Showing : TxDb • reset
0
votes
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482
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How to calculate CDS start and End per transcript from GTF file
dNdScv GenomicFeatures TxDb
7 months ago rohitsatyam102 ▴ 20
2
votes
5
replies
705
views
bambu output
txdb bambu
updated 11 months ago by ▴ 20 • written 11 months ago by • 0
0
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0
replies
617
views
Identify accepted columns in TxDb objects
TxDb
16 months ago Lluís Revilla Sancho ▴ 730
0
votes
1
reply
583
views
TxDb conversion of transcript id to gene id
TxDb.Sscrofa.UCSC.susScr11.refGene TxDb txi
updated 18 months ago by 66k • written 18 months ago by • 0
3
votes
5
replies
1.9k
views
Splitting a TxDB or GRanges by Chromosome
GenomicRanges split chromosome TxDb
updated 2.4 years ago by 16k • written 2.4 years ago by ▴ 40
5
votes
6
replies
2.1k
views
NA transcript values in my Txdb
GFF txdb
updated 2.5 years ago by 66k • written 2.6 years ago by ▴ 20
1
vote
7
replies
2.2k
views
How to get annotations for all genes that overlap a region with annotatePeak
txdb R annotatation
2.9 years ago pegah.taklifi ▴ 30
0
votes
5
replies
2.8k
views
Genomic Features error in TxDbfromGFF
GenomicFeatures TxDb
3.2 years ago sieminsk • 0
0
votes
6
replies
1.2k
views
Splitting TxDb by Strand
GenomicFeatures TxDb
3.3 years ago rproendo ▴ 20
0
votes
3
replies
1.1k
views
Revisiting gene name inclusion in TxDB
Bioconductor GenomicFeatures TxDB
updated 2.6 years ago by • 0 • written 3.6 years ago by ▴ 120
0
votes
1
reply
4.5k
views
Add gene symbol when making TxDb
txdb genomicfeatures
updated 3.8 years ago by 66k • written 3.8 years ago by ▴ 90
0
votes
5
replies
1.5k
views
Error using DRIMSeq with Salmon count data
DRIMSeq tximport txdb Salmon
updated 3.8 years ago by 42k • written 3.8 years ago by • 0
3
votes
6
replies
2.0k
views
TxDb, GenomicFeatures load from GTF file (Mmul_8)
TxDb GenomicFeatures
updated 3.9 years ago by 25k • written 3.9 years ago by ▴ 120
4
votes
6
replies
1.2k
views
Extremely big genes in annotation TxDb packages
annotation txdb AnnotationData Genetics
updated 3.9 years ago by 66k • written 3.9 years ago by ▴ 10
0
votes
2
replies
828
views
Problem in dowloading "TxDb.Hsapiens.UCSC.hg38.knownGene"
annotation software TxDb
updated 4.0 years ago by 66k • written 4.0 years ago by • 0
0
votes
0
replies
875
views
ChIPseeker error when I wnat to get tagMatrix
Chipseeker TxDb getpromoters software error
4.0 years ago hfyuan2016 • 0
0
votes
2
replies
1.1k
views
How to create GRanges for TES
GenomicFeatures TxDb CLIP-Seq
updated 4.0 years ago by ★ 11k • written 4.0 years ago by ▴ 10
1
vote
2
replies
902
views
Any possibility to "cache" TxDb object?
GenomicFeatures TxDb
updated 4.2 years ago by ★ 13k • written 4.2 years ago by ▴ 40
0
votes
2
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998
views
biomart webservice error during makeTxDbFromBiomart in r package GenomicFeatures
biomart txdb makeTxDbFromBiomart GenomicFeatures
updated 4.3 years ago by 66k • written 4.3 years ago by • 0
0
votes
5
replies
2.0k
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 4.3 years ago by 42k • written 4.3 years ago by • 0
6
votes
5
replies
1.0k
views
PTEN missing from TxDb.Hsapiens.UCSC.hg38.knownGene?
TxDb annotation TxDb.Hsapiens.UCSC.hg38.knownGene
updated 4.3 years ago by 3.9k • written 4.3 years ago by ▴ 150
6
votes
4
replies
2.7k
views
the coordinates of exons of RefSeq or ENSEMBL genes
txdb genome exons
updated 4.8 years ago by 25k • written 4.8 years ago by ▴ 670
2
votes
5
replies
2.2k
views
Warning in makeTxDbFromGFF
txdb
updated 3.1 years ago by 16k • written 4.9 years ago by ▴ 10
2
votes
1
reply
898
views
Do TxDb objects contain info about non-transcriptionally active regions?
TxDb GRanges BSGenome variant annotation
updated 5.2 years ago by 66k • written 5.2 years ago by ▴ 40
3
votes
2
replies
1.8k
views
How to use EnsDb in annotatePeak from package "ChIPseeker"
GRanges ChIPseeker annotatePeak TxDb EnsDb
updated 5.3 years ago by ★ 2.0k • written 5.3 years ago by ▴ 100
2
votes
4
replies
1.4k
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 5.5 years ago by 66k • written 5.5 years ago by ▴ 10
0
votes
3
replies
1.4k
views
Error in makeTxDbFromBiomart
software error txdb maketxdbfrombiomart
5.6 years ago katie_emelianova • 0
0
votes
1
reply
1.4k
views
makeTxDbFromGFF error "stop codons that cannot be mapped to an exon"
genomicfeatures txdb maketxdbfromgff
updated 5.9 years ago by ▴ 50 • written 5.9 years ago by • 0
0
votes
1
reply
1.0k
views
TxDb basic question
txdb TxDb.Mmulatta.UCSC.rheMac8.refGene
updated 5.9 years ago by ▴ 50 • written 5.9 years ago by ▴ 120
0
votes
4
replies
1.7k
views
Merging each element of a list of Genomic range
txdb granges cds orf R
updated 6.0 years ago by 66k • written 6.0 years ago by • 0
0
votes
1
reply
1.0k
views
GenomicFeatures: could not find symbol "recursive" in environment of the generic function
genomicfeatures rnaseq txdb
6.2 years ago lucasmacielbiotec • 0
1
vote
5
replies
2.0k
views
Extract genomic features from a TxDb-like object
TxDB genomicfeatures promoter getpromoterseq
updated 6.2 years ago by 16k • written 6.2 years ago by ▴ 40
0
votes
1
reply
3.9k
views
create a txdb using makeTxDbFromGFF
bioconductor txdb maketxdbfromgff
6.4 years ago Nader.Aryamanesh • 0
2
votes
4
replies
2.1k
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 6.5 years ago by ★ 11k • written 6.5 years ago by ▴ 30
2
votes
2
replies
4.5k
views
How to prepare TxDb object using makeTxDbFromGFF with polycistronic transcripts?
txdb gff3 polycistronic transcript
6.6 years ago • updated 6.5 years ago Piotr Gawronski • 0
0
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4
replies
1.7k
views
Cannot extract TxFeatures for a defined GRanges object
TxDB genomicranges genomicfeatures
updated 6.6 years ago by 16k • written 6.6 years ago by ▴ 10
0
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0
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1.3k
views
News: OrgDb and TxDb packages have been added to AnnotationHub for Bioc 3.6
orgdb txdb bioconductor annotation annotationhub News
6.6 years ago shepherl 3.9k
0
votes
2
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1.5k
views
Missing genes from TxDb.Hsapiens.UCSC.hg19.knownGene
txdb txdb.hsapiens.ucsc.hg19.knowngene gviz
updated 6.6 years ago by 66k • written 6.6 years ago by ▴ 10
4
votes
5
replies
1.6k
views
R session crash with SGSeq::convertToTxFeatures
crash SGSeq TxDb makeTxDbFromBiomart TxFeatures
updated 6.7 years ago by ▴ 220 • written 6.7 years ago by ▴ 10
0
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2
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2.0k
views
add annotation features to BSgenome or txdb package
bsgenome txdb annotation orgdb
6.8 years ago Didi ▴ 10
0
votes
2
replies
1.5k
views
makeTxDbFromGFF Error due to incompatible seqnames
summarizedexperiment TxDb gtf genomicfeatures
updated 6.9 years ago by 42k • written 6.9 years ago by • 0
0
votes
1
reply
1.3k
views
makeTxDbFromGFF returns object with wrong seqids (wrong chromosome names)
genomicfeatures txdb canis familiaris rna-seq
updated 7.1 years ago by 66k • written 7.1 years ago by • 0
5
votes
7
replies
2.0k
views
Possible error in TxDb.Mmusculus.UCSC.mm10.ensGene_3.4.0?
txdb genomicfeatures
updated 7.2 years ago by 66k • written 7.2 years ago by ▴ 40
2
votes
1
reply
1.1k
views
makeTxDbPackage() ERROR: values for symbols SOURCEURL are not single strings
genomicfeatures txdb
updated 7.5 years ago by 66k • written 7.5 years ago by ▴ 40
0
votes
2
replies
1.3k
views
Error in TxDb mm10 coordinates?
txdb txdb.mmusculus.ucsc.mm10.knowngene
updated 7.5 years ago by 66k • written 7.5 years ago by ▴ 10
3
votes
3
replies
1.3k
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 7.8 years ago by 25k • written 7.8 years ago by ▴ 450
1
vote
2
replies
2.6k
views
troubleshooting makeTxDbFromGRanges: some exons are linked to transcripts not found in the file
genomicfeatures txdb makeTxDbFromGRanges
updated 7.9 years ago by 16k • written 7.9 years ago by ★ 4.0k
4
votes
2
replies
1.3k
views
distinguish DataSource from Provider and ProviderVersion in makeTxDbPackage
genomicfeatures txdb maketxdbfromgff metadata
updated 8.1 years ago by ★ 6.8k • written 8.1 years ago by ▴ 80
0
votes
5
replies
1.7k
views
makeTxDbFromGFF returns empty object
genomicfeatures txdb maketxdbfromgff
8.1 years ago TimothéeFlutre ▴ 80
0
votes
2
replies
1.2k
views
how to get transcript annotation (unique)
txdb
8.1 years ago KB ▴ 50
50 results • Page 1 of 1
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Comment: Volcano plot of scRNA-seq data not "centered" by ATpoint ★ 4.2k
My comment was generic. If your experiment causes drastic shifts then the situation might be different. The advise is the same: Try to use …
Comment: conumee with Infinium MethylationEPIC v2.0 by Maximus • 0
Hi Sole, If there is a combined mixture of MSet of 450K, EPIC and EPICv2, how should I create an annotation object? I tried to create anno…
Comment: Volcano plot of scRNA-seq data not "centered" by tjl • 0
Thank you both. The code is below, simplified a bit for simplicity. ATpoint, your suggestion re: the top 20% of genes by baseMean makes me …
Comment: Cannot install oligo on Fedora by James W. MacDonald 66k
Wait a minute. The `oligo` package is *supposed to* be using `zlibbioc`, but apparently it is not. I get the same thing as you do, where it…
Comment: Cannot install oligo on Fedora by James W. MacDonald 66k
There is the `zlibbioc` package that provides the headers for zlib 1.2.5, that I think you should be able to use, although that would requi…
Votes
DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Gene symbol
DESeq2 swap ensembl gene id rownames with gene symbol column
A: DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Ge
DESeq2: add annotations (from data frame) to DESeqDataSet
Add new columns to DESeqResults from text file by matching rownames.
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