Showing : TxDB • reset
1
vote
4
replies
337
views
txdb.mmusculus.ucsc.mm10.knowngene issue on X chromosome
TxDb.Mmusculus.UCSC.mm10.ensGene TxDb karyoploteR
7 weeks ago remi-xavier.coux ▴ 10
0
votes
1
reply
851
views
How to calculate CDS start and End per transcript from GTF file
dNdScv GenomicFeatures TxDb
15 months ago rohitsatyam102 ▴ 20
2
votes
5
replies
999
views
bambu output
txdb bambu
updated 19 months ago by ▴ 20 • written 19 months ago by • 0
0
votes
0
replies
850
views
Identify accepted columns in TxDb objects
TxDb
2.1 years ago • updated 2.0 years ago Lluís Revilla Sancho ▴ 760
0
votes
1
reply
770
views
TxDb conversion of transcript id to gene id
TxDb.Sscrofa.UCSC.susScr11.refGene TxDb txi
updated 2.2 years ago by 67k • written 2.2 years ago by • 0
3
votes
5
replies
2.4k
views
Splitting a TxDB or GRanges by Chromosome
GenomicRanges split chromosome TxDb
updated 3.1 years ago by 16k • written 3.1 years ago by ▴ 40
5
votes
6
replies
2.6k
views
NA transcript values in my Txdb
GFF txdb
updated 3.2 years ago by 67k • written 3.3 years ago by ▴ 20
1
vote
7
replies
2.8k
views
How to get annotations for all genes that overlap a region with annotatePeak
txdb R annotatation
3.5 years ago pegah.taklifi ▴ 30
0
votes
5
replies
3.4k
views
Genomic Features error in TxDbfromGFF
GenomicFeatures TxDb
3.8 years ago sieminsk • 0
0
votes
6
replies
1.5k
views
Splitting TxDb by Strand
GenomicFeatures TxDb
4.0 years ago rproendo ▴ 30
0
votes
3
replies
1.4k
views
Revisiting gene name inclusion in TxDB
Bioconductor GenomicFeatures TxDB
updated 3.2 years ago by • 0 • written 4.2 years ago by ▴ 120
0
votes
1
reply
5.3k
views
Add gene symbol when making TxDb
txdb genomicfeatures
updated 4.4 years ago by 67k • written 4.4 years ago by ▴ 90
0
votes
5
replies
1.8k
views
Error using DRIMSeq with Salmon count data
DRIMSeq tximport txdb Salmon
updated 4.5 years ago by 43k • written 4.5 years ago by • 0
3
votes
6
replies
2.5k
views
TxDb, GenomicFeatures load from GTF file (Mmul_8)
TxDb GenomicFeatures
updated 4.5 years ago by 25k • written 4.5 years ago by ▴ 120
4
votes
6
replies
1.5k
views
Extremely big genes in annotation TxDb packages
annotation txdb AnnotationData Genetics
updated 4.6 years ago by 67k • written 4.6 years ago by ▴ 10
0
votes
2
replies
1.0k
views
Problem in dowloading "TxDb.Hsapiens.UCSC.hg38.knownGene"
annotation software TxDb
updated 4.7 years ago by 67k • written 4.7 years ago by • 0
0
votes
0
replies
1.1k
views
ChIPseeker error when I wnat to get tagMatrix
Chipseeker TxDb getpromoters software error
4.7 years ago hfyuan2016 • 0
0
votes
2
replies
1.3k
views
How to create GRanges for TES
GenomicFeatures TxDb CLIP-Seq
updated 4.7 years ago by ★ 11k • written 4.7 years ago by ▴ 10
1
vote
2
replies
1.1k
views
Any possibility to "cache" TxDb object?
GenomicFeatures TxDb
updated 4.9 years ago by ★ 13k • written 4.9 years ago by ▴ 40
0
votes
2
replies
1.2k
views
biomart webservice error during makeTxDbFromBiomart in r package GenomicFeatures
biomart txdb makeTxDbFromBiomart GenomicFeatures
updated 5.0 years ago by 67k • written 5.0 years ago by • 0
0
votes
5
replies
2.4k
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 5.0 years ago by 43k • written 5.0 years ago by • 0
6
votes
5
replies
1.3k
views
PTEN missing from TxDb.Hsapiens.UCSC.hg38.knownGene?
TxDb annotation TxDb.Hsapiens.UCSC.hg38.knownGene
updated 5.0 years ago by 4.1k • written 5.0 years ago by ▴ 150
6
votes
4
replies
3.1k
views
the coordinates of exons of RefSeq or ENSEMBL genes
txdb genome exons
updated 5.5 years ago by 25k • written 5.5 years ago by ▴ 670
2
votes
5
replies
2.5k
views
Warning in makeTxDbFromGFF
txdb
updated 3.8 years ago by 16k • written 5.6 years ago by ▴ 10
2
votes
1
reply
1.1k
views
Do TxDb objects contain info about non-transcriptionally active regions?
TxDb GRanges BSGenome variant annotation
updated 5.8 years ago by 67k • written 5.8 years ago by ▴ 40
3
votes
2
replies
2.1k
views
How to use EnsDb in annotatePeak from package "ChIPseeker"
GRanges ChIPseeker annotatePeak TxDb EnsDb
updated 5.9 years ago by ★ 2.1k • written 5.9 years ago by ▴ 100
2
votes
4
replies
1.7k
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 6.1 years ago by 67k • written 6.1 years ago by ▴ 10
0
votes
3
replies
1.6k
views
Error in makeTxDbFromBiomart
software error txdb maketxdbfrombiomart
6.3 years ago katie_emelianova • 0
0
votes
1
reply
1.6k
views
makeTxDbFromGFF error "stop codons that cannot be mapped to an exon"
genomicfeatures txdb maketxdbfromgff
updated 6.5 years ago by ▴ 50 • written 6.5 years ago by • 0
0
votes
1
reply
1.2k
views
TxDb basic question
txdb TxDb.Mmulatta.UCSC.rheMac8.refGene
updated 6.6 years ago by ▴ 50 • written 6.6 years ago by ▴ 120
0
votes
4
replies
2.0k
views
Merging each element of a list of Genomic range
txdb granges cds orf R
updated 6.6 years ago by 67k • written 6.6 years ago by • 0
0
votes
1
reply
1.2k
views
GenomicFeatures: could not find symbol "recursive" in environment of the generic function
genomicfeatures rnaseq txdb
6.9 years ago lucasmacielbiotec • 0
1
vote
5
replies
2.2k
views
Extract genomic features from a TxDb-like object
TxDB genomicfeatures promoter getpromoterseq
updated 6.9 years ago by 16k • written 6.9 years ago by ▴ 40
0
votes
1
reply
4.3k
views
create a txdb using makeTxDbFromGFF
bioconductor txdb maketxdbfromgff
7.1 years ago Nader.Aryamanesh • 0
2
votes
4
replies
2.4k
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 7.1 years ago by ★ 11k • written 7.1 years ago by ▴ 30
2
votes
2
replies
5.1k
views
How to prepare TxDb object using makeTxDbFromGFF with polycistronic transcripts?
txdb gff3 polycistronic transcript
7.2 years ago Piotr Gawronski • 0
2
votes
4
replies
2.0k
views
Cannot extract TxFeatures for a defined GRanges object
TxDB genomicranges genomicfeatures
updated 7.2 years ago by 16k • written 7.3 years ago by ▴ 40
0
votes
0
replies
1.5k
views
News: OrgDb and TxDb packages have been added to AnnotationHub for Bioc 3.6
orgdb txdb bioconductor annotation annotationhub News
7.2 years ago shepherl 4.1k
0
votes
2
replies
1.8k
views
Missing genes from TxDb.Hsapiens.UCSC.hg19.knownGene
txdb txdb.hsapiens.ucsc.hg19.knowngene gviz
updated 7.3 years ago by 67k • written 7.3 years ago by ▴ 10
4
votes
5
replies
1.8k
views
R session crash with SGSeq::convertToTxFeatures
crash SGSeq TxDb makeTxDbFromBiomart TxFeatures
updated 7.3 years ago by ▴ 260 • written 7.3 years ago by ▴ 40
0
votes
2
replies
2.3k
views
add annotation features to BSgenome or txdb package
bsgenome txdb annotation orgdb
7.5 years ago Didi ▴ 10
0
votes
2
replies
1.6k
views
makeTxDbFromGFF Error due to incompatible seqnames
summarizedexperiment TxDb gtf genomicfeatures
updated 7.5 years ago by 43k • written 7.5 years ago by • 0
0
votes
1
reply
1.4k
views
makeTxDbFromGFF returns object with wrong seqids (wrong chromosome names)
genomicfeatures txdb canis familiaris rna-seq
updated 7.8 years ago by 67k • written 7.8 years ago by • 0
5
votes
7
replies
2.2k
views
Possible error in TxDb.Mmusculus.UCSC.mm10.ensGene_3.4.0?
txdb genomicfeatures
updated 7.9 years ago by 67k • written 7.9 years ago by ▴ 40
2
votes
1
reply
1.3k
views
makeTxDbPackage() ERROR: values for symbols SOURCEURL are not single strings
genomicfeatures txdb
updated 8.1 years ago by 67k • written 8.2 years ago by ▴ 40
0
votes
2
replies
1.5k
views
Error in TxDb mm10 coordinates?
txdb txdb.mmusculus.ucsc.mm10.knowngene
updated 8.2 years ago by 67k • written 8.2 years ago by ▴ 10
3
votes
3
replies
1.5k
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 8.5 years ago by 25k • written 8.5 years ago by ▴ 450
1
vote
2
replies
2.8k
views
troubleshooting makeTxDbFromGRanges: some exons are linked to transcripts not found in the file
genomicfeatures txdb makeTxDbFromGRanges
updated 8.5 years ago by 16k • written 8.5 years ago by ★ 4.1k
4
votes
2
replies
1.5k
views
distinguish DataSource from Provider and ProviderVersion in makeTxDbPackage
genomicfeatures txdb maketxdbfromgff metadata
updated 8.7 years ago by ★ 6.8k • written 8.7 years ago by ▴ 80
0
votes
5
replies
1.9k
views
makeTxDbFromGFF returns empty object
genomicfeatures txdb maketxdbfromgff
8.7 years ago TimothéeFlutre ▴ 80
50 results • Page 1 of 1
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Answer: Error compiling Rbowtie2 in R-4.4 (Bioconductor 3.20 and probably 3.19) by ja.garcia • 0
It has been fixed by the Rbowtie2 maintainers in version 2.12.2. Thank you for the quick fix!
Comment: Announcing GBCC 2025: The first-ever joint conference between Bioconductor and G by Amora • 0
You did a great job giving an overview.....[slope][1] better than the bioconductor group! [1]: https://slopeio.org
Comment: contrast matrix design for a continuous variable by dtzhu337 • 0
Hi Gordon, Thank you very much for your answer. Actually the variable X is the age, which I am also interested in. Somehow, age and V1 are…
Answer: SingleCellExperiment convenience function for metadata+expression? by Peter Hickey ▴ 750
Hi Sarah, `scuttle::makePerCellDF()` / `scuttle::makePerFeatureDF()` and `scater::ggcells()` / `scater::ggfeatures()`, which build upon th…
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Thank you ATpoint for your response! In the result of GSEA, like you indicated, there will be gene sets that have positive NES and gene se…
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