Showing : txdb • reset
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
2
votes
6
replies
1.8k
views
Working with Arabidopsis Databases
bsgenome biomart getPromoterSeq txdb
6.8 years ago oliwindram ▴ 10
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
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
2
votes
1
reply
722
views
makeTxDbPackage() ERROR: values for symbols SOURCEURL are not single strings
genomicfeatures txdb
updated 5.5 years ago by 59k • written 5.5 years ago by ▴ 40
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
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
2
votes
1
reply
421
views
Do TxDb objects contain info about non-transcriptionally active regions?
TxDb GRanges BSGenome variant annotation
updated 3.2 years ago by 59k • written 3.2 years ago by ▴ 40
2
votes
5
replies
996
views
Warning in makeTxDbFromGFF
txdb
updated 13 months ago by 15k • written 2.9 years ago by ▴ 10
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
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
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
1
vote
7
replies
450
views
How to get annotations for all genes that overlap a region with annotatePeak
txdb R annotatation
10 months ago pegah.taklifi ▴ 30
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
0
votes
4
replies
894
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
0
votes
0
replies
759
views
News: OrgDb and TxDb packages have been added to AnnotationHub for Bioc 3.6
orgdb txdb bioconductor annotation annotationhub News
4.6 years ago shepherl 3.1k
0
votes
6
replies
465
views
Splitting TxDb by Strand
GenomicFeatures TxDb
15 months ago rproendo ▴ 20
0
votes
5
replies
753
views
Genomic Features error in TxDbfromGFF
GenomicFeatures TxDb
13 months ago sieminsk • 0
0
votes
1
reply
2.3k
views
create a txdb using makeTxDbFromGFF
bioconductor txdb maketxdbfromgff
4.4 years ago Nader.Aryamanesh • 0
0
votes
1
reply
684
views
GenomicFeatures: could not find symbol "recursive" in environment of the generic function
genomicfeatures rnaseq txdb
4.2 years ago lucasmacielbiotec • 0
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
0
votes
1
reply
542
views
TxDb basic question
txdb TxDb.Mmulatta.UCSC.rheMac8.refGene
updated 3.9 years ago by ▴ 50 • written 3.9 years ago by ▴ 120
0
votes
1
reply
721
views
makeTxDbFromGFF error "stop codons that cannot be mapped to an exon"
genomicfeatures txdb maketxdbfromgff
updated 3.8 years ago by ▴ 50 • written 3.9 years ago by • 0
0
votes
3
replies
818
views
Error in makeTxDbFromBiomart
software error txdb maketxdbfrombiomart
3.6 years ago katie_emelianova • 0
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
0
votes
1
reply
1.3k
views
Add gene symbol when making TxDb
txdb genomicfeatures
updated 21 months ago by 59k • written 21 months ago by ▴ 90
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
684
views
renamed seqlevels (TxDb) don't persist through a save-load cycle
GenomicFeatures TxDb
6.7 years ago Robert K. Bradley ▴ 40
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
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
0
votes
2
replies
309
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
0
replies
351
views
ChIPseeker error when I wnat to get tagMatrix
Chipseeker TxDb getpromoters software error
2.0 years ago hfyuan2016 • 0
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
3
replies
983
views
possible conflict between renameSeqLevels (TxDb) and isActiveSeq (TxDb)
bug txdb genomicfeatures
6.7 years ago Robert K. Bradley ▴ 40
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…
Votes
Answer: Warnings when using "ashr" in lfcshrinkage for DESeq2
Answer: Warnings when using "ashr" in lfcshrinkage for DESeq2
Answer: UniprotKB AC/ID to Entrez ID Conversion
edgeR: what to do with no replicates
Differential gene expression anlaysis?
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