Showing : txdb • reset
0
votes
0
replies
38
views
Inconsistencies between accessor functions for TxDb databases with selected seqlevels.
TxDb GenomicFeatures GenomeInfoDb
2 days ago dbsgtk • 0
1
vote
4
replies
736
views
txdb.mmusculus.ucsc.mm10.knowngene issue on X chromosome
TxDb.Mmusculus.UCSC.mm10.ensGene TxDb karyoploteR
14 months ago remi-xavier.coux ▴ 10
0
votes
1
reply
1.4k
views
How to calculate CDS start and End per transcript from GTF file
dNdScv GenomicFeatures TxDb
2.3 years ago rohitsatyam102 ▴ 20
2
votes
5
replies
1.5k
views
bambu output
txdb bambu
updated 2.6 years ago by ▴ 20 • written 2.6 years ago by • 0
0
votes
0
replies
1.2k
views
Identify accepted columns in TxDb objects
TxDb
3.1 years ago Lluís Revilla Sancho ▴ 760
0
votes
1
reply
1.0k
views
TxDb conversion of transcript id to gene id
TxDb.Sscrofa.UCSC.susScr11.refGene TxDb txi
updated 3.3 years ago by 68k • written 3.3 years ago by • 0
3
votes
5
replies
3.0k
views
Splitting a TxDB or GRanges by Chromosome
GenomicRanges split chromosome TxDb
updated 4.2 years ago by 16k • written 4.2 years ago by ▴ 40
5
votes
6
replies
3.5k
views
NA transcript values in my Txdb
GFF txdb
updated 4.2 years ago by 68k • written 4.3 years ago by ▴ 20
1
vote
7
replies
3.6k
views
How to get annotations for all genes that overlap a region with annotatePeak
txdb R annotatation
4.6 years ago pegah.taklifi ▴ 30
0
votes
5
replies
3.9k
views
Genomic Features error in TxDbfromGFF
GenomicFeatures TxDb
4.9 years ago sieminsk • 0
0
votes
6
replies
2.0k
views
Splitting TxDb by Strand
GenomicFeatures TxDb
5.0 years ago rproendo ▴ 30
0
votes
3
replies
1.8k
views
Revisiting gene name inclusion in TxDB
Bioconductor GenomicFeatures TxDB
updated 4.3 years ago by • 0 • written 5.3 years ago by ▴ 120
0
votes
1
reply
6.2k
views
Add gene symbol when making TxDb
txdb genomicfeatures
updated 5.5 years ago by 68k • written 5.5 years ago by ▴ 90
0
votes
5
replies
2.2k
views
Error using DRIMSeq with Salmon count data
DRIMSeq tximport txdb Salmon
updated 5.5 years ago by 43k • written 5.5 years ago by • 0
3
votes
6
replies
3.4k
views
TxDb, GenomicFeatures load from GTF file (Mmul_8)
TxDb GenomicFeatures
updated 5.6 years ago by 25k • written 5.6 years ago by ▴ 120
4
votes
6
replies
2.0k
views
Extremely big genes in annotation TxDb packages
annotation txdb AnnotationData Genetics
updated 5.6 years ago by 68k • written 5.6 years ago by ▴ 10
0
votes
2
replies
1.3k
views
Problem in dowloading "TxDb.Hsapiens.UCSC.hg38.knownGene"
annotation software TxDb
updated 5.7 years ago by 68k • written 5.7 years ago by • 0
0
votes
0
replies
1.4k
views
ChIPseeker error when I wnat to get tagMatrix
Chipseeker TxDb getpromoters software error
5.8 years ago hfyuan2016 • 0
0
votes
2
replies
1.7k
views
How to create GRanges for TES
GenomicFeatures TxDb CLIP-Seq
updated 5.8 years ago by ★ 11k • written 5.8 years ago by ▴ 10
1
vote
2
replies
1.4k
views
Any possibility to "cache" TxDb object?
GenomicFeatures TxDb
updated 6.0 years ago by ★ 13k • written 6.0 years ago by ▴ 40
0
votes
2
replies
1.4k
views
biomart webservice error during makeTxDbFromBiomart in r package GenomicFeatures
biomart txdb makeTxDbFromBiomart GenomicFeatures
updated 6.0 years ago by 68k • written 6.0 years ago by • 0
0
votes
5
replies
3.0k
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 6.1 years ago by 43k • written 6.1 years ago by • 0
6
votes
5
replies
1.7k
views
PTEN missing from TxDb.Hsapiens.UCSC.hg38.knownGene?
TxDb annotation TxDb.Hsapiens.UCSC.hg38.knownGene
updated 6.1 years ago by 4.3k • written 6.1 years ago by ▴ 150
6
votes
4
replies
4.2k
views
the coordinates of exons of RefSeq or ENSEMBL genes
txdb genome exons
updated 6.5 years ago by 25k • written 6.5 years ago by ▴ 670
2
votes
5
replies
3.1k
views
Warning in makeTxDbFromGFF
txdb
updated 4.9 years ago by 16k • written 6.7 years ago by ▴ 10
2
votes
1
reply
1.4k
views
Do TxDb objects contain info about non-transcriptionally active regions?
TxDb GRanges BSGenome variant annotation
updated 6.9 years ago by 68k • written 6.9 years ago by ▴ 40
3
votes
2
replies
2.6k
views
How to use EnsDb in annotatePeak from package "ChIPseeker"
GRanges ChIPseeker annotatePeak TxDb EnsDb
updated 7.0 years ago by ★ 2.1k • written 7.0 years ago by ▴ 100
2
votes
4
replies
2.0k
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 7.2 years ago by 68k • written 7.2 years ago by ▴ 10
0
votes
3
replies
1.9k
views
Error in makeTxDbFromBiomart
software error txdb maketxdbfrombiomart
7.3 years ago katie_emelianova • 0
0
votes
1
reply
1.9k
views
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
0
votes
1
reply
1.4k
views
TxDb basic question
txdb TxDb.Mmulatta.UCSC.rheMac8.refGene
updated 7.6 years ago by ▴ 50 • written 7.6 years ago by ▴ 120
0
votes
4
replies
2.5k
views
Merging each element of a list of Genomic range
txdb granges cds orf R
updated 7.7 years ago by 68k • written 7.7 years ago by • 0
0
votes
1
reply
1.4k
views
GenomicFeatures: could not find symbol "recursive" in environment of the generic function
genomicfeatures rnaseq txdb
7.9 years ago lucasmacielbiotec • 0
1
vote
5
replies
2.7k
views
Extract genomic features from a TxDb-like object
TxDB genomicfeatures promoter getpromoterseq
updated 7.9 years ago by 16k • written 8.0 years ago by ▴ 50
0
votes
1
reply
4.8k
views
create a txdb using makeTxDbFromGFF
bioconductor txdb maketxdbfromgff
8.2 years ago Nader.Aryamanesh • 0
2
votes
4
replies
2.9k
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
2
votes
2
replies
5.5k
views
How to prepare TxDb object using makeTxDbFromGFF with polycistronic transcripts?
txdb gff3 polycistronic transcript
8.3 years ago Piotr Gawronski • 0
2
votes
4
replies
2.4k
views
Cannot extract TxFeatures for a defined GRanges object
TxDB genomicranges genomicfeatures
updated 8.3 years ago by 16k • written 8.3 years ago by ▴ 40
0
votes
0
replies
1.7k
views
News: OrgDb and TxDb packages have been added to AnnotationHub for Bioc 3.6
orgdb txdb bioconductor annotation annotationhub News
8.3 years ago shepherl 4.3k
0
votes
2
replies
2.1k
views
Missing genes from TxDb.Hsapiens.UCSC.hg19.knownGene
txdb txdb.hsapiens.ucsc.hg19.knowngene gviz
updated 8.4 years ago by 68k • written 8.4 years ago by ▴ 10
4
votes
5
replies
2.2k
views
R session crash with SGSeq::convertToTxFeatures
crash SGSeq TxDb makeTxDbFromBiomart TxFeatures
updated 8.4 years ago by ▴ 260 • written 8.4 years ago by ▴ 40
0
votes
2
replies
2.6k
views
add annotation features to BSgenome or txdb package
bsgenome txdb annotation orgdb
8.6 years ago Didi ▴ 10
0
votes
2
replies
1.9k
views
makeTxDbFromGFF Error due to incompatible seqnames
summarizedexperiment TxDb gtf genomicfeatures
updated 8.6 years ago by 43k • written 8.6 years ago by • 0
0
votes
1
reply
1.6k
views
makeTxDbFromGFF returns object with wrong seqids (wrong chromosome names)
genomicfeatures txdb canis familiaris rna-seq
updated 8.9 years ago by 68k • written 8.9 years ago by • 0
5
votes
7
replies
2.6k
views
Possible error in TxDb.Mmusculus.UCSC.mm10.ensGene_3.4.0?
txdb genomicfeatures
updated 8.9 years ago by 68k • written 8.9 years ago by ▴ 40
2
votes
1
reply
1.5k
views
makeTxDbPackage() ERROR: values for symbols SOURCEURL are not single strings
genomicfeatures txdb
updated 9.2 years ago by 68k • written 9.2 years ago by ▴ 40
0
votes
2
replies
1.8k
views
Error in TxDb mm10 coordinates?
txdb txdb.mmusculus.ucsc.mm10.knowngene
updated 9.2 years ago by 68k • written 9.2 years ago by ▴ 10
3
votes
3
replies
1.8k
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 9.5 years ago by 25k • written 9.5 years ago by ▴ 450
1
vote
2
replies
3.2k
views
troubleshooting makeTxDbFromGRanges: some exons are linked to transcripts not found in the file
genomicfeatures txdb makeTxDbFromGRanges
updated 9.6 years ago by 16k • written 9.6 years ago by ★ 4.1k
4
votes
2
replies
1.9k
views
distinguish DataSource from Provider and ProviderVersion in makeTxDbPackage
genomicfeatures txdb maketxdbfromgff metadata
updated 9.8 years ago by ★ 6.8k • written 9.8 years ago by ▴ 80
68 results • Page 1 of 2
Recent ...
Replies
Comment: Which preprocessing steps are needed before running limpa? by miro165sabo • 0
Hi @gordonsmyth, thank you a lot for very fast and valuable response. I edited the question to provide more details.
Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ? by Gordon Smyth 53k
I tend to use dpcCN(), because it more robust than dpc() to experiments with lots of samples and big differences between samples. You coul…
Answer: Which preprocessing steps are needed before running limpa? by Gordon Smyth 53k
Please see the example limpa analyses given at <http://github.com/smythlab/limpa>, especially the kidney cancer case study. limpa does not…
Comment: Why does IDTaxa trainingSet for SILVA contain "_2" suffixes in the taxonomy name by Korneel • 0
Thanks for the quick reply! If I understand correctly, I think if I keep track of the full lineage, I shouldn't have any risk of collapsin…
Comment: Pathway abundance data from Curatedmetagenomics by yesquokkan • 0
Hello, I was also wondering about the same issue. Did you figure it out?
Votes
Answer: Which preprocessing steps are needed before running limpa?
Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ?
Answer: Which preprocessing steps are needed before running limpa?
Answer: Which preprocessing steps are needed before running limpa?
Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ?
Awards • All
Scholar to Gordon Smyth 53k
Popular Question to Peter Hickey &utrif; 760
Popular Question to Sean Davis 21k
Popular Question to James W. MacDonald 68k
Popular Question to shepherl 4.3k
Locations • All
Slovakia, 10 minutes ago
United States, 1 hour ago
The city by the bay, 2 hours ago
United States, 2 hours ago
spain, 3 hours ago
Traffic: 1004 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats
See More

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6