Showing : TxDb • reset
3
votes
5
replies
561
views
Splitting a TxDB or GRanges by Chromosome
GenomicRanges split chromosome TxDb
updated 8 months ago by 15k • written 8 months ago by ▴ 40
4
votes
6
replies
658
views
NA transcript values in my Txdb
GFF txdb
updated 9 months ago by 60k • written 10 months ago by ▴ 20
1
vote
7
replies
582
views
How to get annotations for all genes that overlap a region with annotatePeak
txdb R annotatation
13 months ago pegah.taklifi ▴ 30
0
votes
5
replies
947
views
Genomic Features error in TxDbfromGFF
GenomicFeatures TxDb
16 months ago sieminsk • 0
0
votes
6
replies
529
views
Splitting TxDb by Strand
GenomicFeatures TxDb
18 months ago rproendo ▴ 20
0
votes
3
replies
379
views
Revisiting gene name inclusion in TxDB
Bioconductor GenomicFeatures TxDB
updated 9 months ago by • 0 • written 21 months ago by ▴ 120
0
votes
1
reply
1.6k
views
Add gene symbol when making TxDb
txdb genomicfeatures
updated 24 months ago by 60k • written 2.0 years ago by ▴ 90
0
votes
5
replies
677
views
Error using DRIMSeq with Salmon count data
DRIMSeq tximport txdb Salmon
updated 2.0 years ago by 37k • written 2.0 years ago by • 0
3
votes
6
replies
629
views
TxDb, GenomicFeatures load from GTF file (Mmul_8)
TxDb GenomicFeatures
updated 2.1 years ago by 25k • written 2.1 years ago by ▴ 120
3
votes
6
replies
522
views
Extremely big genes in annotation TxDb packages
annotation txdb AnnotationData Genetics
updated 2.1 years ago by 60k • written 2.1 years ago by ▴ 10
0
votes
2
replies
285
views
Problem in dowloading "TxDb.Hsapiens.UCSC.hg38.knownGene"
annotation software TxDb
updated 2.2 years ago by 60k • written 2.2 years ago by • 0
0
votes
0
replies
406
views
ChIPseeker error when I wnat to get tagMatrix
Chipseeker TxDb getpromoters software error
2.2 years ago hfyuan2016 • 0
0
votes
2
replies
351
views
How to create GRanges for TES
GenomicFeatures TxDb CLIP-Seq
updated 2.3 years ago by 11k • written 2.3 years ago by ▴ 10
1
vote
2
replies
394
views
Any possibility to "cache" TxDb object?
GenomicFeatures TxDb
updated 2.5 years ago by 13k • written 2.5 years ago by ▴ 40
0
votes
2
replies
469
views
biomart webservice error during makeTxDbFromBiomart in r package GenomicFeatures
biomart txdb makeTxDbFromBiomart GenomicFeatures
updated 2.5 years ago by 60k • written 2.5 years ago by • 0
0
votes
5
replies
644
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 2.6 years ago by 37k • written 2.6 years ago by • 0
6
votes
5
replies
388
views
PTEN missing from TxDb.Hsapiens.UCSC.hg38.knownGene?
TxDb annotation TxDb.Hsapiens.UCSC.hg38.knownGene
updated 2.6 years ago by 3.2k • written 2.6 years ago by ▴ 140
6
votes
4
replies
1.2k
views
the coordinates of exons of RefSeq or ENSEMBL genes
txdb genome exons
updated 3.0 years ago by 25k • written 3.0 years ago by ▴ 640
2
votes
5
replies
1.1k
views
Warning in makeTxDbFromGFF
txdb
updated 16 months ago by 15k • written 3.2 years ago by ▴ 10
2
votes
1
reply
459
views
Do TxDb objects contain info about non-transcriptionally active regions?
TxDb GRanges BSGenome variant annotation
updated 3.4 years ago by 60k • written 3.4 years ago by ▴ 40
3
votes
2
replies
945
views
How to use EnsDb in annotatePeak from package "ChIPseeker"
GRanges ChIPseeker annotatePeak TxDb EnsDb
updated 3.5 years ago by ★ 2.0k • written 3.5 years ago by ▴ 80
2
votes
4
replies
722
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 3.7 years ago by 60k • written 3.7 years ago by ▴ 10
0
votes
3
replies
874
views
Error in makeTxDbFromBiomart
software error txdb maketxdbfrombiomart
3.8 years ago katie_emelianova • 0
0
votes
1
reply
771
views
makeTxDbFromGFF error "stop codons that cannot be mapped to an exon"
genomicfeatures txdb maketxdbfromgff
updated 4.1 years ago by ▴ 50 • written 4.1 years ago by • 0
0
votes
1
reply
576
views
TxDb basic question
txdb TxDb.Mmulatta.UCSC.rheMac8.refGene
updated 4.1 years ago by ▴ 50 • written 4.1 years ago by ▴ 120
0
votes
4
replies
1.0k
views
Merging each element of a list of Genomic range
txdb granges cds orf R
updated 4.2 years ago by 60k • written 4.2 years ago by • 0
0
votes
1
reply
710
views
GenomicFeatures: could not find symbol "recursive" in environment of the generic function
genomicfeatures rnaseq txdb
4.4 years ago lucasmacielbiotec • 0
1
vote
5
replies
1.0k
views
Extract genomic features from a TxDb-like object
TxDB genomicfeatures promoter getpromoterseq
updated 4.4 years ago by 15k • written 4.4 years ago by ▴ 20
0
votes
1
reply
2.4k
views
create a txdb using makeTxDbFromGFF
bioconductor txdb maketxdbfromgff
4.7 years ago Nader.Aryamanesh • 0
2
votes
4
replies
1.4k
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 4.7 years ago by 11k • written 4.7 years ago by ▴ 30
2
votes
2
replies
2.3k
views
How to prepare TxDb object using makeTxDbFromGFF with polycistronic transcripts?
txdb gff3 polycistronic transcript
4.8 years ago Piotr Gawronski • 0
0
votes
4
replies
944
views
Cannot extract TxFeatures for a defined GRanges object
TxDB genomicranges genomicfeatures
updated 4.8 years ago by 15k • written 4.8 years ago by ▴ 10
0
votes
0
replies
797
views
News: OrgDb and TxDb packages have been added to AnnotationHub for Bioc 3.6
orgdb txdb bioconductor annotation annotationhub News
4.8 years ago shepherl 3.2k
0
votes
2
replies
950
views
Missing genes from TxDb.Hsapiens.UCSC.hg19.knownGene
txdb txdb.hsapiens.ucsc.hg19.knowngene gviz
updated 4.8 years ago by 60k • written 4.8 years ago by ▴ 10
3
votes
5
replies
897
views
R session crash with SGSeq::convertToTxFeatures
crash SGSeq TxDb makeTxDbFromBiomart TxFeatures
updated 4.9 years ago by ▴ 110 • written 4.9 years ago by ▴ 10
0
votes
2
replies
1.3k
views
add annotation features to BSgenome or txdb package
bsgenome txdb annotation orgdb
5.1 years ago Didi ▴ 10
0
votes
2
replies
1.1k
views
makeTxDbFromGFF Error due to incompatible seqnames
summarizedexperiment TxDb gtf genomicfeatures
updated 5.1 years ago by 37k • written 5.1 years ago by • 0
0
votes
1
reply
838
views
makeTxDbFromGFF returns object with wrong seqids (wrong chromosome names)
genomicfeatures txdb canis familiaris rna-seq
updated 5.4 years ago by 60k • written 5.4 years ago by • 0
5
votes
7
replies
1.2k
views
Possible error in TxDb.Mmusculus.UCSC.mm10.ensGene_3.4.0?
txdb genomicfeatures
updated 5.4 years ago by 60k • written 5.4 years ago by ▴ 30
2
votes
1
reply
756
views
makeTxDbPackage() ERROR: values for symbols SOURCEURL are not single strings
genomicfeatures txdb
updated 5.7 years ago by 60k • written 5.7 years ago by ▴ 40
0
votes
2
replies
765
views
Error in TxDb mm10 coordinates?
txdb txdb.mmusculus.ucsc.mm10.knowngene
updated 5.7 years ago by 60k • written 5.7 years ago by ▴ 10
3
votes
3
replies
862
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 6.0 years ago by 25k • written 6.0 years ago by ▴ 450
1
vote
2
replies
1.9k
views
troubleshooting makeTxDbFromGRanges: some exons are linked to transcripts not found in the file
genomicfeatures txdb makeTxDbFromGRanges
updated 6.1 years ago by 15k • written 6.1 years ago by ★ 3.3k
4
votes
2
replies
851
views
distinguish DataSource from Provider and ProviderVersion in makeTxDbPackage
genomicfeatures txdb maketxdbfromgff metadata
updated 6.3 years ago by ★ 6.7k • written 6.3 years ago by ▴ 80
0
votes
5
replies
930
views
makeTxDbFromGFF returns empty object
genomicfeatures txdb maketxdbfromgff
6.3 years ago TimothéeFlutre ▴ 80
0
votes
2
replies
844
views
how to get transcript annotation (unique)
txdb
6.3 years ago K ▴ 50
7
votes
4
replies
2.8k
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
6.3 years ago enricoferrero ▴ 620
0
votes
0
replies
806
views
extractUpstreamSeqs with custom genome, no gene_id shown
genomicranges txdb genomicfeatures featureextraction
updated 6.3 years ago by 25k • written 6.3 years ago by ▴ 30
4
votes
4
replies
1.5k
views
Why does Homo.sapiens import TxDb.Hsapiens.UCSC.hg19.knownGene instead of TxDb.Hsapiens.UCSC.hg38.knownGene?
homo.sapiens txdb annotation
updated 6.4 years ago by ★ 6.7k • written 6.4 years ago by ▴ 620
0
votes
1
reply
999
views
How to find index position of desired feature_by in TxDb granges?
granges txdb genomicfeatures
updated 6.4 years ago by 25k • written 6.5 years ago by ▴ 50
50 results • Page 1 of 1
Recent ...
Replies
Comment: DEXseq error unable to find an inherited method for function NSBS for signature by ta_awwad ▴ 10
Hi there, did you manage to solve this problem? thanks TA
Comment: Error in Create switchAnalyzeRlist by k.vitting.seerup ▴ 120
I just double checked and the fasta files found [here][1] should work. Please also take a look at [this][2] if you want to use Ensembl. …
Answer: Correlation between two different datasets: between results of RNAseq and absenc by Michael Love 37k
Re: LFC, if you are working with this and then downstream analysis, I'd recommend `lfcShrink` if you aren't already using this. It will shr…
Answer: Strange Dispersion plot by Michael Love 37k
This indeed looks strange, I would immediately suspect some weird batch effects. Try all kinds of diagnostic plots like, boxplot, PCA, corr…
Answer: Correlation between CpG methylation and gene expression from DESeq2-> Normalizat by Michael Love 37k
In this case, can you say why you want to normalize for gene length? In our tximport/tximeta pipeline, it would correct for differential ge…
Votes
Answer: Error in Create switchAnalyzeRlist
Answer: Error in Create switchAnalyzeRlist
A: DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Ge
DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Gene symbol
Answer: the difference between getGEO and getGEOSuppFiles
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