votes
4
replies
1.2k
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 3.6 years ago by 11k • written 3.7 years ago by ▴ 30
2
votes
2
replies
1.3k
views
How to prepare TxDb object using makeTxDbFromGFF with polycistronic transcripts?
txdb gff3 polycistronic transcript
3.7 years ago Piotr Gawronski • 0
0
votes
4
replies
751
views
Cannot extract TxFeatures for a defined GRanges object
TxDB genomicranges genomicfeatures
updated 3.8 years ago by 15k • written 3.8 years ago by ▴ 10
0
votes
0
replies
575
views
News: OrgDb and TxDb packages have been added to AnnotationHub for Bioc 3.6
orgdb txdb bioconductor annotation annotationhub News
3.8 years ago shepherl 2.8k
0
votes
2
replies
761
views
Missing genes from TxDb.Hsapiens.UCSC.hg19.knownGene
txdb txdb.hsapiens.ucsc.hg19.knowngene gviz
updated 3.8 years ago by 57k • written 3.8 years ago by ▴ 10
3
votes
5
replies
700
views
R session crash with SGSeq::convertToTxFeatures
crash SGSeq TxDb makeTxDbFromBiomart TxFeatures
updated 3.8 years ago by ▴ 110 • written 3.9 years ago by ▴ 10
0
votes
2
replies
1.1k
views
add annotation features to BSgenome or txdb package
bsgenome txdb annotation orgdb
4.0 years ago Didi ▴ 10
0
votes
2
replies
768
views
makeTxDbFromGFF Error due to incompatible seqnames
summarizedexperiment TxDb gtf genomicfeatures
updated 4.0 years ago by 33k • written 4.0 years ago by • 0
0
votes
1
reply
709
views
makeTxDbFromGFF returns object with wrong seqids (wrong chromosome names)
genomicfeatures txdb canis familiaris rna-seq
updated 4.3 years ago by 57k • written 4.3 years ago by • 0
5
votes
7
replies
1.1k
views
Possible error in TxDb.Mmusculus.UCSC.mm10.ensGene_3.4.0?
txdb genomicfeatures
updated 4.4 years ago by 57k • written 4.4 years ago by ▴ 30
2
votes
1
reply
611
views
makeTxDbPackage() ERROR: values for symbols SOURCEURL are not single strings
genomicfeatures txdb
updated 4.7 years ago by 57k • written 4.7 years ago by ▴ 40
0
votes
2
replies
605
views
Error in TxDb mm10 coordinates?
txdb txdb.mmusculus.ucsc.mm10.knowngene
updated 4.7 years ago by 57k • written 4.7 years ago by ▴ 10
3
votes
3
replies
713
views
Genes found on particular chromosome using two methods in TxDb.Hsapiens.UCSC.hg19.knownGene were not identical
txdb.hsapiens.ucsc.hg19.knowngene txdb
updated 5.0 years ago by 25k • written 5.0 years ago by ▴ 450
1
vote
2
replies
1.7k
views
troubleshooting makeTxDbFromGRanges: some exons are linked to transcripts not found in the file
genomicfeatures txdb makeTxDbFromGRanges
updated 5.1 years ago by 15k • written 5.1 years ago by ★ 3.0k
4
votes
2
replies
697
views
distinguish DataSource from Provider and ProviderVersion in makeTxDbPackage
genomicfeatures txdb maketxdbfromgff metadata
updated 5.2 years ago by ★ 6.7k • written 5.2 years ago by ▴ 70
0
votes
5
replies
754
views
makeTxDbFromGFF returns empty object
genomicfeatures txdb maketxdbfromgff
5.3 years ago TimothéeFlutre ▴ 70
0
votes
2
replies
741
views
how to get transcript annotation (unique)
txdb
5.3 years ago K ▴ 50
7
votes
4
replies
1.9k
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
5.3 years ago enricoferrero ▴ 570
0
votes
0
replies
687
views
extractUpstreamSeqs with custom genome, no gene_id shown
genomicranges txdb genomicfeatures featureextraction
updated 5.3 years ago by 25k • written 5.3 years ago by ▴ 30
4
votes
4
replies
1.3k
views
Why does Homo.sapiens import TxDb.Hsapiens.UCSC.hg19.knownGene instead of TxDb.Hsapiens.UCSC.hg38.knownGene?
homo.sapiens txdb annotation
updated 5.3 years ago by ★ 6.7k • written 5.3 years ago by ▴ 570
0
votes
1
reply
863
views
How to find index position of desired feature_by in TxDb granges?
granges txdb genomicfeatures
updated 5.4 years ago by 25k • written 5.4 years ago by ▴ 50
2
votes
2
replies
778
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
5.4 years ago vinod.acear ▴ 50
1
vote
6
replies
1.0k
views
problem creating txdb object and bsgenome for solanum pennellii
bsgenome txdb promoter
updated 5.5 years ago by 25k • written 5.5 years ago by ▴ 20
50 results • Page 1 of 1
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Mouse genes are not typically all capitals, but I was able to find a reference to a mouse gene in NCBI to [CH36-217G15][1]. Maybe this is …
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