Showing : txdb • reset
7
votes
16
replies
1.6k
views
Setting package name in makeTxDbPackage
genomicfeatures txdb
updated 7.0 years ago by ★ 7.2k • written 7.0 years ago by ▴ 760
5
votes
7
replies
1.2k
views
Possible error in TxDb.Mmusculus.UCSC.mm10.ensGene_3.4.0?
txdb genomicfeatures
updated 5.2 years ago by 59k • written 5.2 years ago by ▴ 30
1
vote
7
replies
451
views
How to get annotations for all genes that overlap a region with annotatePeak
txdb R annotatation
10 months ago pegah.taklifi ▴ 30
4
votes
7
replies
1.9k
views
How to get Genomic feature in txdb format from biomart for sacCer2 (EF4) assembly?
makeTxDbFromBiomart genomicfeatures txdb biomart
updated 6.6 years ago by 59k • written 6.6 years ago by ▴ 50
0
votes
6
replies
465
views
Splitting TxDb by Strand
GenomicFeatures TxDb
15 months ago rproendo ▴ 20
4
votes
6
replies
526
views
NA transcript values in my Txdb
GFF txdb
updated 6 months ago by 59k • written 7 months ago by ▴ 20
3
votes
6
replies
537
views
TxDb, GenomicFeatures load from GTF file (Mmul_8)
TxDb GenomicFeatures
updated 22 months ago by 25k • written 22 months ago by ▴ 120
2
votes
6
replies
1.8k
views
Working with Arabidopsis Databases
bsgenome biomart getPromoterSeq txdb
6.8 years ago oliwindram ▴ 10
3
votes
6
replies
464
views
Extremely big genes in annotation TxDb packages
annotation txdb AnnotationData Genetics
updated 23 months ago by 59k • written 23 months ago by ▴ 10
1
vote
6
replies
1.2k
views
problem creating txdb object and bsgenome for solanum pennellii
bsgenome txdb promoter
updated 6.3 years ago by 25k • written 6.3 years ago by ▴ 20
3
votes
5
replies
377
views
Splitting a TxDB or GRanges by Chromosome
GenomicRanges split chromosome TxDb
updated 5 months ago by 15k • written 5 months ago by ▴ 30
0
votes
5
replies
896
views
makeTxDbFromGFF returns empty object
genomicfeatures txdb maketxdbfromgff
6.1 years ago TimothéeFlutre ▴ 80
3
votes
5
replies
856
views
R session crash with SGSeq::convertToTxFeatures
crash SGSeq TxDb makeTxDbFromBiomart TxFeatures
updated 4.7 years ago by ▴ 110 • written 4.7 years ago by ▴ 10
1
vote
5
replies
962
views
Extract genomic features from a TxDb-like object
TxDB genomicfeatures promoter getpromoterseq
updated 4.2 years ago by 15k • written 4.2 years ago by ▴ 20
2
votes
5
replies
996
views
Warning in makeTxDbFromGFF
txdb
updated 13 months ago by 15k • written 2.9 years ago by ▴ 10
6
votes
5
replies
343
views
PTEN missing from TxDb.Hsapiens.UCSC.hg38.knownGene?
TxDb annotation TxDb.Hsapiens.UCSC.hg38.knownGene
updated 2.3 years ago by 3.1k • written 2.3 years ago by ▴ 140
0
votes
5
replies
519
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 2.3 years ago by 37k • written 2.3 years ago by • 0
0
votes
5
replies
601
views
Error using DRIMSeq with Salmon count data
DRIMSeq tximport txdb Salmon
updated 21 months ago by 37k • written 21 months ago by • 0
0
votes
5
replies
753
views
Genomic Features error in TxDbfromGFF
GenomicFeatures TxDb
13 months ago sieminsk • 0
7
votes
4
replies
2.7k
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
6.1 years ago enricoferrero ▴ 610
0
votes
4
replies
885
views
threeUTRsByTranscript appears to not work after invoking setter seqlevelsStyle
txdb threeutrsbytranscript seqlevelsstyle seqlevels
6.7 years ago • updated 6.6 years ago Robert K. Bradley ▴ 40
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 6.1 years ago by ★ 6.7k • written 6.1 years ago by ▴ 610
0
votes
4
replies
895
views
Cannot extract TxFeatures for a defined GRanges object
TxDB genomicranges genomicfeatures
updated 4.6 years ago by 15k • written 4.6 years ago by ▴ 10
6
votes
4
replies
1.0k
views
the coordinates of exons of RefSeq or ENSEMBL genes
txdb genome exons
updated 2.8 years ago by 25k • written 2.8 years ago by ▴ 640
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 4.4 years ago by 11k • written 4.5 years ago by ▴ 30
2
votes
4
replies
660
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 3.4 years ago by 59k • written 3.4 years ago by ▴ 10
0
votes
4
replies
944
views
Merging each element of a list of Genomic range
txdb granges cds orf R
updated 3.9 years ago by 59k • written 3.9 years ago by • 0
3
votes
3
replies
826
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 5.8 years ago by 25k • written 5.8 years ago by ▴ 450
0
votes
3
replies
983
views
possible conflict between renameSeqLevels (TxDb) and isActiveSeq (TxDb)
bug txdb genomicfeatures
6.7 years ago Robert K. Bradley ▴ 40
0
votes
3
replies
330
views
Revisiting gene name inclusion in TxDB
Bioconductor GenomicFeatures TxDB
updated 6 months ago by • 0 • written 18 months ago by ▴ 100
3
votes
3
replies
2.9k
views
Installation of TxDb.Hsapiens.UCSC.hg19.knownGene fails.
biocinstaller installation TxDb
updated 7.3 years ago by ★ 7.2k • written 7.3 years ago by 1.5k
0
votes
3
replies
818
views
Error in makeTxDbFromBiomart
software error txdb maketxdbfrombiomart
3.6 years ago katie_emelianova • 0
0
votes
3
replies
1.1k
views
extracting promoter region error for A.thaliana
promoter region txdb
updated 6.3 years ago by 25k • written 6.3 years ago by ▴ 20
0
votes
2
replies
814
views
how to get transcript annotation (unique)
txdb
6.1 years ago K ▴ 50
4
votes
2
replies
817
views
distinguish DataSource from Provider and ProviderVersion in makeTxDbPackage
genomicfeatures txdb maketxdbfromgff metadata
updated 6.1 years ago by ★ 6.7k • written 6.1 years ago by ▴ 80
1
vote
2
replies
1.8k
views
troubleshooting makeTxDbFromGRanges: some exons are linked to transcripts not found in the file
genomicfeatures txdb makeTxDbFromGRanges
updated 5.9 years ago by 15k • written 5.9 years ago by ★ 3.2k
0
votes
2
replies
739
views
Error in TxDb mm10 coordinates?
txdb txdb.mmusculus.ucsc.mm10.knowngene
updated 5.5 years ago by 59k • written 5.5 years ago by ▴ 10
0
votes
2
replies
1.0k
views
makeTxDbFromGFF Error due to incompatible seqnames
summarizedexperiment TxDb gtf genomicfeatures
updated 4.9 years ago by 37k • written 4.9 years ago by • 0
0
votes
2
replies
1.2k
views
add annotation features to BSgenome or txdb package
bsgenome txdb annotation orgdb
4.8 years ago Didi ▴ 10
0
votes
2
replies
899
views
Missing genes from TxDb.Hsapiens.UCSC.hg19.knownGene
txdb txdb.hsapiens.ucsc.hg19.knowngene gviz
updated 4.6 years ago by 59k • written 4.6 years ago by ▴ 10
2
votes
2
replies
2.1k
views
How to prepare TxDb object using makeTxDbFromGFF with polycistronic transcripts?
txdb gff3 polycistronic transcript
4.5 years ago Piotr Gawronski • 0
3
votes
2
replies
866
views
How to use EnsDb in annotatePeak from package "ChIPseeker"
GRanges ChIPseeker annotatePeak TxDb EnsDb
updated 3.3 years ago by ★ 1.9k • written 3.3 years ago by ▴ 80
2
votes
2
replies
1.0k
views
Setting genome information on a TxDb object
genomicfeatures txdb
updated 7.0 years ago by 15k • written 7.0 years ago by ▴ 760
0
votes
2
replies
427
views
biomart webservice error during makeTxDbFromBiomart in r package GenomicFeatures
biomart txdb makeTxDbFromBiomart GenomicFeatures
updated 2.3 years ago by 59k • written 2.3 years ago by • 0
1
vote
2
replies
346
views
Any possibility to "cache" TxDb object?
GenomicFeatures TxDb
updated 2.2 years ago by 13k • written 2.2 years ago by ▴ 40
0
votes
2
replies
310
views
How to create GRanges for TES
GenomicFeatures TxDb CLIP-Seq
updated 2.0 years ago by 11k • written 2.0 years ago by ▴ 10
0
votes
2
replies
242
views
Problem in dowloading "TxDb.Hsapiens.UCSC.hg38.knownGene"
annotation software TxDb
updated 24 months ago by 59k • written 24 months ago by • 0
0
votes
2
replies
684
views
renamed seqlevels (TxDb) don't persist through a save-load cycle
GenomicFeatures TxDb
6.7 years ago Robert K. Bradley ▴ 40
2
votes
2
replies
871
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
6.2 years ago vinod.acear ▴ 50
0
votes
2
replies
1.7k
views
makeTxDbpackage after makeTxDbfromGFF --> Error in spc[[2]] : subscript out of bounds
gtf TxDb maketxdbfromgff
updated 6.9 years ago by 15k • written 6.9 years ago by • 0
50 results • Page 1 of 1
Recent ...
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Answer: regression analysis for epic array methylation data using limma by Basti ▴ 280
Which package do you intend to use ? There are many tutorials in packages vignette that show you how to perform differential methylation an…
Comment: scRNASeq reference at a transcript level by Basti ▴ 280
I believe this question is not related to any Bioconductor package, I think the only solution to this question is to search yourself in Pub…
Comment: Warnings when using "ashr" in lfcshrinkage for DESeq2 by andrebolerbarros ▴ 10
Upgrading the package solved the issue, thanks!
Answer: Warnings when using "ashr" in lfcshrinkage for DESeq2 by ATpoint ★ 1.2k
The error comes from the `mixsqp` package, see https://github.com/stephens999/ashr/issues/131. Upgrading the package to the most recent 0.3…
Comment: Warnings when using "ashr" in lfcshrinkage for DESeq2 by andrebolerbarros ▴ 10
Thanks for the suggestion. I ran the following filtering criteria: ``` keep <- rowSums(counts(dds) >= 10) >= 5 dds <- dds[keep,] ``` It ga…
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Answer: Warnings when using "ashr" in lfcshrinkage for DESeq2
Answer: Warnings when using "ashr" in lfcshrinkage for DESeq2
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edgeR: what to do with no replicates
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