Showing : TxDb • reset
0
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460
views
How to calculate CDS start and End per transcript from GTF file
dNdScv GenomicFeatures TxDb
6 months ago rohitsatyam102 ▴ 20
2
votes
5
replies
685
views
bambu output
txdb bambu
updated 10 months ago by ▴ 20 • written 10 months ago by • 0
0
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0
replies
588
views
Identify accepted columns in TxDb objects
TxDb
16 months ago • updated 15 months ago Lluís Revilla Sancho ▴ 730
0
votes
1
reply
564
views
TxDb conversion of transcript id to gene id
TxDb.Sscrofa.UCSC.susScr11.refGene TxDb txi
updated 18 months ago by 65k • written 18 months ago by • 0
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
5
votes
6
replies
2.1k
views
NA transcript values in my Txdb
GFF txdb
updated 2.5 years ago by 65k • written 2.6 years ago by ▴ 20
1
vote
7
replies
2.2k
views
How to get annotations for all genes that overlap a region with annotatePeak
txdb R annotatation
2.8 years ago pegah.taklifi ▴ 30
0
votes
5
replies
2.8k
views
Genomic Features error in TxDbfromGFF
GenomicFeatures TxDb
3.1 years ago sieminsk • 0
0
votes
6
replies
1.2k
views
Splitting TxDb by Strand
GenomicFeatures TxDb
3.2 years ago rproendo ▴ 20
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
0
votes
1
reply
4.5k
views
Add gene symbol when making TxDb
txdb genomicfeatures
updated 3.7 years ago by 65k • written 3.7 years ago by ▴ 90
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
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
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
2
replies
818
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
0
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0
replies
861
views
ChIPseeker error when I wnat to get tagMatrix
Chipseeker TxDb getpromoters software error
4.0 years ago hfyuan2016 • 0
0
votes
2
replies
1.1k
views
How to create GRanges for TES
GenomicFeatures TxDb CLIP-Seq
updated 4.0 years ago by ★ 11k • written 4.0 years ago by ▴ 10
1
vote
2
replies
894
views
Any possibility to "cache" TxDb object?
GenomicFeatures TxDb
updated 4.2 years ago by ★ 13k • written 4.2 years ago by ▴ 40
0
votes
2
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984
views
biomart webservice error during makeTxDbFromBiomart in r package GenomicFeatures
biomart txdb makeTxDbFromBiomart GenomicFeatures
updated 4.3 years ago by 65k • written 4.3 years ago by • 0
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
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 3.9k • written 4.3 years ago by ▴ 150
6
votes
4
replies
2.7k
views
the coordinates of exons of RefSeq or ENSEMBL genes
txdb genome exons
updated 4.8 years ago by 25k • written 4.8 years ago by ▴ 670
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
2
votes
1
reply
886
views
Do TxDb objects contain info about non-transcriptionally active regions?
TxDb GRanges BSGenome variant annotation
updated 5.1 years ago by 65k • written 5.1 years ago by ▴ 40
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
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
Error in makeTxDbFromBiomart
software error txdb maketxdbfrombiomart
5.5 years ago katie_emelianova • 0
0
votes
1
reply
1.4k
views
makeTxDbFromGFF error "stop codons that cannot be mapped to an exon"
genomicfeatures txdb maketxdbfromgff
updated 5.8 years ago by ▴ 50 • written 5.8 years ago by • 0
0
votes
1
reply
1.0k
views
TxDb basic question
txdb TxDb.Mmulatta.UCSC.rheMac8.refGene
updated 5.8 years ago by ▴ 50 • written 5.9 years ago by ▴ 120
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
0
votes
1
reply
1.0k
views
GenomicFeatures: could not find symbol "recursive" in environment of the generic function
genomicfeatures rnaseq txdb
6.1 years ago lucasmacielbiotec • 0
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
0
votes
1
reply
3.9k
views
create a txdb using makeTxDbFromGFF
bioconductor txdb maketxdbfromgff
6.4 years ago Nader.Aryamanesh • 0
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
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
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0
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1.3k
views
News: OrgDb and TxDb packages have been added to AnnotationHub for Bioc 3.6
orgdb txdb bioconductor annotation annotationhub News
6.5 years ago shepherl 3.9k
0
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4
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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
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
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
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
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
1
reply
1.2k
views
makeTxDbFromGFF returns object with wrong seqids (wrong chromosome names)
genomicfeatures txdb canis familiaris rna-seq
updated 7.1 years ago by 65k • written 7.1 years ago by • 0
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
2
votes
1
reply
1.1k
views
makeTxDbPackage() ERROR: values for symbols SOURCEURL are not single strings
genomicfeatures txdb
updated 7.4 years ago by 65k • written 7.4 years ago by ▴ 40
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
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
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
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
5
replies
1.7k
views
makeTxDbFromGFF returns empty object
genomicfeatures txdb maketxdbfromgff
8.0 years ago TimothéeFlutre ▴ 80
0
votes
2
replies
1.2k
views
how to get transcript annotation (unique)
txdb
8.0 years ago KB ▴ 50
50 results • Page 1 of 1
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Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0
Thank you Tim, this is a great help in getting me started!
Comment: Too many significant genes when integrating gtex and tcga by Michael Love 41k
Yes, this was one of the aspects we highlighted in the 2014 paper, and it's also in the workflow. Check these places first. Also take a st…
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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