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Showing :
TxDb
•
reset
0
votes
5
replies
94
views
Genomic Features error in TxDbfromGFF
GenomicFeatures
TxDb
9 days ago
sieminsk
• 0
0
votes
6
replies
130
views
Splitting TxDb by Strand
GenomicFeatures
TxDb
9 weeks ago
rproendo
• 0
0
votes
2
replies
91
views
Revisiting gene name inclusion in TxDB
Bioconductor
GenomicFeatures
TxDB
5 months ago
k.vitting.seerup
▴ 100
0
votes
1
reply
255
views
Add gene symbol when making TxDb
txdb
genomicfeatures
updated 7 months ago by
James W. MacDonald
56k • written 7 months ago by
Jake
▴ 70
0
votes
5
replies
138
views
Error using DRIMSeq with Salmon count data
DRIMSeq
tximport
txdb
Salmon
updated 8 months ago by
Michael Love
32k • written 8 months ago by
Charlotte
• 0
3
votes
6
replies
171
views
TxDb, GenomicFeatures load from GTF file (Mmul_8)
TxDb
GenomicFeatures
updated 9 months ago by
Martin Morgan
25k • written 9 months ago by
Brian Smith
▴ 120
3
votes
6
replies
141
views
Extremely big genes in annotation TxDb packages
annotation
txdb
AnnotationData
Genetics
updated 9 months ago by
James W. MacDonald
56k • written 9 months ago by
Papyrus
▴ 10
0
votes
2
replies
72
views
Problem in dowloading "TxDb.Hsapiens.UCSC.hg38.knownGene"
annotation
software
TxDb
updated 10 months ago by
James W. MacDonald
56k • written 10 months ago by
AmalAbdel-Aziz
• 0
0
votes
0
replies
141
views
ChIPseeker error when I wnat to get tagMatrix
Chipseeker
TxDb
getpromoters
software error
10 months ago
hfyuan2016
• 0
0
votes
2
replies
111
views
How to create GRanges for TES
GenomicFeatures
TxDb
CLIP-Seq
updated 11 months ago by
Michael Lawrence
11k • written 11 months ago by
mar.pieraccioli
▴ 10
1
vote
2
replies
101
views
Any possibility to "cache" TxDb object?
GenomicFeatures
TxDb
updated 13 months ago by
Steve Lianoglou
13k • written 13 months ago by
aush
▴ 40
0
votes
2
replies
87
views
biomart webservice error during makeTxDbFromBiomart in r package GenomicFeatures
biomart
txdb
makeTxDbFromBiomart
GenomicFeatures
updated 14 months ago by
James W. MacDonald
56k • written 14 months ago by
ksomi47
• 0
0
votes
5
replies
100
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 14 months ago by
Michael Love
32k • written 14 months ago by
holmkn
• 0
6
votes
5
replies
116
views
PTEN missing from TxDb.Hsapiens.UCSC.hg38.knownGene?
TxDb
annotation
TxDb.Hsapiens.UCSC.hg38.knownGene
updated 14 months ago by
shepherl
2.6k • written 14 months ago by
bernatgel
▴ 130
6
votes
4
replies
454
views
the coordinates of exons of RefSeq or ENSEMBL genes
txdb
genome
exons
updated 20 months ago by
Martin Morgan
25k • written 20 months ago by
Bogdan
▴ 610
2
votes
5
replies
526
views
Warning in makeTxDbFromGFF
txdb
updated 6 days ago by
Hervé Pagès
14k • written 22 months ago by
weir
▴ 10
2
votes
1
reply
257
views
Do TxDb objects contain info about non-transcriptionally active regions?
TxDb
GRanges
BSGenome
variant annotation
updated 2.1 years ago by
James W. MacDonald
56k • written 2.1 years ago by
jacorvar
▴ 40
3
votes
2
replies
498
views
How to use EnsDb in annotatePeak from package "ChIPseeker"
GRanges
ChIPseeker
annotatePeak
TxDb
EnsDb
updated 2.1 years ago by
Johannes Rainer
★ 1.8k • written 2.1 years ago by
foehn
▴ 60
2
votes
4
replies
412
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 2.3 years ago by
James W. MacDonald
56k • written 2.3 years ago by
olavur
▴ 10
0
votes
3
replies
574
views
Error in makeTxDbFromBiomart
software error
txdb
maketxdbfrombiomart
2.5 years ago
katie_emelianova
• 0
0
votes
1
reply
477
views
makeTxDbFromGFF error "stop codons that cannot be mapped to an exon"
genomicfeatures
txdb
maketxdbfromgff
updated 2.7 years ago by
daniel.vantwisk
▴ 50 • written 2.7 years ago by
marisa.e.miller
• 0
0
votes
1
reply
381
views
TxDb basic question
txdb
TxDb.Mmulatta.UCSC.rheMac8.refGene
updated 2.8 years ago by
daniel.vantwisk
▴ 50 • written 2.8 years ago by
Brian Smith
▴ 120
0
votes
4
replies
614
views
Merging each element of a list of Genomic range
txdb
granges
cds
orf
R
updated 2.8 years ago by
James W. MacDonald
56k • written 2.8 years ago by
q.thomas
• 0
0
votes
1
reply
556
views
GenomicFeatures: could not find symbol "recursive" in environment of the generic function
genomicfeatures
rnaseq
txdb
3.1 years ago
lucasmacielbiotec
• 0
1
vote
5
replies
680
views
Extract genomic features from a TxDb-like object
TxDB
genomicfeatures
promoter
getpromoterseq
updated 3.1 years ago by
Hervé Pagès
14k • written 3.1 years ago by
rbenel
▴ 20
0
votes
1
reply
1.9k
views
create a txdb using makeTxDbFromGFF
bioconductor
txdb
maketxdbfromgff
3.3 years ago
Nader.Aryamanesh
• 0
2
votes
4
replies
1.1k
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 3.3 years ago by
Michael Lawrence
11k • written 3.3 years ago by
james.dalgleish
▴ 30
2
votes
2
replies
1.2k
views
How to prepare TxDb object using makeTxDbFromGFF with polycistronic transcripts?
txdb
gff3
polycistronic transcript
3.4 years ago
Piotr Gawronski
• 0
0
votes
4
replies
674
views
Cannot extract TxFeatures for a defined GRanges object
TxDB
genomicranges
genomicfeatures
updated 3.4 years ago by
Hervé Pagès
14k • written 3.5 years ago by
oolongoni
▴ 10
0
votes
0
replies
514
views
News:
OrgDb and TxDb packages have been added to AnnotationHub for Bioc 3.6
orgdb
txdb
bioconductor
annotation
annotationhub
News
3.5 years ago
shepherl
2.6k
0
votes
2
replies
669
views
Missing genes from TxDb.Hsapiens.UCSC.hg19.knownGene
txdb
txdb.hsapiens.ucsc.hg19.knowngene
gviz
updated 3.5 years ago by
James W. MacDonald
56k • written 3.5 years ago by
izzy.yichao.cai
▴ 10
3
votes
5
replies
610
views
R session crash with SGSeq::convertToTxFeatures
crash
SGSeq
TxDb
makeTxDbFromBiomart
TxFeatures
updated 3.5 years ago by
Leonard Goldstein
▴ 110 • written 3.5 years ago by
oolongoni
▴ 10
0
votes
2
replies
1.0k
views
add annotation features to BSgenome or txdb package
bsgenome
txdb
annotation
orgdb
3.7 years ago
Didi
▴ 10
0
votes
2
replies
698
views
makeTxDbFromGFF Error due to incompatible seqnames
summarizedexperiment
TxDb
gtf
genomicfeatures
updated 3.7 years ago by
Michael Love
32k • written 3.7 years ago by
filipeje
• 0
0
votes
1
reply
665
views
makeTxDbFromGFF returns object with wrong seqids (wrong chromosome names)
genomicfeatures
txdb
canis familiaris
rna-seq
updated 4.0 years ago by
James W. MacDonald
56k • written 4.0 years ago by
jggomeza
• 0
5
votes
7
replies
962
views
Possible error in TxDb.Mmusculus.UCSC.mm10.ensGene_3.4.0?
txdb
genomicfeatures
updated 4.1 years ago by
James W. MacDonald
56k • written 4.1 years ago by
Chao-Jen Wong
▴ 30
2
votes
1
reply
561
views
makeTxDbPackage() ERROR: values for symbols SOURCEURL are not single strings
genomicfeatures
txdb
updated 4.4 years ago by
James W. MacDonald
56k • written 4.4 years ago by
gtho123
▴ 40
0
votes
2
replies
549
views
Error in TxDb mm10 coordinates?
txdb
txdb.mmusculus.ucsc.mm10.knowngene
updated 4.4 years ago by
James W. MacDonald
56k • written 4.4 years ago by
Mark
▴ 10
3
votes
3
replies
629
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 4.7 years ago by
Martin Morgan
25k • written 4.7 years ago by
li lilingdu
▴ 450
1
vote
2
replies
1.6k
views
troubleshooting makeTxDbFromGRanges: some exons are linked to transcripts not found in the file
genomicfeatures
txdb
makeTxDbFromGRanges
updated 4.8 years ago by
Hervé Pagès
14k • written 4.8 years ago by
Guido Hooiveld
★ 2.9k
4
votes
2
replies
629
views
distinguish DataSource from Provider and ProviderVersion in makeTxDbPackage
genomicfeatures
txdb
maketxdbfromgff
metadata
updated 4.9 years ago by
Valerie Obenchain
★ 6.7k • written 4.9 years ago by
TimothéeFlutre
▴ 70
0
votes
5
replies
690
views
makeTxDbFromGFF returns empty object
genomicfeatures
txdb
maketxdbfromgff
5.0 years ago
TimothéeFlutre
▴ 70
0
votes
2
replies
670
views
how to get transcript annotation (unique)
txdb
5.0 years ago
K
▴ 50
7
votes
4
replies
1.8k
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
5.0 years ago
enricoferrero
▴ 570
0
votes
0
replies
649
views
extractUpstreamSeqs with custom genome, no gene_id shown
genomicranges
txdb
genomicfeatures
featureextraction
updated 5.0 years ago by
Martin Morgan
25k • written 5.0 years ago by
wd
▴ 30
4
votes
4
replies
1.2k
views
Why does Homo.sapiens import TxDb.Hsapiens.UCSC.hg19.knownGene instead of TxDb.Hsapiens.UCSC.hg38.knownGene?
homo.sapiens
txdb
annotation
updated 5.0 years ago by
Valerie Obenchain
★ 6.7k • written 5.0 years ago by
enricoferrero
▴ 570
0
votes
1
reply
812
views
How to find index position of desired feature_by in TxDb granges?
granges
txdb
genomicfeatures
updated 5.1 years ago by
Martin Morgan
25k • written 5.1 years ago by
vinod.acear
▴ 50
2
votes
2
replies
714
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
5.1 years ago
vinod.acear
▴ 50
1
vote
6
replies
907
views
problem creating txdb object and bsgenome for solanum pennellii
bsgenome
txdb
promoter
updated 5.2 years ago by
Martin Morgan
25k • written 5.2 years ago by
sekawaiwai2006
▴ 20
0
votes
3
replies
929
views
extracting promoter region error for A.thaliana
promoter region
txdb
updated 5.2 years ago by
Martin Morgan
25k • written 5.2 years ago by
sekawaiwai2006
▴ 20
59 results • Page
1 of 2
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Thanks Martin. Yes, that works.
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