Showing : txdb • reset
3
votes
5
replies
236
views
Splitting a TxDB or GRanges by Chromosome
GenomicRanges split chromosome TxDb
updated 6 weeks ago by 15k • written 6 weeks ago by ▴ 30
4
votes
6
replies
338
views
NA transcript values in my Txdb
GFF txdb
updated 10 weeks ago by 58k • written 3 months ago by ▴ 20
1
vote
7
replies
330
views
How to get annotations for all genes that overlap a region with annotatePeak
txdb R annotatation
6 months ago pegah.taklifi ▴ 30
0
votes
5
replies
538
views
Genomic Features error in TxDbfromGFF
GenomicFeatures TxDb
10 months ago sieminsk • 0
0
votes
6
replies
393
views
Splitting TxDb by Strand
GenomicFeatures TxDb
11 months ago rproendo ▴ 20
0
votes
3
replies
278
views
Revisiting gene name inclusion in TxDB
Bioconductor GenomicFeatures TxDB
updated 12 weeks ago by • 0 • written 14 months ago by ▴ 100
0
votes
1
reply
865
views
Add gene symbol when making TxDb
txdb genomicfeatures
updated 17 months ago by 58k • written 17 months ago by ▴ 90
0
votes
5
replies
470
views
Error using DRIMSeq with Salmon count data
DRIMSeq tximport txdb Salmon
updated 17 months ago by 35k • written 17 months ago by • 0
3
votes
6
replies
456
views
TxDb, GenomicFeatures load from GTF file (Mmul_8)
TxDb GenomicFeatures
updated 18 months ago by 25k • written 18 months ago by ▴ 120
3
votes
6
replies
407
views
Extremely big genes in annotation TxDb packages
annotation txdb AnnotationData Genetics
updated 19 months ago by 58k • written 19 months ago by ▴ 10
0
votes
2
replies
190
views
Problem in dowloading "TxDb.Hsapiens.UCSC.hg38.knownGene"
annotation software TxDb
updated 20 months ago by 58k • written 20 months ago by • 0
0
votes
0
replies
317
views
ChIPseeker error when I wnat to get tagMatrix
Chipseeker TxDb getpromoters software error
20 months ago hfyuan2016 • 0
0
votes
2
replies
272
views
How to create GRanges for TES
GenomicFeatures TxDb CLIP-Seq
updated 20 months ago by 11k • written 20 months ago by ▴ 10
1
vote
2
replies
306
views
Any possibility to "cache" TxDb object?
GenomicFeatures TxDb
updated 23 months ago by 13k • written 23 months ago by ▴ 40
0
votes
2
replies
325
views
biomart webservice error during makeTxDbFromBiomart in r package GenomicFeatures
biomart txdb makeTxDbFromBiomart GenomicFeatures
updated 24 months ago by 58k • written 24 months ago by • 0
0
votes
5
replies
380
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 2.0 years ago by 35k • written 2.0 years ago by • 0
6
votes
5
replies
292
views
PTEN missing from TxDb.Hsapiens.UCSC.hg38.knownGene?
TxDb annotation TxDb.Hsapiens.UCSC.hg38.knownGene
updated 2.0 years ago by 2.9k • written 2.0 years ago by ▴ 130
6
votes
4
replies
864
views
the coordinates of exons of RefSeq or ENSEMBL genes
txdb genome exons
updated 2.5 years ago by 25k • written 2.5 years ago by ▴ 620
2
votes
5
replies
866
views
Warning in makeTxDbFromGFF
txdb
updated 9 months ago by 15k • written 2.6 years ago by ▴ 10
2
votes
1
reply
383
views
Do TxDb objects contain info about non-transcriptionally active regions?
TxDb GRanges BSGenome variant annotation
updated 2.9 years ago by 58k • written 2.9 years ago by ▴ 40
3
votes
2
replies
753
views
How to use EnsDb in annotatePeak from package "ChIPseeker"
GRanges ChIPseeker annotatePeak TxDb EnsDb
updated 2.9 years ago by ★ 1.9k • written 3.0 years ago by ▴ 80
2
votes
4
replies
604
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 3.1 years ago by 58k • written 3.1 years ago by ▴ 10
0
votes
3
replies
769
views
Error in makeTxDbFromBiomart
software error txdb maketxdbfrombiomart
3.3 years ago katie_emelianova • 0
0
votes
1
reply
662
views
makeTxDbFromGFF error "stop codons that cannot be mapped to an exon"
genomicfeatures txdb maketxdbfromgff
updated 3.5 years ago by ▴ 50 • written 3.6 years ago by • 0
0
votes
1
reply
505
views
TxDb basic question
txdb TxDb.Mmulatta.UCSC.rheMac8.refGene
updated 3.6 years ago by ▴ 50 • written 3.6 years ago by ▴ 120
0
votes
4
replies
859
views
Merging each element of a list of Genomic range
txdb granges cds orf R
updated 3.6 years ago by 58k • written 3.6 years ago by • 0
0
votes
1
reply
662
views
GenomicFeatures: could not find symbol "recursive" in environment of the generic function
genomicfeatures rnaseq txdb
3.9 years ago lucasmacielbiotec • 0
1
vote
5
replies
905
views
Extract genomic features from a TxDb-like object
TxDB genomicfeatures promoter getpromoterseq
updated 3.9 years ago by 15k • written 3.9 years ago by ▴ 20
0
votes
1
reply
2.2k
views
create a txdb using makeTxDbFromGFF
bioconductor txdb maketxdbfromgff
4.1 years ago Nader.Aryamanesh • 0
2
votes
4
replies
1.3k
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 4.1 years ago by 11k • written 4.1 years ago by ▴ 30
2
votes
2
replies
1.8k
views
How to prepare TxDb object using makeTxDbFromGFF with polycistronic transcripts?
txdb gff3 polycistronic transcript
4.2 years ago Piotr Gawronski • 0
0
votes
4
replies
847
views
Cannot extract TxFeatures for a defined GRanges object
TxDB genomicranges genomicfeatures
updated 4.2 years ago by 15k • written 4.3 years ago by ▴ 10
0
votes
0
replies
726
views
News: OrgDb and TxDb packages have been added to AnnotationHub for Bioc 3.6
orgdb txdb bioconductor annotation annotationhub News
4.3 years ago shepherl 2.9k
0
votes
2
replies
856
views
Missing genes from TxDb.Hsapiens.UCSC.hg19.knownGene
txdb txdb.hsapiens.ucsc.hg19.knowngene gviz
updated 4.3 years ago by 58k • written 4.3 years ago by ▴ 10
3
votes
5
replies
807
views
R session crash with SGSeq::convertToTxFeatures
crash SGSeq TxDb makeTxDbFromBiomart TxFeatures
updated 4.3 years ago by ▴ 110 • written 4.4 years ago by ▴ 10
0
votes
2
replies
1.2k
views
add annotation features to BSgenome or txdb package
bsgenome txdb annotation orgdb
4.5 years ago Didi ▴ 10
0
votes
2
replies
957
views
makeTxDbFromGFF Error due to incompatible seqnames
summarizedexperiment TxDb gtf genomicfeatures
updated 4.5 years ago by 35k • written 4.5 years ago by • 0
0
votes
1
reply
774
views
makeTxDbFromGFF returns object with wrong seqids (wrong chromosome names)
genomicfeatures txdb canis familiaris rna-seq
updated 4.8 years ago by 58k • written 4.8 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 4.9 years ago by 58k • written 4.9 years ago by ▴ 30
2
votes
1
reply
666
views
makeTxDbPackage() ERROR: values for symbols SOURCEURL are not single strings
genomicfeatures txdb
updated 5.2 years ago by 58k • written 5.2 years ago by ▴ 40
0
votes
2
replies
711
views
Error in TxDb mm10 coordinates?
txdb txdb.mmusculus.ucsc.mm10.knowngene
updated 5.2 years ago by 58k • written 5.2 years ago by ▴ 10
3
votes
3
replies
787
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 5.5 years ago by 25k • written 5.5 years ago by ▴ 450
1
vote
2
replies
1.8k
views
troubleshooting makeTxDbFromGRanges: some exons are linked to transcripts not found in the file
genomicfeatures txdb makeTxDbFromGRanges
updated 5.6 years ago by 15k • written 5.6 years ago by ★ 3.2k
4
votes
2
replies
782
views
distinguish DataSource from Provider and ProviderVersion in makeTxDbPackage
genomicfeatures txdb maketxdbfromgff metadata
updated 5.7 years ago by ★ 6.7k • written 5.7 years ago by ▴ 70
0
votes
5
replies
847
views
makeTxDbFromGFF returns empty object
genomicfeatures txdb maketxdbfromgff
5.8 years ago TimothéeFlutre ▴ 70
0
votes
2
replies
793
views
how to get transcript annotation (unique)
txdb
5.8 years ago K ▴ 50
7
votes
4
replies
2.6k
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
5.8 years ago enricoferrero ▴ 590
0
votes
0
replies
750
views
extractUpstreamSeqs with custom genome, no gene_id shown
genomicranges txdb genomicfeatures featureextraction
updated 5.8 years ago by 25k • written 5.8 years ago by ▴ 30
4
votes
4
replies
1.4k
views
Why does Homo.sapiens import TxDb.Hsapiens.UCSC.hg19.knownGene instead of TxDb.Hsapiens.UCSC.hg38.knownGene?
homo.sapiens txdb annotation
updated 5.8 years ago by ★ 6.7k • written 5.8 years ago by ▴ 590
0
votes
1
reply
920
views
How to find index position of desired feature_by in TxDb granges?
granges txdb genomicfeatures
updated 5.9 years ago by 25k • written 5.9 years ago by ▴ 50
50 results • Page 1 of 1
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Comment: Multi-factor paired RNAseq differential analysis with DEseq2 by Matthew • 0
Thanks for the suggestion, I'll give that a try! Based on the PCA, all three factors do tend to influence the results, so I'll try the colu…
Comment: fgsea not downloading due to new r version. Is there a way around this? by amir.khan • 0
Seems to have done the trick and worked. thanks!
Comment: Multi-factor paired RNAseq differential analysis with DEseq2 by Michael Love 35k
Just to underscore swbarnes2 advice above, I'd also recommend discussing statistical design with a local statistician or someone familiar w…
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First, I'd start by looking at all your samples in PCA. Does sex have a strong effect? Does it make sense to compare one tissue with anot…
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Thank you for your input I appreciate it. I will revise and make changes to this post as you suggested. Unfortunately I am not able to do t…
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Answer: fgsea not downloading due to new r version. Is there a way around this?
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Answer: fgsea not downloading due to new r version. Is there a way around this?
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