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TxDb
•
reset
0
votes
1
reply
461
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
andre_sim
▴ 20 • written 10 months ago by
camilia.savitri
• 0
0
votes
0
replies
591
views
Identify accepted columns in TxDb objects
TxDb
16 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
James W. MacDonald
65k • written 18 months ago by
Luke
• 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
Hervé Pagès
16k • written 2.4 years ago by
jon.klonowski
▴ 40
5
votes
6
replies
2.1k
views
NA transcript values in my Txdb
GFF
txdb
updated 2.5 years ago by
James W. MacDonald
65k • written 2.6 years ago by
A.J.
▴ 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
3.3 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
fabian.grammes
• 0 • written 3.5 years ago by
k.vitting.seerup
▴ 120
0
votes
1
reply
4.5k
views
Add gene symbol when making TxDb
txdb
genomicfeatures
updated 3.7 years ago by
James W. MacDonald
65k • written 3.7 years ago by
Jake
▴ 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
Michael Love
41k • written 3.7 years ago by
Charlotte
• 0
3
votes
6
replies
2.0k
views
TxDb, GenomicFeatures load from GTF file (Mmul_8)
TxDb
GenomicFeatures
updated 3.8 years ago by
Martin Morgan
25k • written 3.8 years ago by
Brian Smith
▴ 120
4
votes
6
replies
1.2k
views
Extremely big genes in annotation TxDb packages
annotation
txdb
AnnotationData
Genetics
updated 3.9 years ago by
James W. MacDonald
65k • written 3.9 years ago by
epibio
▴ 10
0
votes
2
replies
818
views
Problem in dowloading "TxDb.Hsapiens.UCSC.hg38.knownGene"
annotation
software
TxDb
updated 3.9 years ago by
James W. MacDonald
65k • written 3.9 years ago by
AmalAbdel-Aziz
• 0
0
votes
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
Michael Lawrence
★ 11k • written 4.0 years ago by
mar.pieraccioli
▴ 10
1
vote
2
replies
894
views
Any possibility to "cache" TxDb object?
GenomicFeatures
TxDb
updated 4.2 years ago by
Steve Lianoglou
★ 13k • written 4.2 years ago by
aush
▴ 40
0
votes
2
replies
984
views
biomart webservice error during makeTxDbFromBiomart in r package GenomicFeatures
biomart
txdb
makeTxDbFromBiomart
GenomicFeatures
updated 4.3 years ago by
James W. MacDonald
65k • written 4.3 years ago by
ksomi47
• 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
Michael Love
41k • written 4.3 years ago by
holmkn
• 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
shepherl
3.9k • written 4.3 years ago by
bernatgel
▴ 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
Martin Morgan
25k • written 4.8 years ago by
Bogdan
▴ 670
2
votes
5
replies
2.1k
views
Warning in makeTxDbFromGFF
txdb
updated 3.1 years ago by
Hervé Pagès
16k • written 4.9 years ago by
weir
▴ 10
2
votes
1
reply
888
views
Do TxDb objects contain info about non-transcriptionally active regions?
TxDb
GRanges
BSGenome
variant annotation
updated 5.1 years ago by
James W. MacDonald
65k • written 5.1 years ago by
jacorvar
▴ 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
Johannes Rainer
★ 2.0k • written 5.2 years ago by
foehn
▴ 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
James W. MacDonald
65k • written 5.4 years ago by
olavur
▴ 10
0
votes
3
replies
1.4k
views
Error in makeTxDbFromBiomart
software error
txdb
maketxdbfrombiomart
5.6 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
daniel.vantwisk
▴ 50 • written 5.8 years ago by
marisa.e.miller
• 0
0
votes
1
reply
1.0k
views
TxDb basic question
txdb
TxDb.Mmulatta.UCSC.rheMac8.refGene
updated 5.8 years ago by
daniel.vantwisk
▴ 50 • written 5.9 years ago by
Brian Smith
▴ 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
James W. MacDonald
65k • written 5.9 years ago by
q.thomas
• 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
Hervé Pagès
16k • written 6.2 years ago by
rbenel
▴ 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
Michael Lawrence
★ 11k • written 6.4 years ago by
james.dalgleish
▴ 30
2
votes
2
replies
4.5k
views
How to prepare TxDb object using makeTxDbFromGFF with polycistronic transcripts?
txdb
gff3
polycistronic transcript
6.5 years ago
Piotr Gawronski
• 0
0
votes
4
replies
1.6k
views
Cannot extract TxFeatures for a defined GRanges object
TxDB
genomicranges
genomicfeatures
updated 6.5 years ago by
Hervé Pagès
16k • written 6.5 years ago by
oolongoni
▴ 10
0
votes
0
replies
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
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
James W. MacDonald
65k • written 6.6 years ago by
izzy.yichao.cai
▴ 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
Leonard Goldstein
▴ 200 • written 6.6 years ago by
oolongoni
▴ 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
Michael Love
41k • written 6.8 years ago by
filipeje
• 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
James W. MacDonald
65k • written 7.1 years ago by
jggomeza
• 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
James W. MacDonald
65k • written 7.2 years ago by
Chao-Jen Wong
▴ 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
James W. MacDonald
65k • written 7.4 years ago by
gtho123
▴ 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
James W. MacDonald
65k • written 7.4 years ago by
Mark
▴ 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
Martin Morgan
25k • written 7.7 years ago by
li lilingdu
▴ 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
Hervé Pagès
16k • written 7.8 years ago by
Guido Hooiveld
★ 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
Valerie Obenchain
★ 6.8k • written 8.0 years ago by
TimothéeFlutre
▴ 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
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Comment: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
Chris
• 0
Intent to delete when going home. Sorry for that!
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
Gordon Smyth
50k
Please ask you own question. Inserting your own dataset into someone else's question like this is very impolite. I have already answered m…
Comment: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
limma most certainly is available. It installs in R 4.4.0 and Bioc 3.19 for all platforms without any issues. It has not had any period of …
Comment: package goseq seems to be not available on the latest version of R
by
Patrycja
▴ 20
limma package also isn't available.Is there any information when these packages will be available?
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
Chris
• 0
Thanks Gordon for the advice!
Votes
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Handling multiple differential expression comparisons
Answer: fgsea significant result
Answer: fgsea significant result
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