Showing : TxDB • reset
8
votes
16
replies
2.7k
views
Setting package name in makeTxDbPackage
genomicfeatures txdb
updated 9.0 years ago by ★ 7.2k • written 9.0 years ago by ▴ 760
1
vote
7
replies
2.1k
views
How to get annotations for all genes that overlap a region with annotatePeak
txdb R annotatation
2.8 years ago pegah.taklifi ▴ 30
5
votes
7
replies
1.9k
views
Possible error in TxDb.Mmusculus.UCSC.mm10.ensGene_3.4.0?
txdb genomicfeatures
updated 7.2 years ago by 65k • written 7.2 years ago by ▴ 40
4
votes
7
replies
2.7k
views
How to get Genomic feature in txdb format from biomart for sacCer2 (EF4) assembly?
makeTxDbFromBiomart genomicfeatures txdb biomart
updated 8.5 years ago by 65k • written 8.5 years ago by ▴ 50
4
votes
6
replies
1.2k
views
Extremely big genes in annotation TxDb packages
annotation txdb AnnotationData Genetics
updated 3.8 years ago by 65k • written 3.8 years ago by ▴ 10
0
votes
6
replies
1.2k
views
Splitting TxDb by Strand
GenomicFeatures TxDb
3.2 years ago rproendo ▴ 20
5
votes
6
replies
2.1k
views
NA transcript values in my Txdb
GFF txdb
updated 2.5 years ago by 65k • written 2.5 years ago by ▴ 20
2
votes
6
replies
2.5k
views
Working with Arabidopsis Databases
bsgenome biomart getPromoterSeq txdb
8.7 years ago oliwindram ▴ 10
1
vote
6
replies
1.8k
views
problem creating txdb object and bsgenome for solanum pennellii
bsgenome txdb promoter
updated 8.2 years ago by 25k • written 8.2 years ago by ▴ 20
3
votes
6
replies
2.0k
views
TxDb, GenomicFeatures load from GTF file (Mmul_8)
TxDb GenomicFeatures
updated 3.8 years ago by 25k • written 3.8 years ago by ▴ 120
4
votes
5
replies
1.6k
views
R session crash with SGSeq::convertToTxFeatures
crash SGSeq TxDb makeTxDbFromBiomart TxFeatures
updated 6.6 years ago by ▴ 200 • written 6.6 years ago by ▴ 10
1
vote
5
replies
1.9k
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
3
votes
5
replies
1.8k
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
0
votes
5
replies
2.7k
views
Genomic Features error in TxDbfromGFF
GenomicFeatures TxDb
3.1 years ago sieminsk • 0
0
votes
5
replies
1.5k
views
Error using DRIMSeq with Salmon count data
DRIMSeq tximport txdb Salmon
updated 3.7 years ago by 41k • written 3.7 years ago by • 0
0
votes
5
replies
1.7k
views
makeTxDbFromGFF returns empty object
genomicfeatures txdb maketxdbfromgff
8.0 years ago TimothéeFlutre ▴ 80
0
votes
5
replies
1.9k
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 41k • written 4.3 years ago by • 0
2
votes
5
replies
683
views
bambu output
txdb bambu
updated 10 months ago by ▴ 20 • written 10 months 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 3.8k • written 4.3 years ago by ▴ 150
2
votes
5
replies
2.1k
views
Warning in makeTxDbFromGFF
txdb
updated 3.1 years ago by 16k • written 4.9 years ago by ▴ 10
0
votes
4
replies
1.6k
views
Cannot extract TxFeatures for a defined GRanges object
TxDB genomicranges genomicfeatures
updated 6.5 years ago by 16k • written 6.5 years ago by ▴ 10
6
votes
4
replies
2.7k
views
the coordinates of exons of RefSeq or ENSEMBL genes
txdb genome exons
updated 4.7 years ago by 25k • written 4.8 years ago by ▴ 670
0
votes
4
replies
1.3k
views
threeUTRsByTranscript appears to not work after invoking setter seqlevelsStyle
txdb threeutrsbytranscript seqlevelsstyle seqlevels
8.6 years ago Robert K. Bradley ▴ 40
4
votes
4
replies
2.0k
views
Why does Homo.sapiens import TxDb.Hsapiens.UCSC.hg19.knownGene instead of TxDb.Hsapiens.UCSC.hg38.knownGene?
homo.sapiens txdb annotation
updated 8.1 years ago by ★ 6.8k • written 8.1 years ago by ▴ 660
0
votes
4
replies
1.7k
views
Merging each element of a list of Genomic range
txdb granges cds orf R
updated 5.9 years ago by 65k • written 5.9 years ago by • 0
7
votes
4
replies
3.5k
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
8.0 years ago enricoferrero ▴ 660
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 6.4 years ago by ★ 11k • written 6.4 years ago by ▴ 30
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 5.4 years ago by 65k • written 5.4 years ago by ▴ 10
0
votes
3
replies
1.4k
views
possible conflict between renameSeqLevels (TxDb) and isActiveSeq (TxDb)
bug txdb genomicfeatures
8.7 years ago • updated 8.6 years ago Robert K. Bradley ▴ 40
3
votes
3
replies
3.8k
views
Installation of TxDb.Hsapiens.UCSC.hg19.knownGene fails.
biocinstaller installation TxDb
updated 9.3 years ago by ★ 7.2k • written 9.3 years ago by 1.6k
0
votes
3
replies
1.5k
views
extracting promoter region error for A.thaliana
promoter region txdb
updated 8.3 years ago by 25k • written 8.3 years ago by ▴ 20
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 7.7 years ago by 25k • written 7.7 years ago by ▴ 450
0
votes
3
replies
1.4k
views
Error in makeTxDbFromBiomart
software error txdb maketxdbfrombiomart
5.5 years ago katie_emelianova • 0
0
votes
3
replies
1.1k
views
Revisiting gene name inclusion in TxDB
Bioconductor GenomicFeatures TxDB
updated 2.5 years ago by • 0 • written 3.5 years ago by ▴ 120
2
votes
2
replies
4.4k
views
How to prepare TxDb object using makeTxDbFromGFF with polycistronic transcripts?
txdb gff3 polycistronic transcript
6.5 years ago Piotr Gawronski • 0
0
votes
2
replies
816
views
Problem in dowloading "TxDb.Hsapiens.UCSC.hg38.knownGene"
annotation software TxDb
updated 3.9 years ago by 65k • written 3.9 years ago by • 0
4
votes
2
replies
1.3k
views
distinguish DataSource from Provider and ProviderVersion in makeTxDbPackage
genomicfeatures txdb maketxdbfromgff metadata
updated 8.0 years ago by ★ 6.8k • written 8.0 years ago by ▴ 80
0
votes
2
replies
1.2k
views
how to get transcript annotation (unique)
txdb
8.0 years ago KB ▴ 50
2
votes
2
replies
1.4k
views
Setting genome information on a TxDb object
genomicfeatures txdb
updated 9.0 years ago by 16k • written 9.0 years ago by ▴ 760
3
votes
2
replies
1.7k
views
How to use EnsDb in annotatePeak from package "ChIPseeker"
GRanges ChIPseeker annotatePeak TxDb EnsDb
updated 5.2 years ago by ★ 2.0k • written 5.2 years ago by ▴ 100
0
votes
2
replies
2.0k
views
add annotation features to BSgenome or txdb package
bsgenome txdb annotation orgdb
6.8 years ago Didi ▴ 10
2
votes
2
replies
1.4k
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
8.2 years ago vinod.acear ▴ 50
0
votes
2
replies
1.0k
views
renamed seqlevels (TxDb) don't persist through a save-load cycle
GenomicFeatures TxDb
8.7 years ago • updated 8.6 years ago Robert K. Bradley ▴ 40
0
votes
2
replies
2.2k
views
makeTxDbpackage after makeTxDbfromGFF --> Error in spc[[2]] : subscript out of bounds
gtf TxDb maketxdbfromgff
updated 8.9 years ago by 16k • written 8.9 years ago by • 0
0
votes
2
replies
1.5k
views
Missing genes from TxDb.Hsapiens.UCSC.hg19.knownGene
txdb txdb.hsapiens.ucsc.hg19.knowngene gviz
updated 6.6 years ago by 65k • written 6.6 years ago by ▴ 10
0
votes
2
replies
1.5k
views
makeTxDbFromGFF Error due to incompatible seqnames
summarizedexperiment TxDb gtf genomicfeatures
updated 6.8 years ago by 41k • written 6.8 years ago by • 0
0
votes
2
replies
1.3k
views
Error in TxDb mm10 coordinates?
txdb txdb.mmusculus.ucsc.mm10.knowngene
updated 7.4 years ago by 65k • written 7.4 years ago by ▴ 10
1
vote
2
replies
2.5k
views
troubleshooting makeTxDbFromGRanges: some exons are linked to transcripts not found in the file
genomicfeatures txdb makeTxDbFromGRanges
updated 7.8 years ago by 16k • written 7.8 years ago by ★ 3.9k
0
votes
2
replies
982
views
biomart webservice error during makeTxDbFromBiomart in r package GenomicFeatures
biomart txdb makeTxDbFromBiomart GenomicFeatures
updated 4.2 years ago by 65k • written 4.3 years ago by • 0
1
vote
2
replies
890
views
Any possibility to "cache" TxDb object?
GenomicFeatures TxDb
updated 4.2 years ago by ★ 13k • written 4.2 years ago by ▴ 40
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Answer: SGSeq: moving toward diffex from SGSeq analysis by Leonard Goldstein ▴ 200
`vid` and `eid` are unique identifiers for splice variants and splicing events respectively. They are analogous to exon bin and gene identi…
Comment: Help with error using camera() in limma by Chris • 0
Thanks James! I fixed the error. I try gene symbol instead of entrez and it worked.
Comment: limma for gene expression analysis with big and unbalanced sample size by XW • 0
Could you explain more about the comment "there are no problems with using limma for unbalanced data sets" ? thanks.
Comment: Limma, eBayes different sample size of groups and adjustment by XW • 0
Could you explain more about how the analysis self-correct the different sample sizes when calling DEGs in limma? Thanks
Answer: How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy) by James W. MacDonald 65k
The section of the vignette that is *directly above the one you quote* says that you can use the HMMcopy utils to do all three things. And …
Votes
Answer: Fold change calculation in Diffbind vs. DESEQ2?
C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB
C: Extremely big genes in annotation TxDb packages
Make custom Txdb class objects from Txdb
Comment: Help with error using camera() in limma
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