Showing : TxDb • reset
1
vote
7
replies
190
views
How to get annotations for all genes that overlap a region with annotatePeak
txdb R annotatation
10 weeks ago pegah.taklifi ▴ 30
0
votes
5
replies
357
views
Genomic Features error in TxDbfromGFF
GenomicFeatures TxDb
5 months ago sieminsk • 0
0
votes
6
replies
272
views
Splitting TxDb by Strand
GenomicFeatures TxDb
7 months ago rproendo ▴ 20
0
votes
2
replies
191
views
Revisiting gene name inclusion in TxDB
Bioconductor GenomicFeatures TxDB
10 months ago k.vitting.seerup ▴ 100
0
votes
1
reply
530
views
Add gene symbol when making TxDb
txdb genomicfeatures
updated 13 months ago by 58k • written 13 months ago by ▴ 90
0
votes
5
replies
285
views
Error using DRIMSeq with Salmon count data
DRIMSeq tximport txdb Salmon
updated 13 months ago by 34k • written 13 months ago by • 0
3
votes
6
replies
337
views
TxDb, GenomicFeatures load from GTF file (Mmul_8)
TxDb GenomicFeatures
updated 14 months ago by 25k • written 14 months ago by ▴ 120
3
votes
6
replies
283
views
Extremely big genes in annotation TxDb packages
annotation txdb AnnotationData Genetics
updated 15 months ago by 58k • written 15 months ago by ▴ 10
0
votes
2
replies
148
views
Problem in dowloading "TxDb.Hsapiens.UCSC.hg38.knownGene"
annotation software TxDb
updated 16 months ago by 58k • written 16 months ago by • 0
0
votes
0
replies
241
views
ChIPseeker error when I wnat to get tagMatrix
Chipseeker TxDb getpromoters software error
16 months ago hfyuan2016 • 0
0
votes
2
replies
208
views
How to create GRanges for TES
GenomicFeatures TxDb CLIP-Seq
updated 16 months ago by 11k • written 16 months ago by ▴ 10
1
vote
2
replies
243
views
Any possibility to "cache" TxDb object?
GenomicFeatures TxDb
updated 19 months ago by 13k • written 19 months ago by ▴ 40
0
votes
2
replies
173
views
biomart webservice error during makeTxDbFromBiomart in r package GenomicFeatures
biomart txdb makeTxDbFromBiomart GenomicFeatures
updated 20 months ago by 58k • written 20 months ago by • 0
0
votes
5
replies
262
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 20 months ago by 34k • written 20 months ago by • 0
6
votes
5
replies
220
views
PTEN missing from TxDb.Hsapiens.UCSC.hg38.knownGene?
TxDb annotation TxDb.Hsapiens.UCSC.hg38.knownGene
updated 20 months ago by 2.8k • written 20 months ago by ▴ 130
6
votes
4
replies
729
views
the coordinates of exons of RefSeq or ENSEMBL genes
txdb genome exons
updated 2.2 years ago by 25k • written 2.2 years ago by ▴ 620
2
votes
5
replies
741
views
Warning in makeTxDbFromGFF
txdb
updated 5 months ago by 15k • written 2.3 years ago by ▴ 10
2
votes
1
reply
333
views
Do TxDb objects contain info about non-transcriptionally active regions?
TxDb GRanges BSGenome variant annotation
updated 2.5 years ago by 58k • written 2.5 years ago by ▴ 40
3
votes
2
replies
655
views
How to use EnsDb in annotatePeak from package "ChIPseeker"
GRanges ChIPseeker annotatePeak TxDb EnsDb
updated 2.6 years ago by ★ 1.9k • written 2.6 years ago by ▴ 80
2
votes
4
replies
519
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 2.8 years ago by 58k • written 2.8 years ago by ▴ 10
0
votes
3
replies
698
views
Error in makeTxDbFromBiomart
software error txdb maketxdbfrombiomart
2.9 years ago katie_emelianova • 0
0
votes
1
reply
600
views
makeTxDbFromGFF error "stop codons that cannot be mapped to an exon"
genomicfeatures txdb maketxdbfromgff
updated 3.2 years ago by ▴ 50 • written 3.2 years ago by • 0
0
votes
1
reply
456
views
TxDb basic question
txdb TxDb.Mmulatta.UCSC.rheMac8.refGene
updated 3.2 years ago by ▴ 50 • written 3.3 years ago by ▴ 120
0
votes
4
replies
736
views
Merging each element of a list of Genomic range
txdb granges cds orf R
updated 3.3 years ago by 58k • written 3.3 years ago by • 0
0
votes
1
reply
625
views
GenomicFeatures: could not find symbol "recursive" in environment of the generic function
genomicfeatures rnaseq txdb
3.5 years ago lucasmacielbiotec • 0
1
vote
5
replies
819
views
Extract genomic features from a TxDb-like object
TxDB genomicfeatures promoter getpromoterseq
updated 3.6 years ago by 15k • written 3.6 years ago by ▴ 20
0
votes
1
reply
2.1k
views
create a txdb using makeTxDbFromGFF
bioconductor txdb maketxdbfromgff
3.8 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 3.8 years ago by 11k • written 3.8 years ago by ▴ 30
2
votes
2
replies
1.4k
views
How to prepare TxDb object using makeTxDbFromGFF with polycistronic transcripts?
txdb gff3 polycistronic transcript
3.9 years ago Piotr Gawronski • 0
0
votes
4
replies
783
views
Cannot extract TxFeatures for a defined GRanges object
TxDB genomicranges genomicfeatures
updated 3.9 years ago by 15k • written 3.9 years ago by ▴ 10
0
votes
0
replies
605
views
News: OrgDb and TxDb packages have been added to AnnotationHub for Bioc 3.6
orgdb txdb bioconductor annotation annotationhub News
3.9 years ago shepherl 2.8k
0
votes
2
replies
793
views
Missing genes from TxDb.Hsapiens.UCSC.hg19.knownGene
txdb txdb.hsapiens.ucsc.hg19.knowngene gviz
updated 4.0 years ago by 58k • written 4.0 years ago by ▴ 10
3
votes
5
replies
737
views
R session crash with SGSeq::convertToTxFeatures
crash SGSeq TxDb makeTxDbFromBiomart TxFeatures
updated 4.0 years ago by ▴ 110 • written 4.0 years ago by ▴ 10
0
votes
2
replies
1.1k
views
add annotation features to BSgenome or txdb package
bsgenome txdb annotation orgdb
4.2 years ago Didi ▴ 10
0
votes
2
replies
797
views
makeTxDbFromGFF Error due to incompatible seqnames
summarizedexperiment TxDb gtf genomicfeatures
updated 4.2 years ago by 34k • written 4.2 years ago by • 0
0
votes
1
reply
730
views
makeTxDbFromGFF returns object with wrong seqids (wrong chromosome names)
genomicfeatures txdb canis familiaris rna-seq
updated 4.5 years ago by 58k • written 4.5 years ago by • 0
5
votes
7
replies
1.1k
views
Possible error in TxDb.Mmusculus.UCSC.mm10.ensGene_3.4.0?
txdb genomicfeatures
updated 4.6 years ago by 58k • written 4.6 years ago by ▴ 30
2
votes
1
reply
628
views
makeTxDbPackage() ERROR: values for symbols SOURCEURL are not single strings
genomicfeatures txdb
updated 4.8 years ago by 58k • written 4.8 years ago by ▴ 40
0
votes
2
replies
625
views
Error in TxDb mm10 coordinates?
txdb txdb.mmusculus.ucsc.mm10.knowngene
updated 4.8 years ago by 58k • written 4.8 years ago by ▴ 10
3
votes
3
replies
737
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 5.1 years ago by 25k • written 5.1 years ago by ▴ 450
1
vote
2
replies
1.7k
views
troubleshooting makeTxDbFromGRanges: some exons are linked to transcripts not found in the file
genomicfeatures txdb makeTxDbFromGRanges
updated 5.2 years ago by 15k • written 5.2 years ago by ★ 3.0k
4
votes
2
replies
723
views
distinguish DataSource from Provider and ProviderVersion in makeTxDbPackage
genomicfeatures txdb maketxdbfromgff metadata
updated 5.4 years ago by ★ 6.7k • written 5.4 years ago by ▴ 70
0
votes
5
replies
785
views
makeTxDbFromGFF returns empty object
genomicfeatures txdb maketxdbfromgff
5.4 years ago TimothéeFlutre ▴ 70
0
votes
2
replies
761
views
how to get transcript annotation (unique)
txdb
5.4 years ago K ▴ 50
7
votes
4
replies
2.0k
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
5.4 years ago enricoferrero ▴ 570
0
votes
0
replies
699
views
extractUpstreamSeqs with custom genome, no gene_id shown
genomicranges txdb genomicfeatures featureextraction
updated 5.4 years ago by 25k • written 5.5 years ago by ▴ 30
4
votes
4
replies
1.3k
views
Why does Homo.sapiens import TxDb.Hsapiens.UCSC.hg19.knownGene instead of TxDb.Hsapiens.UCSC.hg38.knownGene?
homo.sapiens txdb annotation
updated 5.5 years ago by ★ 6.7k • written 5.5 years ago by ▴ 570
0
votes
1
reply
881
views
How to find index position of desired feature_by in TxDb granges?
granges txdb genomicfeatures
updated 5.6 years ago by 25k • written 5.6 years ago by ▴ 50
2
votes
2
replies
797
views
How to rename seqlevels style (I, II, III, ...,XVI, Mito to 1,2,3,...16, 17.) in txdb granges?
renameSeqlevels mapSeqlevels grangeslist granges txdb
5.6 years ago vinod.acear ▴ 50
1
vote
6
replies
1.0k
views
problem creating txdb object and bsgenome for solanum pennellii
bsgenome txdb promoter
updated 5.6 years ago by 25k • written 5.6 years ago by ▴ 20
50 results • Page 1 of 1
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Replies
Comment: How similar or disimilar are two sets of DEG? by ATpoint ▴ 850
Sounds like a job for gene set enrichment analysis, e.g. via http://bioconductor.org/packages/release/bioc/html/fgsea.html That will check…
Comment: Correct annotation of DGEList object from edgeR package regarding an RNA-Seq dat by IIart.hubII • 0
What is "coad_clear" in this case? What data have you allotted to it? Can you please share the whole code? Or can anyone answer this questi…
Comment: GenomicScores package: availableGScores and getGScores functions not working by Robert Castelo ★ 2.7k
hi, Indeed you were using an outdated version of the package. Regarding how to install current release version, please read first carefull…
Answer: Unable to install Bioconductor packages by shepherl 2.8k
This normally occurs when R was installed with a different account or an admin account. Unless on this account you won't be able to update…
Comment: GenomicScores package: availableGScores and getGScores functions not working by nattzy94 • 0
I tried to install the latest version of GenomicScores (2.4.0) by downloading the tar.gz and running `install.packages('GenomicScores_2.4.0…
Votes
A: Differential expression analysis starting from TPM data
Comment: deseq2 machine sizing best practices for very large data set
Comment: Extracting normalized counts in MEDIPS
Comment: "full model matrix is less than full rank"
A: Extracting normalized counts in MEDIPS
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