Showing : TxDb • reset
0
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511
views
How to calculate CDS start and End per transcript from GTF file
dNdScv GenomicFeatures TxDb
7 months ago rohitsatyam102 ▴ 20
2
votes
5
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728
views
bambu output
txdb bambu
updated 11 months ago by ▴ 20 • written 11 months ago by • 0
0
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0
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634
views
Identify accepted columns in TxDb objects
TxDb
17 months ago Lluís Revilla Sancho ▴ 730
0
votes
1
reply
594
views
TxDb conversion of transcript id to gene id
TxDb.Sscrofa.UCSC.susScr11.refGene TxDb txi
updated 19 months ago by 66k • written 19 months ago by • 0
3
votes
5
replies
1.9k
views
Splitting a TxDB or GRanges by Chromosome
GenomicRanges split chromosome TxDb
updated 2.5 years ago by 16k • written 2.5 years ago by ▴ 40
5
votes
6
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2.2k
views
NA transcript values in my Txdb
GFF txdb
updated 2.6 years ago by 66k • written 2.7 years ago by ▴ 20
1
vote
7
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2.3k
views
How to get annotations for all genes that overlap a region with annotatePeak
txdb R annotatation
2.9 years ago pegah.taklifi ▴ 30
0
votes
5
replies
2.8k
views
Genomic Features error in TxDbfromGFF
GenomicFeatures TxDb
3.2 years ago sieminsk • 0
0
votes
6
replies
1.2k
views
Splitting TxDb by Strand
GenomicFeatures TxDb
3.4 years ago rproendo ▴ 20
0
votes
3
replies
1.1k
views
Revisiting gene name inclusion in TxDB
Bioconductor GenomicFeatures TxDB
updated 2.6 years ago by • 0 • written 3.6 years ago by ▴ 120
0
votes
1
reply
4.6k
views
Add gene symbol when making TxDb
txdb genomicfeatures
updated 3.8 years ago by 66k • written 3.8 years ago by ▴ 90
0
votes
5
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1.5k
views
Error using DRIMSeq with Salmon count data
DRIMSeq tximport txdb Salmon
updated 3.9 years ago by 42k • written 3.9 years ago by • 0
3
votes
6
replies
2.1k
views
TxDb, GenomicFeatures load from GTF file (Mmul_8)
TxDb GenomicFeatures
updated 3.9 years ago by 25k • written 3.9 years ago by ▴ 120
4
votes
6
replies
1.2k
views
Extremely big genes in annotation TxDb packages
annotation txdb AnnotationData Genetics
updated 4.0 years ago by 66k • written 4.0 years ago by ▴ 10
0
votes
2
replies
841
views
Problem in dowloading "TxDb.Hsapiens.UCSC.hg38.knownGene"
annotation software TxDb
updated 4.1 years ago by 66k • written 4.1 years ago by • 0
0
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0
replies
891
views
ChIPseeker error when I wnat to get tagMatrix
Chipseeker TxDb getpromoters software error
4.1 years ago hfyuan2016 • 0
0
votes
2
replies
1.1k
views
How to create GRanges for TES
GenomicFeatures TxDb CLIP-Seq
updated 4.1 years ago by ★ 11k • written 4.1 years ago by ▴ 10
1
vote
2
replies
915
views
Any possibility to "cache" TxDb object?
GenomicFeatures TxDb
updated 4.3 years ago by ★ 13k • written 4.3 years ago by ▴ 40
0
votes
2
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1.0k
views
biomart webservice error during makeTxDbFromBiomart in r package GenomicFeatures
biomart txdb makeTxDbFromBiomart GenomicFeatures
updated 4.4 years ago by 66k • written 4.4 years ago by • 0
0
votes
5
replies
2.0k
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 4.4 years ago by 42k • written 4.4 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 4.4 years ago by 3.9k • written 4.4 years ago by ▴ 150
6
votes
4
replies
2.7k
views
the coordinates of exons of RefSeq or ENSEMBL genes
txdb genome exons
updated 4.9 years ago by 25k • written 4.9 years ago by ▴ 670
2
votes
5
replies
2.2k
views
Warning in makeTxDbFromGFF
txdb
updated 3.2 years ago by 16k • written 5.0 years ago by ▴ 10
2
votes
1
reply
911
views
Do TxDb objects contain info about non-transcriptionally active regions?
TxDb GRanges BSGenome variant annotation
updated 5.2 years ago by 66k • written 5.2 years ago by ▴ 40
3
votes
2
replies
1.8k
views
How to use EnsDb in annotatePeak from package "ChIPseeker"
GRanges ChIPseeker annotatePeak TxDb EnsDb
updated 5.3 years ago by ★ 2.1k • written 5.3 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 5.5 years ago by 66k • written 5.5 years ago by ▴ 10
0
votes
3
replies
1.4k
views
Error in makeTxDbFromBiomart
software error txdb maketxdbfrombiomart
5.7 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 5.9 years ago by ▴ 50 • written 5.9 years ago by • 0
0
votes
1
reply
1.0k
views
TxDb basic question
txdb TxDb.Mmulatta.UCSC.rheMac8.refGene
updated 5.9 years ago by ▴ 50 • written 6.0 years ago by ▴ 120
0
votes
4
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1.8k
views
Merging each element of a list of Genomic range
txdb granges cds orf R
updated 6.0 years ago by 66k • written 6.0 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
6.2 years ago lucasmacielbiotec • 0
1
vote
5
replies
2.0k
views
Extract genomic features from a TxDb-like object
TxDB genomicfeatures promoter getpromoterseq
updated 6.3 years ago by 16k • written 6.3 years ago by ▴ 40
0
votes
1
reply
4.0k
views
create a txdb using makeTxDbFromGFF
bioconductor txdb maketxdbfromgff
6.5 years ago Nader.Aryamanesh • 0
2
votes
4
replies
2.2k
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 6.5 years ago by ★ 11k • written 6.5 years ago by ▴ 30
2
votes
2
replies
4.6k
views
How to prepare TxDb object using makeTxDbFromGFF with polycistronic transcripts?
txdb gff3 polycistronic transcript
6.6 years ago Piotr Gawronski • 0
0
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4
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1.7k
views
Cannot extract TxFeatures for a defined GRanges object
TxDB genomicranges genomicfeatures
updated 6.6 years ago by 16k • written 6.6 years ago by ▴ 10
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
6.6 years ago shepherl 3.9k
0
votes
2
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1.6k
views
Missing genes from TxDb.Hsapiens.UCSC.hg19.knownGene
txdb txdb.hsapiens.ucsc.hg19.knowngene gviz
updated 6.7 years ago by 66k • written 6.7 years ago by ▴ 10
4
votes
5
replies
1.6k
views
R session crash with SGSeq::convertToTxFeatures
crash SGSeq TxDb makeTxDbFromBiomart TxFeatures
updated 6.7 years ago by ▴ 220 • written 6.7 years ago by ▴ 10
0
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2
replies
2.0k
views
add annotation features to BSgenome or txdb package
bsgenome txdb annotation orgdb
6.9 years ago Didi ▴ 10
0
votes
2
replies
1.5k
views
makeTxDbFromGFF Error due to incompatible seqnames
summarizedexperiment TxDb gtf genomicfeatures
updated 6.9 years ago by 42k • written 6.9 years ago by • 0
0
votes
1
reply
1.3k
views
makeTxDbFromGFF returns object with wrong seqids (wrong chromosome names)
genomicfeatures txdb canis familiaris rna-seq
updated 7.2 years ago by 66k • written 7.2 years ago by • 0
5
votes
7
replies
2.0k
views
Possible error in TxDb.Mmusculus.UCSC.mm10.ensGene_3.4.0?
txdb genomicfeatures
updated 7.3 years ago by 66k • written 7.3 years ago by ▴ 40
2
votes
1
reply
1.1k
views
makeTxDbPackage() ERROR: values for symbols SOURCEURL are not single strings
genomicfeatures txdb
updated 7.5 years ago by 66k • written 7.5 years ago by ▴ 40
0
votes
2
replies
1.3k
views
Error in TxDb mm10 coordinates?
txdb txdb.mmusculus.ucsc.mm10.knowngene
updated 7.6 years ago by 66k • written 7.6 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 7.9 years ago by 25k • written 7.9 years ago by ▴ 450
1
vote
2
replies
2.6k
views
troubleshooting makeTxDbFromGRanges: some exons are linked to transcripts not found in the file
genomicfeatures txdb makeTxDbFromGRanges
updated 7.9 years ago by 16k • written 7.9 years ago by ★ 4.0k
4
votes
2
replies
1.3k
views
distinguish DataSource from Provider and ProviderVersion in makeTxDbPackage
genomicfeatures txdb maketxdbfromgff metadata
updated 8.1 years ago by ★ 6.8k • written 8.1 years ago by ▴ 80
0
votes
5
replies
1.7k
views
makeTxDbFromGFF returns empty object
genomicfeatures txdb maketxdbfromgff
8.1 years ago TimothéeFlutre ▴ 80
0
votes
2
replies
1.2k
views
how to get transcript annotation (unique)
txdb
8.1 years ago KB ▴ 50
50 results • Page 1 of 1
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Comment: gds in GEOmetadb 2023-06-26 version is empty by Frederico Moraes Ferreira ▴ 100
Try axel -n 20 https://gbnci.cancer.gov/geo/GEOmetadb.sqlite.gz
Comment: Most enriched pathway is not expressed when modifying universe parameter by James W. MacDonald 66k
The default for `enrichGO` is to subset to those with a p-value<0.05. You don't adjust that default argument, so you shouldn't have any GO …
Answer: In a 3 group DEG analysis with three batches, can I use 1 group in all three bat by Michael Love 42k
You can compare A and C thanks to the sharing of samples from B across 1, 2 and 3.
Comment: Most enriched pathway is not expressed when modifying universe parameter by adripel • 0
In the enrichGO results we have significant and non-significant enriched terms that are displayed. So why would an enriched term (significa…
Answer: Design formula, numeric contrast, and lfcshrink in deseq2 by Michael Love 42k
For questions about how to construct the correct contrasts correspond to particular hypotheses, I recommend consulting with a local statist…
Votes
Comment: Most enriched pathway is not expressed when modifying universe parameter
Time-course, comparison of two groups
Answer: Behaviour of featureCounts when quantifying multi-mapping reads
Answer: GESA with certain gene list returns no result with human genom, but many result
Answer: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
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